WO2013041844A2 - Antibodies, variable domains & chains tailored for human use - Google Patents
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- WO2013041844A2 WO2013041844A2 PCT/GB2012/052296 GB2012052296W WO2013041844A2 WO 2013041844 A2 WO2013041844 A2 WO 2013041844A2 GB 2012052296 W GB2012052296 W GB 2012052296W WO 2013041844 A2 WO2013041844 A2 WO 2013041844A2
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Classifications
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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
- C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
-
- A—HUMAN NECESSITIES
- A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
- A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
- A01K67/00—Rearing or breeding animals, not otherwise provided for; New or modified breeds of animals
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Definitions
- the present invention relates to the provision of antibody therapeutics and prophylactics that are tailored specifically for human use.
- the present invention provides libraries, vertebrates and cells, such as transgenic mice or rats or transgenic mouse or rat cells. Furthermore, the invention relates to methods of using the vertebrates to isolate antibodies or nucleotide sequences encoding antibodies. Antibodies, heavy chains, polypeptides, nucleotide sequences, pharmaceutical compositions and uses are also provided by the invention.
- non-human vertebrates eg, mice and rats
- cells comprising transgenic immunoglobulin loci, such loci comprising human variable (V), diversity (D) and/or joining (J) segments, and optionally human constant regions.
- endogenous constant regions of the host vertebrate eg, mouse or rat constant regions
- the transgenic loci are provided in the transgenic loci.
- transgenic loci in the art include varying amounts of the human V(D) J repertoire.
- Existing transgenic immunoglobulin loci are based on a single human DNA source. The potential diversity of human antibody variable regions in non-human vertebrates bearing such transgenic loci is thus confined.
- the present invention has been developed from extensive bioinformatics analysis of natural antibody gene segment distributions across a myriad of different human populations and across more than two thousand samples from human individuals.
- the inventors have undertaken this huge task to more thoroughly understand and design non-human vertebrate systems and resultant antibodies to better address human medical therapeutics as a whole, as well as to enable rational design to address specific ethnic populations of humans.
- the inventors have constructed transgenic non-human vertebrates and isolated antibodies, antibody chains and cells expressing these in a way that yields products that utilise gene segments that have been purposely included on the basis of the human bioinformatics analysis.
- the examples illustrate worked experiments where the inventors isolated many cells and antibodies to this effect.
- the invention also relates to synthetically-extended & ethnically-diverse superhuman
- the present invention thus provides for novel and potentially expanded synthetic immunoglobulin diversities, thus providing a pool of diversity from which human antibody therapeutic leads can be selected.
- This expanded pool is useful when seeking to find antibodies with desirable characteristics, such as relatively high affinity to target antigen without the need for further affinity maturation (eg, using laborious in vitro techniques such as phage or ribosome display), or improved biophysical characteristics, or to address targets and new epitopes that have previously been difficult to address with antibodies are not reached by prior antibody binding sites.
- the invention also provides for diversity that is potentially biased towards variable gene usage common to members of a specific human population, which is useful for generating antibodies for treating and/or preventing diseases or conditions within such population. This ability to bias the antibody repertoire allows one to tailor antibody therapeutics with the aim of more effectively treating and/or preventing disease or medical conditions in specific human populations.
- the present inventors realised the possibility of providing immunoglobulin gene segments from disparate sources in transgenic loci, in order to provide for novel and potentially-expanded antibody diversities from which antibody therapeutics (and antibody tool reagents) could be generated. This- opens up the potential of transgenic human-mouse/rat technologies to the possibility of interrogating different and possibly larger antibody sequence-spaces than has hitherto been possible.
- HCDR3 length at least 20 amino acids
- naturally-occurring antibodies have been isolated from humans infected with infectious disease pathogens, such antibodies having a long HCDR3 length.
- Neutralising antibodies have been found in this respect.
- a long HCDR3 length would be desirable to address other antigens (eg, receptor clefts or enzyme active sites), not just limited to infectious disease pathogens, and thus the inventors realised the general desirability of the possibility of engineering transgenic loci to be able to produce long HCDR3 antibodies and heavy chains.
- the inventors through laborious execution of bioinformatics on in excess of 2000 human DNA samples via the 1000 Genomes project together with rational sequence choices, identified that the inclusion of the specific human gene segment variant JH6*02 is desirable for producing long HCDR3 antibodies and chains.
- antibodies are humanised with an arbitrary choice of human constant region (presumably derived from one (often unknown) ethnic population or non-naturally occurring) that does not function as well in patients of a different human ethnic population. This is important, since the constant region has the major role in providing antibody effector functions, eg, for antibody recycling, cellular and complement recruitment and for cell killing.
- a non-human vertebrate or vertebrate cell (optionally an ES cell or antibody-producing cell) comprising a genome having a superhuman immunoglobulin heavy chain human VH and/or D and/or J gene repertoire.
- a non-human vertebrate or vertebrate cell (optionally an ES cell or antibody-producing cell) comprising a genome having a superhuman immunoglobulin light chain human VL gene repertoire; optionally wherein the vertebrate or cell is according to the first configuration.
- a non-human vertebrate or vertebrate cell (optionally an ES cell or antibody-producing cell) whose genome comprises a transgenic immunoglobulin locus (eg, a heavy chain locus or a light chain locus), said locus comprising immunoglobulin gene segments according to the first and second human immunoglobulin gene segments (optionally V segments) as mentioned below operably connected upstream of an immunoglobulin constant region; optionally wherein the genome is homozygous for said transgenic immunoglobulin locus;
- a transgenic immunoglobulin locus eg, a heavy chain locus or a light chain locus
- said locus comprising immunoglobulin gene segments according to the first and second human immunoglobulin gene segments (optionally V segments) as mentioned below operably connected upstream of an immunoglobulin constant region; optionally wherein the genome is homozygous for said transgenic immunoglobulin locus;
- immunoglobulin locus comprises more than the natural human complement of functional V gene segments;
- immunoglobulin locus comprises more than the natural human complement of functional D gene segments;
- the immunoglobulin locus comprises more than the natural human complement of functional J gene segments.
- a transgenic non-human vertebrate eg, a mouse or rat
- vertebrate cell optionally an ES cell or antibody-producing cell
- the transgenic locus comprises one or more human immunoglobulin V gene segments, one or more human J gene segments and optionally one or more human D gene segments, a first (optionally a V segment) of said gene segments and a second (optionally a V segment) of said gene segments being different and derived from the genomes of first and second human individuals respectively, wherein the individuals are different; and optionally not related;
- immunoglobulin locus comprises more than the natural human complement of functional V gene segments;
- immunoglobulin locus comprises more than the natural human complement of functional D gene segments;
- immunoglobulin locus comprises more than the natural human complement of functional J gene segments.
- a transgenic non-human vertebrate eg, a mouse or rat
- vertebrate cell eg. an ES cell or antibody-producing cell
- each locus comprising a plurality of human immunoglobulin gene segments operably connected upstream of a non-human vertebrate constant region for the production of a repertoire of chimaeric antibodies, or chimaeric light or heavy chains, having a non-human vertebrate constant region and a human variable region
- the first transgenic locus comprises one or more human immunoglobulin V gene segments, one or more human J gene segments and optionally one or more human D gene segments
- the second transgenic locus comprises one or more human immunoglobulin V gene segments, one or more human J gene segments and optionally one or more human D gene segments
- each immunoglobulin locus comprises more than the natural human
- each immunoglobulin locus comprises more than the natural human
- a method of constructing a cell eg, an ES cell according to the invention, the method comprising
- the gene segment(s) in step (b) are identified from an immunoglobulin gene database selected from the 1000 Genomes, Ensembl, Genbank and IMGT databases.
- Genbank is a reference to Genbank release number 185.0 or 191.0; the 1000 Genomes database is Phase 1, release v3, 16 th March 2012; the Ensembl database is assembly GRCh37.p8 (10/04/2012); the IMGT database is available at www.imgt.org .
- the first and second human individuals are members of first and second ethnic populations respectively, wherein the populations are different, optionally wherein the human immunoglobulin gene segment derived from the genome sequence of the second individual is low- frequency (optionally rare) within the second ethnic population.
- This configuration of the invention also provides a method of making a transgenic non-human vertebrate (eg, a mouse or rat), the method comprising
- an ES cell eg, a mouse C57BL/6N, C57BL/6J, 129S5 or 129Sv strain ES cell
- a donor non-human vertebrate blastocyst eg, a mouse C57BL/6N, C57BL/6J, 129S5 or 129Sv strain blastocyst
- the invention provides a method of isolating an antibody that binds a predetermined antigen (eg, a bacterial or viral pathogen antigen), the method comprising immunising a non-human vertebrate according to the invention.
- a predetermined antigen eg, a bacterial or viral pathogen antigen
- a first transgenic cell expresses a first antibody having a chain encoded by a first immunoglobulin gene, the gene comprising a first variable domain nucleotide sequence produced following recombination of a first human unrearranged immunoglobulin gene segment;
- a second transgenic cell expresses a second antibody having a chain encoded by a second immunoglobulin gene, the second gene comprising a second variable domain nucleotide sequence produced following recombination of a second human unrearranged immunoglobulin gene segment, the first and second antibodies being non-identical;
- the first and second gene segments are different and derived from the genome sequences of first and second human individuals respectively, wherein the individuals are different; and optionally not related; (d) wherein the cells are non-human vertebrate (eg, mouse or rat) cells.
- non-human vertebrate eg, mouse or rat
- the first and second human individuals are members of first and second ethnic populations respectively, wherein the populations are different; optionally wherein the ethnic populations are selected from those identified in the 1000 Genomes database.
- the second human immunoglobulin gene segment is a polymorphic variant of the first human immunoglobulin gene segment; optionally wherein the second gene segment is selected from the group consisting of a gene segment in any of Tables 1 to 7 and 9 to 14 below (eg, selected from Table 13 or Table 14), eg, the second gene segment is a polymorphic variant of VH1- 69.
- the heavy chain constant regions are gamma-type constant regions.
- the invention also provides an isolated nucleotide sequence encoding the antibody, optionally wherein the sequence is provided in an antibody expression vector, optionally in a host cell.
- the invention also provides a method of producing a human antibody, the method comprising replacing the non-human vertebrate constant regions of the antibody of the third configuration with human antibody constant regions.
- the invention also provides a pharmaceutical composition
- a pharmaceutical composition comprising an antibody according to the third configuration, or an antibody produced according to the method above and a diluent, excipient or carrier; optionally wherein the composition is provided in a container connected to an IV needle or syringe or in an IV bag.
- the invention also provides an antibody-producing cell that expresses the second antibody recited in any one of the configurations.
- the invention contemplates the combination of nucleotide sequences of first and second immunoglobulin gene segments (eg, two or more polymorphic variants of a particular human germline VH or VL gene segment) to provide a synthetic gene segment.
- synthetic gene segment is used, in one embodiment, to build a transgenic immunoglobulin locus, wherein the synthetic gene segment is provided in combination with one or more human variable and J regions (and optionally one or more human D regions) operably connected upstream of a constant region.
- the invention provides for superhuman gene segment diversity.
- sequences to be combined can be selected from gene segments that have been observed to be commonly used in human antibodies raised against a particular antigen (eg, a flu antigen, such as haemaglutinin).
- a flu antigen such as haemaglutinin
- the synthetic gene segment may recombine in vivo to produce an antibody that is well suited to the treatment and/or prevention of a disease or condition (eg, influenza) mediated by said antigen.
- a disease or condition eg, influenza
- a non-human vertebrate (optionally a mouse or a rat) or vertebrate cell whose genome comprises an immunoglobulin heavy chain locus comprising human gene segment JH6*02, one or more VH gene segments and one or more D gene segments upstream of a constant region; wherein the gene segments in the heavy chain locus are operably linked to the constant region thereof so that the mouse is capable of producing an antibody heavy chain produced by recombination of the human JH6*02 with a D segment and a VH segment.
- a non-human vertebrate cell (optionally a mouse cell or a rat cell) whose genome comprises an immunoglobulin heavy chain locus comprising human gene segment JH6*02, one or more VH gene segments and one or more D gene segments upstream of a constant region; wherein the gene segments in the heavy chain locus are operably linked to the constant region thereof for producing (eg, in a subsequent progeny cell) an antibody heavy chain produced by recombination of the human JH6*02 with a D segment and a VH segment.
- a heavy chain (eg, comprised by an antibody) isolated from a vertebrate of the invention wherein the heavy chain comprises a HCD 3 of at least 20 amino acids.
- a method for producing a heavy chain, VH domain or an antibody specific to a target antigen comprising immunizing a non-human vertebrate according to the invention with the antigen and isolating the heavy chain, VH domain or an antibody specific to a target antigen or a cell producing the heavy chain, VH domain or an antibody, wherein the heavy chain, VH domain or an antibody comprises a HCDR3 that is derived from the recombination of human JH6*02 with a VH gene segment and a D gene segment.
- a heavy chain, VH domain or an antibody produced by the method comprising immunizing a non-human vertebrate according to the invention with the antigen and isolating the heavy chain, VH domain or an antibody specific to a target antigen or a cell producing the heavy chain, VH domain or an antibody, wherein the heavy chain, VH domain or an antibody comprises a HCDR3 that is derived from the recombination of human JH6*02 with a VH gene segment and a
- a vector (eg, a CHO cell or HEK293 cell vector) comprising the nucleic acid; optionally wherein the vector is in a host cell (eg, a CHO cell or HEK293 cell).
- a pharmaceutical composition comprising the antibody, heavy chain or VH domain (eg, comprised by an antibody), together with a pharmaceutically-acceptable excipient, diluent or a medicament (eg, a further antigen-specific variable domain, heavy chain or antibody).
- the antibody, heavy chain or VH domain (eg, comprised by an antibody) as above for use in medicine.
- an antibody, heavy chain or VH domain eg, comprised by an antibody
- a method of producing an antibody heavy chain comprising
- variable domain (b) combining the variable domain with a human heavy chain constant region to produce an antibody heavy chain comprising (in N- to C-terminal direction) the variable domain and the constant region;
- human heavy chain constant region is an IGHGlref, IGHG2ref, IGHG2a, IGHG3ref, IGHG3a, IGHG3b, IGHG4ref or IGHG4a constant region.
- an antibody comprising a human heavy chain, the heavy chain comprising a variable domain that is specific for an antigen and a constant region that is an IGHGlref, IGHG2ref, IGHG2a, IGHG3ref, IGHG3a, IGHG3b, IGHG4ref or IGHG4a constant region .
- the variable domain comprises mouse-pattern AID somatic mutations.
- a polypeptide comprising (in N- to C- terminal direction) a leader sequence, a human variable domain that is specific for an antigen and a human constant region that is an IGHGlref, IGHG2ref, IGHG2a, IGHG3ref, IGHG3a, IGHG3b, IGHG4ref or IGHG4a constant region wherein (i) the leader sequence is not the native human variable domain leader sequence; and/or (ii) the variable domain comprises mouse AID-pattern somatic mutations and/or mouse Terminal deoxynucleotidyl transferase (TdT)- pattern junctional mutations.
- TdT Terminal deoxynucleotidyl transferase
- a vector (eg, a CHO cell or HEK293 cell vector) comprising a IGHGlref, IGHG2ref, IGHG2a, IGHG3ref, IGHG3a, IGHG3b, IGHG4ref or IGHG4a constant region nucleotide sequence that is 3' of a cloning site for the insertion of a human antibody heavy chain variable domain nucleotide sequence, such that upon insertion of such a variable domain sequence the vector comprises (in 5' to 3' direction) a promoter, a leader sequence, the variable domain sequence and the constant region sequence so that the vector is capable of expressing a human antibody heavy chain when present in a host cell.
- a non-human vertebrate eg, a mouse or rat
- a non-human vertebrate cell eg, an ES cell or a B- cell
- having a genome comprising at least 3 human variable region gene segments of the same type (eg, at least 3 human VH6-1 gene segments, at least 3 human JH6 gene segments, at least 3 human VK1-39 gene segments, at least 3 human D2-2 gene segments or at least 3 human JKI gene segments), wherein at least two of the human gene segments are variants that are not identical to each other.
- a non-human vertebrate eg, a mouse or rat
- a non-human vertebrate cell eg, an ES cell or a B- cell
- having a genome comprising at least 2 different non-endogenous variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 3 human JH6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments) cis at the same Ig locus.
- a non-human vertebrate eg, a mouse or rat
- a non-human vertebrate cell eg, an ES cell or a B- cell
- having a genome comprising at least 2 different human variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human JH6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments) trans at the same Ig locus; and optionally a third human gene segment of the same type, wherein the third gene segment is cis with one of said 2 different gene segments.
- a population of non-human vertebrates comprising a repertoire of human variable region gene segments, wherein the plurality comprises at least 2 human variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human JH6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments), a first of said different gene segments is provided in the genome of a first vertebrate of the population, and a second of said different gene segments being provided in the genome of a second vertebrate of the population, wherein the genome of the first vertebrate does not comprise the second gene segment.
- the plurality comprises at least 2 human variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human JH6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments)
- a first of said different gene segments is provided in the genome of a first vertebrate
- a non-human vertebrate eg, a mouse or rat
- a non-human vertebrate cell eg, an ES cell or a B- cell
- having a genome comprising at least 2 different non-endogenous variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human J H6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments), wherein the gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
- a method of enhancing the human immunoglobulin gene diversity of a non-human vertebrate comprising providing the vertebrate with a genome comprising at least 3 human variable region gene segments of the same type (eg, at least 3 human VH6-1 gene segments, at least 3 human J H6 gene segments, at least 3 human VK1-39 gene segments, at least 3 human D2-2 gene segments or at least 3 human JKI gene segments), wherein at least two of the human gene segments are variants that are not identical to each other.
- a method of enhancing the immunoglobulin gene diversity of a non-human vertebrate comprising providing the vertebrate with a genome comprising at least 2 different non-endogenous variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human J H6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments) cis at the same Ig locus.
- a non-human vertebrate eg, a mouse or rat
- a method of enhancing the immunoglobulin gene diversity of a non-human vertebrate comprising providing the vertebrate with a genome comprising at least 2 different human variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human JH6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments) trans at the same Ig locus; and optionally a third human gene segment of the same type, wherein the third gene segment is cis with one of said 2 different gene segments.
- a non-human vertebrate eg, a mouse or rat
- a method of providing an enhanced human immunoglobulin variable region gene segment repertoire comprising providing a population of non-human vertebrates (eg, a mouse or rat) comprising a repertoire of human variable region gene segments, wherein the method comprises providing at least 2 different human variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human JH6 gene segments, at least 2 human VKI- 39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments), wherein a first of said different gene segments is provided in the genome of a first vertebrate of the population, and a second of said different gene segments is provided in the genome of a second vertebrate of the population, wherein the genome of the first vertebrate does not comprise the second gene segment.
- a population of non-human vertebrates eg, a mouse or rat
- the method comprises providing at least 2 different human variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human
- a method of enhancing the human immunoglobulin gene diversity of a non-human vertebrate comprising providing the vertebrate with a genome comprising at least 2 different non-endogenous variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human J H6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments), wherein the gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
- a method of enhancing the human immunoglobulin gene diversity of a non-human vertebrate comprising providing the vertebrate with a genome comprising at least 2 human variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human J H6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments), wherein the gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations; optionally wherein at least 2 or 3 of said different gene segments are provided at the same Ig locus in said genome.
- a non-human vertebrate eg, a mouse or rat
- a non-human vertebrate eg, a mouse or rat
- a non-human vertebrate cell eg, an ES cell or a B- cell
- having a genome comprising first and second human Ig locus gene segments of the same type (eg, first and second human JH6 gene segments; or first and second lgG2 gene segments; or first and second human J ⁇ 7 gene segments)
- the first gene segment is a gene segment selected from any one of Tables 1 and 9 to 14 (eg, selected from Table 13 or Table 14) (eg, IGHJ6-a)
- the second gene segment is the corresponding reference sequence.
- a population of non-human vertebrates comprising first and second human Ig locus gene segments of the same type (eg, first and second human JH6 gene segments; or first and second lgG2 gene segments; or first and second human J ⁇ 7 gene segments), wherein the first gene segment is a gene segment selected from any one of Tables 1 and 9 to 14 (eg, selected from Table 13 or Table 14) (eg, IGHJ6-a) and the second gene segment is the corresponding reference sequence, wherein the first gene segment is provided in the genome of a first vertebrate of the population, and the second gene segment is provided in the genome of a second vertebrate of the population.
- first and second human Ig locus gene segments of the same type eg, first and second human JH6 gene segments; or first and second lgG2 gene segments; or first and second human J ⁇ 7 gene segments
- the first gene segment is a gene segment selected from any one of Tables 1 and 9 to 14 (eg, selected from Table 13 or Table 14) (eg,
- a method of enhancing the human immunoglobulin gene diversity of a non-human vertebrate comprising providing the vertebrate with a genome comprising first and second human Ig locus gene segments of the same type (eg, first and second human JH6 gene segments; or first and second lgG2 gene segments; or first and second human J ⁇ 7 gene segments), wherein the first gene segment is a gene segment selected from any one of Tables 1 and 9 to 14 (eg, selected from Table 13 or Table 14) (eg, IGHJ6-a) and the second gene segment is the corresponding reference sequence.
- first and second human Ig locus gene segments of the same type eg, first and second human JH6 gene segments; or first and second lgG2 gene segments; or first and second human J ⁇ 7 gene segments
- the first gene segment is a gene segment selected from any one of Tables 1 and 9 to 14 (eg, selected from Table 13 or Table 14) (eg, IGHJ6-a) and the second gene segment is the corresponding reference sequence.
- the invention relates to human D gene segment variants as described further below.
- the invention relates to human V gene segment variants as described further below. In one aspect of this configuration, the invention relates to human J gene segment variants as described further below.
- Figures 1 to 3 Schematic illustrating a protocol for producing recombineered BAC vectors to add V gene segments into a mouse genome
- FIG. 4 Schematic illustrating a protocol for adding V gene segments to a mouse genome using sequential recombinase mediated cassette exchange (s MCE).
- Figure 5 Alignment of 13 IGHVl-69 variants showing the variable (V) coding region only. Nucleotides that differ from VH1-69 variant *01 are indicated at the appropriate position whereas identical nucleotides are marked with a dash. Where nucleotide changes result in amino acid differences, the encoded amino acid is shown above the corresponding triplet. Boxed regions correspond to CDR1, CDR2 and CDR3 as indicated.
- Figure 6 is a schematic illustrating gene segment diversity and the effect of including variant variants in cis according to the invention:-
- V4-4 can only be recombined within variant 1 to form for instance for instance V4-4-D-J6 or V4-4-D-J2 A .
- the variant V4-4 A can't be recombined with either J6 or J2 A from variant 1 and can only be joined with J-genes from variant 2 to form V4-4 A -D-J6 A and V4-4 A -D-J2.
- V4-4-J2/J6 complexity 4.
- (c) Supra mouse of the invention The variants are added in cis and thus can be recombined in every combination, expanding the repertoire.
- V4-4 can be combined with J6A, J6, J2A or J2 and similarly V4-4A can be recombined with these same J-genes.
- the V4-4-J6/J2 complexity 8 which in this simple example is double that of a person and 4X that of a mouse with a single variant.
- Figure 7 Alignment of human JH6*02 variants. Nucleotides that differ from JH6 *01 are indicated at the appropriate position whereas identical nucleotides are marked with a dash. Where nucleotide changes result in amino acid differences, the encoded amino acid is shown above. Accession numbers (eg, J00256) are shown to the left of the IMGT variant name.
- Figure 8 Alignment of JH sequences from various species.
- Table 13 Variant Frequency Analyses & Human Population Distributions
- Table 14 Frequent Human Variant Distributions
- a suitable source of JH6*02 and other human DNA sequences for use in the invention will be readily apparent to the skilled person.
- a DNA sample from a consenting human donor (eg, a cheek swab sample as per the Example herein) from which can be obtained suitable DNA sequences for use in constructing a locus of the invention.
- Other sources of human DNA are commercially available, as will be known to the skilled person.
- the skilled person is able to construct gene segment sequence by referring to one or more databases of human Ig gene segment sequences disclosed herein.
- An example source for human V, D and J gene segments according to the invention are Bacterial Artificial Chromosomes (RPCI-11 BACs) obtained from Roswell Park Cancer Institute
- Male blood was obtained via a double-blind selection protocol. Male blood DNA was isolated from one randomly chosen donor (out of 10 male donors)".
- the invention relates to synthetically-extended & ethnically-diverse superhuman immunoglobulin gene repertoires.
- the human immunoglobulin repertoires are beyond those found in nature (ie, "Superhuman"), for example, they are more diverse than a natural human repertoire or they comprise combinations of human immunoglobulin gene segments from disparate sources in a way that is non-natural.
- the repertoires of the invention are "superhuman” immunoglobulin repertoires, and the invention relates to the application of these in transgenic cells and non-human vertebrates for utility in producing chimaeric antibodies (with the possibility of converting these into fully-human, isolated antibodies using recombinant DNA technology).
- the present invention thus provides for novel and potentially expanded synthetic immunoglobulin diversities, which provides for a pool of diversity from which antibody therapeutic leads (antibody therapeutics and antibody tool reagents) can be selected.
- This opens up the potential of transgenic human-mouse/rat technologies to the possibility of interrogating different and possibly larger antibody sequence- spaces than has hitherto been possible.
- the invention provides a SUPERHUMAN MOUSETM (aka SUPRA-MOUSETM) and a SUPERHUMAN RATTM (aka SUPRA-RATTM)
- SUPRA-RATTM aka SUPRA-RATTM
- the present inventors have realised the possibility of mining the huge genetics resources now available to the skilled person thanks to efforts such as the HapMap Project, 1000 Genomes Project and sundry other immunoglobulin gene databases (see below for more details).
- the inventors realised the application of these genome sequencing developments in the present invention to generate synthetically-produced and ethnically-diverse artificial immunoglobulin gene repertoires.
- the inventors realised that such repertoires are useful for the production of antibodies having improved affinity and/or biophysical characteristics, and/or wherein the range of epitope specificities produced by means of such repertoire is novel, provides for antibodies to epitopes that have hitherto been intractable by prior transgenic immunoglobulin loci or difficult to address.
- the present invention provides libraries, vertebrates and cells, such as transgenic mice or rats or transgenic mouse or rat cells. Furthermore, the invention relates to methods of using the vertebrates to isolate antibodies or nucleotide sequences encoding antibodies. Antibodies, nucleotide sequences, pharmaceutical compositions and uses are also provided by the invention.
- the present inventors have realized methods and antibody loci designs that harness the power of genetic variation analysis.
- the reference human genome provides a foundation for experimental work and genetic analysis of human samples.
- the reference human is a compilation of the genomes from a small number of individuals and for any one segment of the genome a high quality single reference genome for one of the two chromosomes is available. Because the reference genome was assembled from a series of very large insert clones, the identity of these clones is known.
- the 1000-Genomes Project has the objective of identifying the most frequent variations in the human genome.
- This public domain project involved sequencing the genomes of more than 1000 individuals from diverse ethnic groups, comparing these sequences to the reference and assembling a catalogue of variants. This has enabled the annotation of variants in coding regions, but because this sequence wasn't derived from large clones of DNA, the analysis of the sequence from diploid individuals can't discriminate the distribution of the variation between the maternal and paternally inherited chromosomes. Where more than one variant is identified in a protein coding gene, it is not possible to illuminate the distribution of the pattern of variants in each version of the protein.
- the 1000-Genome Project has sequenced mother-father-child trios. This allows one to "phase" the sequence variants, in other words identify blocks of sequence that are inherited from one or other parent and deconvolute the variants.
- the inventors' analysis of the 1000-genome data for the individual human coding segments of the C, V D and J genes from the heavy and light chains reveals that there is significant variation in these segments. Individuals will usually have two different heavy chain alleles and also different light chain alleles at both kappa and lambda loci. The repertoire of antibodies that can be generated from each allele will be different. This variation will contribute to a better or differing immune response to certain antigens.
- mice that have hitherto been generated with immunoglobulin heavy and light chain loci contain just one type of immunoglobulin locus. Even if these mice contain a full human heavy chain locus, the variation will be less than contained in a typical human because only one set of C, V, D and J genes are available, while a typical human would have two sets.
- the inventors have devised ways to improve on this limitation when constructing transgenic non- human vertebrates and cells for human antibody and variable region production in vivo.
- mice can be generated with two different loci, each engineered to have a different repertoire of V, D and J segments. This could be in a single mouse or two or more separate mouse strains and would be analogous to or beyond the repertoire found in a normal human. The engineering of such a mouse would go beyond the repertoire described in humanized mice to date which only have one set of alleles.
- JH gene segments eg, see the examples
- this addresses compatibility with human patients since the inventor's analysis has drawn out candidate variants that are naturally conserved and sometimes very prevalent amongst human ethnic populations. Additionally this enables one to tailor the configurations of the invention to provide for antibody-based drugs that better address specific human ethnic populations.
- loci and cells and vertebrates comprising these
- gene segments are provided in which gene segments from different human populations are used. This is desirable to increase antibody gene diversity to better address more diverse human patients.
- the gene segments are from first and second different human populations respectively, and thus the second gene segment is found in the second human population, but not so (or rarely) in the first human population. Rarely means, for example, that the gene segment is found in 5, 4, 3, 2, or 1 or zero individuals in the first population in the 1000 Genomes database.
- the first gene segment may be shown as present in a first population by reference to Table 13 or 14 herein
- the second gene segment may be shown as present in the second population by reference to Table 13 and not in the first population.
- the first gene segment may also be shown as being present in the second population by reference to Table 13 or 14.
- V gene segment In any configuration or aspect of the invention, where a V gene segment is used, this may be used optionally with the native leader sequence.
- genomic DNA eg, from BACs as in the examples
- the native leader will be used for each V gene segment incorporated into the locus and genomes of the invention.
- the skilled person may wish to inert a non-native leader sequence together with one or more of the V gene segments.
- this may be used optionally with the native 5' UTR sequence.
- genomic DNA eg, from BACs as in the examples
- native 5' UTR sequence will be used for each V gene segment incorporated into the locus and genomes of the invention.
- skilled person may wish to exclude the native 5' UTR sequence.
- the present invention provides, in a first configuration (a) Superhuman heavy chain gene repertoires
- a non-human vertebrate or vertebrate cell (optionally an ES cell or antibody-producing cell) comprising a genome having a superhuman immunoglobulin heavy chain human VH and/or D and/or J gene repertoire.
- the cell of the invention is an embryonic stem cell.
- the ES cell is derived from the mouse C57BL/6N, C57BL/6J, 129S5 or 129Sv strain.
- the non-human vertebrate is a rodent, suitably a mouse, and cells of the invention, are rodent cells or ES cells, suitably mouse ES cells.
- the ES cells of the present invention can be used to generate animals using techniques well known in the art, which comprise injection of the ES cell into a blastocyst followed by implantation of chimaeric blastocystys into females to produce offspring which can be bred and selected for homozygous recombinants having the required insertion.
- the invention relates to a transgenic animal comprised of ES cell-derived tissue and host embryo derived tissue. In one aspect the invention relates to genetically-altered subsequent generation animals, which include animals having a homozygous recombinants for the VDJ and/or VJ regions.
- the natural human immunoglobulin gene segment repertoire consists of (see eg, www.imgt.org 3 ⁇ 4:-
- V lambda total-75; functional-31 J lambda: total-7; functional-5
- the vertebrate or cell genome comprises a transgenic immunoglobulin heavy chain locus comprising a plurality of human immunoglobulin VH gene segments, one or more human D gene segments and one or more human J gene segments, wherein the plurality of VH gene segments consists of more than the natural human repertoire of functional VH gene segments; optionally wherein the genome is homozygous for said transgenic heavy chain locus.
- the VH gene repertoire consists of a plurality of VH gene segments derived from the genome sequence of a first human individual, supplemented with one or more different VH gene segments derived from the genome sequence of a second, different human individual.
- the D and J segments are derived from the genome sequence of the first human individual.
- the VH gene segments from the genome sequence of the second individual are selected from the VH gene segments listed in Table 1, 13 or 14. In this way, the locus provides a superhuman repertoire of D gene segments.
- the individuals are not related.
- Individuals are "not related" in the context of any configuration or aspect of the invention, for example, if one of the individuals does not appear in a family tree of the other individual in the same generation or going back one, two, three or four generations.
- are not related for example, if they do not share a common ancestor in the present generation or going back one, two, three or four generations.
- the transgenic locus comprises more than 41 functional human VH gene segment species, and thus more than the natural human functional repertoire.
- the locus comprises at least 42, 43, 44, 45, 46, 47, 48, 49 or 50 functional human VH gene segment species (eg, wherein the locus comprises the full functional VH repertoire of said first individual supplemented with one or more VH gene segments derived from the genome sequence of the second human individual and optionally with one or more VH gene segments derived from the genome sequence of a third human individual).
- the locus provides a superhuman repertoire of VH gene segments that is useful for generating a novel gene and antibody diversity for use in therapeutic and tool antibody selection.
- the transgenic locus comprises a first VH gene segment derived from the genome sequence of the first individual and a second VH gene segment derived from the genome sequence of the second individual, wherein the second VH gene segment is a polymorphic variant of the first VH gene segment.
- the VH gene segments are polymorphic variants of VHl-69 as illustrated in the examples below.
- the locus comprises a further polymorphic variant of the first VH gene segment (eg, a variant derived from the genome sequence of a third human individual). In this way, the locus provides a superhuman repertoire of VH gene segments.
- the genome (alternatively or additionally to the superhuman VH diversity) comprises a transgenic immunoglobulin heavy chain locus comprising a plurality of human immunoglobulin VH gene segments, a plurality of human D gene segments and one or more human J gene segments, wherein the plurality of D gene segments consists of more than the natural human repertoire of functional D gene segments.
- the genome is homozygous for said transgenic heavy chain locus.
- the D gene repertoire consists of a plurality of D gene segments derived from the genome sequence of a (or said) first human individual, supplemented with one or more different D gene segments derived from the genome sequence of a (or said) second, different human individual.
- the individuals are not related.
- the J segments are derived from the genome sequence of the first human individual.
- the D gene segments from the genome sequence of the second individual are selected from the D gene segments listed in Table 2, 13 or 14. In this way, the locus provides a superhuman repertoire of D gene segments.
- the transgenic locus comprises more than 23 functional human D gene segment species; optionally wherein the locus comprises at least 24, 25, 26, 27, 28, 29, 30 or 31 functional human D gene segment species (eg, wherein the locus comprises the full functional D repertoire of said first individual supplemented with one or more D gene segments derived from the genome sequence of the second human individual and optionally with one or more D gene segments derived from the genome sequence of a third human individual).
- the locus provides a superhuman repertoire of D gene segments.
- the transgenic locus comprises a first D gene segment derived from the genome sequence of the first individual and a second D gene segment derived from the genome sequence of the second individual, wherein the second D gene segment is a polymorphic variant of the first D gene segment.
- the locus comprises a further polymorphic variant of the first D gene segment (eg, a variant derived from the genome sequence of a third human individual). In this way, the locus provides a superhuman repertoire of D gene segments.
- the genome comprises a (or said) transgenic immunoglobulin heavy chain locus comprising a plurality of human immunoglobulin VH gene segments, one or more human D gene segments and a plurality of human JH gene segments, wherein the plurality of J gene segments consists of more than the natural human repertoire of functional J gene segments; optionally wherein the genome is homozygous for said transgenic heavy chain locus.
- the JH gene repertoire consists of a plurality of J gene segments derived from the genome sequence of a (or said) first human individual, supplemented with one or more different J gene segments derived from the genome sequence of a (or said) second, different human individual.
- the individuals are not related.
- D segments are derived from the genome sequence of the first human individual.
- the J gene segments from the genome sequence of the second individual are selected from the J gene segments listed in Table 3 13 or 14. In this way, the locus provides a superhuman repertoire of JH gene segments.
- the transgenic locus comprises more than 6 functional human JH gene segment segments.
- the locus comprises at least 7, 8, 9, 10, 11, 12, 13, 14, 15, or 16 functional human JH gene segments (eg, wherein the locus comprises the full functional JH repertoire of said first individual supplemented with one or more J H gene segments derived from the genome sequence of the second human individual and optionally with one or more J H gene segments derived from the genome sequence of a third human individual).
- the locus provides a superhuman repertoire of JH gene segments.
- the transgenic locus comprises a first J H gene segment derived from the genome sequence of the first individual and a second JH gene segment derived from the genome sequence of the second individual, wherein the second J H gene segment is a polymorphic variant of the first JH gene segment.
- the locus comprises a further polymorphic variant of the first JH gene segment (eg, a variant derived from the genome sequence of a third human individual). In this way, the locus provides a superhuman repertoire of JH gene segments.
- the first configuration of the invention also provides:-
- a non-human vertebrate or vertebrate cell (optionally an ES cell or antibody-producing cell) comprising a genome having a superhuman immunoglobulin light chain human VL gene repertoire.
- the vertebrate or cell comprises a heavy chain transgene according to aspect (a) of the first configuration.
- superhuman diversity is provided in both the heavy and light chain immunoglobulin gene segments in the cell and vertebrate.
- the genome of the cell or vertebrate is homozygous for the heavy and light chain transgenes and endogenous antibody expression is inactivated.
- Such a vertebrate is useful for immunisation with a predetermined antigen to produce one or more selected antibodies that bind the antigen and have human variable regions resulting from recombination within the superhuman gene segment repertoire. This provides potentially for a novel antibody and gene sequence space from which to select therapeutic, prophylactic and tool antibodies.
- the vertebrate or cell genome comprises a transgenic immunoglobulin kappa light chain locus comprising a plurality of human immunoglobulin VK gene segments and one or more human J gene segments, wherein the plurality of VK gene segments consists of more than the natural human repertoire of functional VK gene segments; optionally wherein the genome is homozygous for said transgenic kappa light chain locus; and/or
- transgenic immunoglobulin lambda light chain locus comprising a plurality of human immunoglobulin V ⁇ gene segments and one or more human J gene segments, wherein the plurality of V ⁇ gene segments consists of more than the natural human repertoire of functional V ⁇ gene segments; optionally wherein the genome is homozygous for said transgenic lambda light chain locus.
- the locus provides a superhuman repertoire of VL gene segments.
- the VK gene repertoire consists of a plurality of VK gene segments derived from the genome sequence of a first human individual, supplemented with one or more VK gene segments derived from the genome sequence of a second, different human individual; optionally wherein the individuals are not related; optionally wherein the J segments are derived from the genome sequence of the first human individual; and optionally wherein the VK gene segments from the genome sequence of the second individual are selected from the VK gene segments listed in Table 4, 13 or 14; and
- the V ⁇ gene repertoire consists of a plurality of V ⁇ gene segments derived from the genome sequence of a first human individual, supplemented with one or more V ⁇ gene segments derived from the genome sequence of a second, different human individual; optionally wherein the individuals are not related; optionally wherein the J segments are derived from the genome sequence of the first human individual; and optionally wherein the V ⁇ gene segments from the genome sequence of the second individual are selected from the V ⁇ gene segments listed in Table 5, 13 or 14.
- the locus provides a superhuman repertoire of VL gene segments.
- the vertebrate or cell In one embodiment of the vertebrate or cell,
- the kappa light transgenic locus comprises more than 38 functional human VK gene segment species; optionally wherein the locus comprises at least 39, 40, 41, 42, 43, 44, 45, 46, 47 or 48 functional human VK gene segment species (eg, wherein the locus comprises the full functional VK repertoire of said first individual supplemented with one or more VK gene segments derived from the genome sequence of the second human individual and optionally with one or more VK gene segments derived from the genome sequence of a third human individual); and
- the lambda light transgenic locus comprises more than 31 functional human V ⁇ gene segment species; optionally wherein the locus comprises at least 32, 33, 34, 35, 36, 37, 38, 39, 40 or 41 functional human V ⁇ gene segment species (eg, wherein the locus comprises the full functional V ⁇ repertoire of said first individual supplemented with one or more V ⁇ gene segments derived from the genome sequence of the second human individual and optionally with one or more V ⁇ gene segments derived from the genome sequence of a third human individual).
- the locus provides a superhuman repertoire of VL gene segments.
- the kappa light transgenic locus comprises a first VK gene segment derived from the genome sequence of the first individual and a second VK gene segment derived from the genome sequence of the second individual, wherein the second VK gene segment is a polymorphic variant of the first VK gene segment; optionally wherein the locus comprises a further polymorphic variant of the first VK gene segment (eg, a variant derived from the genome sequence of a third human individual); and
- the lambda light transgenic locus comprises a first V ⁇ gene segment derived from the genome sequence of the first individual and a second V ⁇ gene segment derived from the genome sequence of the second individual, wherein the second V ⁇ gene segment is a polymorphic variant of the first V ⁇ gene segment; optionally wherein the locus comprises a further polymorphic variant of the first VX gene segment (eg, a variant derived from the genome sequence of a third human individual).
- the locus provides a superhuman repertoire of VL gene segments.
- the genome comprises a (or said) transgenic immunoglobulin light chain locus comprising a plurality of human immunoglobulin VL gene segments and a plurality of human JL gene segments, wherein the plurality of J gene segments consists of more than the natural human repertoire of functional J gene segments; optionally wherein the genome is homozygous for said transgenic heavy chain locus.
- the JK gene repertoire consists of a plurality of JK gene segments derived from the genome sequence of a (or said) first human individual, supplemented with one or more J K gene segments derived from the genome sequence of a (or said) second, different human individual; optionally wherein the individuals are not related; optionally wherein the VK segments are derived from the genome sequence of the first human individual; optionally wherein the J K gene segments from the genome sequence of the second individual are selected from the J K gene segments listed in Table 6, 13 or 14; and
- the JK gene repertoire consists of a plurality of iX gene segments derived from the genome sequence of a (or said) first human individual, supplemented with one or more iX gene segments derived from the genome sequence of a (or said) second, different human individual; optionally wherein the individuals are not related; optionally wherein the V ⁇ segments are derived from the genome sequence of the first human individual; optionally wherein the iX gene segments from the genome sequence of the second individual are selected from the iX gene segments listed in Table 7, 13 or 14.
- the locus provides a superhuman repertoire of J L gene segments.
- the transgenic light chain locus comprises more than 5 functional human J K gene segment species; optionally wherein the locus comprises at least 6, 7, 8, 9, 10, 11, 12, 13, 14 or 15 functional human JK gene segment species (eg, wherein the locus comprises the full functional J K repertoire of said first individual supplemented with one or more JK gene segments derived from the genome sequence of the second human individual and optionally with one or more J K gene segments derived from the genome sequence of a third human individual); and/or
- the transgenic light chain locus comprises more than 5 functional human iX gene segment species; optionally wherein the locus comprises at least 6, 7, 8, 9, 10, 11, 12, 13, 14 or 15 functional human iX gene segment species (eg, wherein the locus comprises the full functional iX repertoire of said first individual supplemented with one or more iX gene segments derived from the genome sequence of the second human individual and optionally with one or more iX gene segments derived from the genome sequence of a third human individual).
- the locus provides a superhuman repertoire of J L gene segments.
- the kappa light transgenic locus comprises a first JK gene segment derived from the genome sequence of the first individual and a second JK gene segment derived from the genome sequence of the second individual, wherein the second JK gene segment is a polymorphic variant of the first J K gene segment; optionally wherein the locus comprises a further polymorphic variant of the first J ⁇ gene segment (eg, a variant derived from the genome sequence of a third human individual); and
- the lambda light transgenic locus comprises a first iX gene segment derived from the genome sequence of the first individual and a second iX gene segment derived from the genome sequence of the second individual, wherein the second JK gene segment is a polymorphic variant of the first iX gene segment; optionally wherein the locus comprises a further polymorphic variant of the first iX gene segment (eg, a variant derived from the genome sequence of a third human individual).
- the locus provides a superhuman repertoire of J L gene segments.
- the present invention provides, in a second configuration
- a library of antibody-producing transgenic cells whose genomes collectively encode a repertoire of antibodies, wherein (a) a first transgenic cell expresses a first antibody having a chain (eg, heavy chain) encoded by a first immunoglobulin gene, the gene comprising a first variable domain nucleotide sequence produced following recombination of a first human unrearranged immunoglobulin gene segment (eg, a VH);
- a first transgenic cell expresses a first antibody having a chain (eg, heavy chain) encoded by a first immunoglobulin gene, the gene comprising a first variable domain nucleotide sequence produced following recombination of a first human unrearranged immunoglobulin gene segment (eg, a VH);
- a second transgenic cell expresses a second antibody having a chain (eg, a heavy chain) encoded by a second immunoglobulin gene, the second gene comprising a second variable domain nucleotide sequence produced following recombination of a second human unrearranged immunoglobulin gene segment (eg, a VH), the first and second antibodies being non-identical;
- the first and second gene segments are different and derived from the genome sequences of first and second human individuals respectively, wherein the individuals are different; and optionally not related;
- cells are non-human vertebrate (eg, mouse or rat) cells (eg, B-cells or hybridomas).
- the library is provided in vitro.
- the library is provided in vivo by one or a plurality of transgenic non-human vertebrates.
- the or each vertebrate is according to any aspect of the first configuration of the invention.
- the library encodes an antibody repertoire of from 10 to 10 9 antibodies, for example, 10, 20, 30, 40, 50, 100 or 1000 to 10 s ; or 10, 20, 30, 40, 50, 100 or 1000 to 10 7 ; or 10, 20, 30, 40, 50, 100 or 1000 to 10 s ; or 10, 20, 30, 40, 50, 100 or 1000 to 10 s ; or 10, 20, 30, 40, 50, 100 or 1000 to 10 4 antibodies.
- library encodes an antibody repertoire of at least 10 3 , 10 4 , 10 s , 10 s , 10 7 , 10 s , 10 9 ' or 10 10 antibodies.
- the first variable domain nucleotide sequence is produced following recombination of the first human unrearranged immunoglobulin gene segment with one or more other immunoglobulin gene segments (for example, human immunoglobulin gene segments).
- the first gene segment is a VH
- the first variable domain nucleotide sequence (a VH domain) is produced following recombination of the VH with a human D and JH segments in vivo, optionally with somatic hypermutation, in the first transgenic cell or an ancestor thereof.
- the first variable domain nucleotide sequence (a VL domain) is produced following recombination of the VL with a human JL segment in vivo, optionally with somatic hypermutation, in e first transgenic cell or an ancestor thereof.
- the second variable domain nucleotide sequence is produced following recombination of the second human unrearranged immunoglobulin gene segment with one or more other immunoglobulin gene segments (for example, human immunoglobulin gene segments).
- the second gene segment is a VH
- the second variable domain nucleotide sequence (a VH domain) is produced following recombination of the VH with a human D and JH segments in vivo, optionally with somatic hypermutation, in the second transgenic cell or an ancestor thereof.
- the second variable domain nucleotide sequence (a VL domain) is produced following recombination of the VL with a human JL segment in vivo, optionally with somatic hypermutation, in the second transgenic cell or an ancestor thereof.
- the first and second gene segments are respectively derived from genome sequences of first and second human individuals.
- a gene segment is isolated or cloned from a sample cell taken from said individual using standard molecular biology techniques as know to the skilled person.
- the sequence of the gene segment may be mutated (eg, by the introduction of up to 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 or 15 nucleotide changes) prior to use in the present invention.
- a gene segment is derived by identifying a candidate human immunoglobulin gene segment in a database (see guidance below) and a nucleotide sequence encoding a gene segment for use in the present invention is made by reference (eg, to be identical or a mutant with up to 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 or 15 nucleotide changes to the reference sequence) to the database sequence.
- a nucleotide sequence encoding a gene segment for use in the present invention is made by reference (eg, to be identical or a mutant with up to 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 or 15 nucleotide changes to the reference sequence) to the database sequence.
- the skilled person will be aware of methods of obtaining nucleotide sequences by reference to databases or by obtaining from cellular samples.
- the first and second human individuals are members of first and second ethnic populations respectively, wherein the populations are different. This, therefore, provides for superhuman gene diversity in transgenic loci, cells and vertebrates as per the invention.
- the ethnic populations are selected from those identified in the 1000 Genomes Project of database.
- Table 8 which provides details of the ethnic populations on which the 1000 Genomes database is based.
- the International HapMap Project discloses that goal of the HapMap Project: to determine the common patterns of DNA sequence variation in the human genome by determining the genotypes of one million or more sequence variants, their frequencies and the degree of association between them in DNA samples from populations with ancestry from parts of Africa, Asia and Europe.
- the relevant human populations of differing geographical ancestry include Yoruba, Japanese, Chinese, Northern European and Western European populations. More specifically:- Utah population with Northern or Western European ancestry (samples collected in 1980 by the
- a suitable sample of human populations from which the populations used in the present invention are selected is as follows:-
- each human population is selected from a population marked "(a)" above.
- each human population is selected from a population marked "(b)" above.
- each human population is selected from a population marked "(c)" above.
- the first and second ethnic populations are selected from the group consisting of an ethnic population with European ancestry, an ethnic population with East Asian, an ethnic population with West African ancestry, an ethnic population with Americas ancestry and an ethnic population with South Asian ancestry.
- the first and second ethnic populations are selected from the group consisting of an ethnic population with Northern European ancestry; or an ethnic population with Western European ancestry; or an ethnic population with Toscani ancestry; or an ethnic population with British ancestry; or an ethnic population with Icelandic ancestry; or an ethnic population with Finnish ancestry; or an ethnic population with Iberian ancestry; or an ethnic population with Japanese ancestry; or an ethnic population with Chinese ancestry; or an ethnic population Vietnamese ancestry; or an ethnic population with Yoruba ancestry; or an ethnic population with Luhya ancestry; or an ethnic population with Gambian ancestry; or an ethnic population with Malawian ancestry; or an ethnic population with Native American ancestry; or an ethnic population with Afro-Caribbean ancestry; or an ethnic population with Mexican ancestry; or an ethnic population with Puerto ican ancestry;
- the human immunoglobulin gene segment derived from the genome sequence of the second individual is low-frequency (optionally rare) within the second ethnic population.
- human immunoglobulin gene segment has a Minor Allele Frequency (MAF) (cumulative frequency) of between 0.5% - 5%, optionally less than 0.5%, in the second human population, eg, as in the 1000 Genomes database.
- MAF Minor Allele Frequency
- the first variable region nucleotide sequence is produced by recombination of the first human
- immunoglobulin gene segment with a first J gene segment and optionally a first D gene segment, wherein the first human immunoglobulin gene segment is a V gene segment and the V, D and J segments are derived from the first human population, optionally from the genome of one individual the first human populati
- the second variable region nucleotide sequence is produced by recombination of the second human immunoglobulin gene segment with a second J gene segment and optionally a second D gene segment, wherein the second human immunoglobulin gene segment is a V gene segment derived from the second population and the D and/or J segments are derived from the first human population, optionally the D and J gene segments being from the genome of one individual of the first human population.
- all of the D and J segments that have been recombined with the first and second V gene segments are D and J segments derived from the first human population, optionally the D and J gene segments being from the genome of one individual of the first human population.
- the second human immunoglobulin gene segment is a polymorphic variant of the first human immunoglobulin gene segment; optionally wherein the second gene segment is selected from the group consisting of a gene segment in any of Tables 1 to 7 and 9 to 14 (eg, selected from Table 13 or 14).
- the first and second human immunoglobulin gene segments are both (i) V H gene segments; (ii) D segments; (iii) J segments (optionally both J H segments, both J K segments or both ⁇ ⁇ segments); (iv) constant regions (optionally both a gamma constant region, optionally both a C gamma-1 constant region); (v) CHI regions; (vi) CH2 regions; or (vii) CH3 regions.
- the library is, for example, a naive and optionally has a library size of from 10 or 10 2 to 10 9 cells.
- the library has, for example, been selected against a predetermined antigen and optionally has a library size of from 10 or 10 2 to 10 9 cells.
- said first and second cells are progeny of first and second ancestor non-human vertebrate cells respectively, wherein the first ancestor cell comprises a genome comprising said first human immunoglobulin gene segment; and the second ancestor cell comprises a genome comprising said second human immunoglobulin gene segment.
- the invention further provides a library of antibody-producing transgenic cells whose genomes collectively encode a repertoire of antibodies, wherein the library comprises the first and second ancestor cells described above.
- the invention further provides a library of hybridoma cells produced by fusion of the library of the invention (eg, a B-cell library) with fusion partner cells and optionally has a library size of from 10 or 10 2 to 10 9 cells.
- a library size of from 10 or 10 2 to 10 9 cells.
- 10 or 10 2 to 10 9 cells For example, from 10, 20, 30, 40, 50, 100 or 1000 to 10 s ; or 10, 20, 30, 40, 50, 100 or 1000 to 10 7 ; or 10, 20, 30, 40, 50, 100 or 1000 to 10 s ; or 10, 20, 30, 40, 50, 100 or 1000 to 10 s ; or 10, 20, 30, 40, 50, 100 or 1000 to 10 4 cells.
- Production of hybridomas is well known to the skilled person.
- fusion partners are SP2/0-gl4 (obtainable from ECACC), P3X63-Ag8.653 (obtainable from LGC Standards; C L-1580), NS1 and NS0 cells.
- PEG fusion or electrofusion can be carried out, as is conventional.
- the invention provides, in a third confieuration:- An isolated antibody having
- each variable domain of the antibody is a human variable domain.
- heavy chain constant regions are mu- or gamma-type constant regions.
- the invention also provides an isolated nucleotide sequence encoding the antibody of the third configuration, optionally wherein the sequence is provided in an antibody expression vector, optionally in a host cell.
- Suitable vectors are mammalian expression vectors (eg, CHO cell vectors or HEK293 cell vectors), yeast vectors (eg, a vector for expression in Picchia pastoris, or a bacterial expression vector, eg, a vector for E. coli expression.
- the invention also provides a method of producing a human antibody, the method comprising replacing the non-human vertebrate constant regions of the antibody of the third configuration with human antibody constant regions (eg, a C variant disclosed in table 13 or 18).
- human antibody constant regions eg, a C variant disclosed in table 13 or 18.
- the skilled person will be aware of standard molecular biology techniques to do this. For example, see Harlow, E. & Lane, D. 1998, 5 th edition, Antibodies: A Laboratory Manual, Cold Spring Harbor Lab. Press, Plainview, NY; and Pasqualini and Arap, Proceedings of the National Academy of Sciences (2004) 101:257-259 for standard immunisation.
- Joining of the variable regions of an antibody to a human constant region can be effected by techniques readily available in the art, such as using conventional recombinant DNA and NA technology as will be apparent to the skilled person. See e.g. Sambrook, J and Russell, D. (2001, 3'd edition) Molecular Cloning: A Laboratory Manual (Cold Spring Harbor Lab. Press, Plainview, NY).
- the method comprises further making a mutant or derivative of the antibody.
- the invention also provides a pharmaceutical composition
- a pharmaceutical composition comprising an antibody according to the third configuration, or a human antibody of the invention and a diluent, excipient or carrier;
- composition is provided in a container connected to an IV needle or syringe or in an IV bag.
- the invention also provides an antibody-producing cell (eg, a mammalian cell, eg, CHO or HEK293; a yeast cell, eg, P pastoris; a bacterial cell, eg, E coli; a B-cell; or a hybridoma) that expresses the second antibody of the third configuration or the isolated antibody of the invention.
- an antibody-producing cell eg, a mammalian cell, eg, CHO or HEK293; a yeast cell, eg, P pastoris; a bacterial cell, eg, E coli; a B-cell; or a hybridoma
- the first configuration of the invention also provides:-
- a non-human vertebrate or vertebrate cell (optionally an ES cell or antibody-producing cell) whose genome comprises a transgenic immunoglobulin locus (eg, a heavy chain locus or a light chain locus), said locus comprising immunoglobulin gene segments according to the first and second human immunoglobulin gene segments (optionally V segments) described above in connection with the third configuration.
- the gene segments are operably connected upstream of an immunoglobulin constant region; optionally wherein the genome is homozygous for said transgenic immunoglobulin locus.
- the immunoglobulin locus comprises more than the natural human complement of functional V gene segments; and/or
- immunoglobulin locus comprises more than the natural human complement of functional D gene segments;
- immunoglobulin locus comprises more than the natural human complement of functional J gene segments.
- the first configuration also provides:-
- a transgenic non-human vertebrate eg, a mouse or rat
- vertebrate cell eg. an ES cell or antibody-producing cell
- a transgenic immunoglobulin locus comprising a plurality of human immunoglobulin gene segments operably connected upstream of a non-human vertebrate constant region for the production of a repertoire of chimaeric antibodies, or chimaeric light or heavy chains, having a non-human vertebrate constant region and a human variable region
- the transgenic locus comprises one or more human immunoglobulin V gene segments, one or more human J gene segments and optionally one or more human D gene segments, a first (optionally a V segment) of said gene segments and a second (optionally a V segment) of said gene segments being different and derived from the genomes of first and second human individuals respectively, wherein the individuals are different; and optionally not related; optionally wherein the immunoglobulin locus comprises more than the natural human complement of functional V gene segments; and/or optionally where
- a superhuman immunoglobulin gene repertoire is provided in a transgenic non-human vertebrate or vertebrate cell according to the invention.
- the first configuration also provides:-
- a transgenic non-human vertebrate eg, a mouse or rat
- vertebrate cell eg. an ES cell or antibody-producing cell
- each locus comprising a plurality of human immunoglobulin gene segments operably connected upstream of a non-human vertebrate constant region for the production of a repertoire of chimaeric antibodies, or chimaeric light or heavy chains, having a non-human vertebrate constant region and a human variable region
- the first transgenic locus comprises one or more human immunoglobulin V gene segments, one or more human J gene segments and optionally one or more human D gene segments
- the second transgenic locus comprises one or more human immunoglobulin V gene segments, one or more human J gene segments and optionally one or more human D gene segments
- each immunoglobulin locus comprises more than the natural human
- each immunoglobulin locus comprises more than the natural human
- a superhuman immunoglobulin gene repertoire is provided in a transgenic non-human vertebrate or vertebrate cell according to the invention.
- the immunoglobulin gene segments are optionally as described for the third configuration.
- the genome optionally comprises a third immunoglobulin gene segment (optionally a V segment), the third gene segment being derived from a human individual that is different from the individual from which the first (and optionally also the second) gene segment is derived; optionally wherein the first, second and third gene segments are polymorphic variants of a human immunoglobulin gene segment (eg, VH1-69 - see the examples for further description).
- a human immunoglobulin gene segment eg, VH1-69 - see the examples for further description.
- the genome of the vertebrate or cell is optionally homozygous for the first, second and optional third gene segment, wherein a copy of the first, second and optional third gene segments are provided together on the same chromosome operably connected upstream of a common non-human vertebrate constant region.
- each first, second and optional third gene segment is a V gene segment.
- the library of the invention is provided by a collection of non-human vertebrates (optionally a collection of rodents, mice or rats); optionally, wherein a first member of said collection produces said first antibody but not said second antibody, and a second member of the collection produces said second antibody (but optionally not said first antibody). It is therefore contemplated to make non-human vertebrates where different human genomes have been used as a source for building the transgenic loci in the vertebrates.
- a first vertebrate comprises a transgenic heavy chain locus having gene segments only from a first (and optionally a second) human population or individual;
- a second vertebrate comprises a transgenic heavy chain locus having gene segments only from a third (and optionally a fourth) human population or individual; and optionally third and more vertebrates can be built similarly based on unique or overlapping human population genomes.
- the mixed population provides a collective pool of human immunoglobulin genes that is greater than found in a natural human repertoire. This is useful to extend the antibody and gene sequence space beyond those possible with prior transgenic mice and rats bearing human immunoglobulin loci. As explained above, these have been based on a single human genome.
- the collection of non-human vertebrates bear human immunoglobulin genes confined to human populations that are together grouped under the same population genus "(a)" mentioned above.
- This provides for a gene repertoire that is biased to producing human antibody variable regions prevalent in the population genus (a) and thus useful for generating antibody therapeutics/prophylactics for members of said population.
- gene segments from different human populations are provided in a single transgene according to the invention (not necessarily in a collection of vertebrates)
- the different human populations are for example together grouped under the same population genus "(a)" mentioned above.
- the invention also provides a repertoire of antibodies expressed from a library of cells according to the invention.
- the constant region of the transgenic locus is, in one example, an endogenous constant region of said vertebrate (eg, endogenous mouse or rat constant region, eg, from the same strain of mouse or rat as the non- human vertebrate itself).
- an endogenous constant region of said vertebrate eg, endogenous mouse or rat constant region, eg, from the same strain of mouse or rat as the non- human vertebrate itself.
- the invention also provides a method of constructing a cell (eg, an ES cell) according to the invention, the method comprising
- the cell comprises a heavy chain locus constructed according to steps (a) to (c) and/or a light chain locus (kappa and/or lambda loci) constructed according to steps (a) to (c).
- the cell is homozygous for the or each transgenic locus; optionally wherein antibody expression from loci endogenous to said cell has been inactivated. This is useful for confining the functional antibody gene repertoire, and thus antibody production, to antibodies bearing human variable regions.
- the gene segment(s) in step (b) are identified from an immunoglobulin gene database selected from the 1000 Genomes, Ensembl, Genbank and IMGT databases.
- the first and second human individuals are members of first and second ethnic populations respectively, wherein the populations are different, optionally wherein the human immunoglobulin gene segment derived from the genome sequence of the second individual is low- frequency (optionally rare) within the second ethnic population.
- the invention also provides a method of making a transgenic non-human vertebrate (eg, a mouse or rat), the method comprising
- an ES cell eg, a mouse C57BL/6N, C57BL/6J, 129S5 or 129Sv strain ES cell
- a donor non-human vertebrate blastocyst eg, a mouse C57BL/6N, C57BL/6J, 129S5 or 129Sv strain blastocyst
- the invention provides a transgenic non-human vertebrate (eg, a mouse or rat) made by the method or a progeny thereof.
- the invention also provides a population of such non-human vertebrates.
- the invention also provides a method of isolating an antibody that binds a predetermined antigen (eg, a bacterial or viral pathogen antigen), the method comprising
- This method optionally further comprises after step (e) the step of isolating from said B lymphocytes nucleic acid encoding said antibody that binds said antigen; optionally exchanging the heavy chain constant region nucleotide sequence of the antibody with a nucleotide sequence encoding a human or humanised heavy chain constant region and optionally affinity maturing the variable region of said antibody; and optionally inserting said nucleic acid into an expression vector and optionally a host.
- GenBank www.ncbi.nlm.nih.gov/genbank
- Bioinformatics tools for database manipulation are also readily available and known to the skilled person, eg, as publicly available from the 1000 Genomes Project/EBI (www.100Qgenomes.org)
- IMGT International ImMunoGeneTics Information System 9 ; M.-P. Lefranc, 2002;
- IMGT is an integrated information system that specializes in antibodies, T cell receptors, and MHC molecules of all vertebrate species. It provides a common portal to standardized data that include nucleotide and protein sequences, oligonucleotide primers, gene maps, genetic polymorphisms, specificities, and two-dimensional (2D) and three-dimensional (3D) structures.
- IMGT includes three sequence databases (IMGT/LIGM-DB, IMGT/MHC-DB, IMGT/PRIMERDB), one genome database (IMGT/GENE-DB), one 3D structure database (IMGT/3Dstructure-DB), and a range of web resources ("/MGf Marie-Paule page”) and interactive tools.
- V-BASE (I. M. Tomlinson, 2002;https://www.mrc-cpe.cam. ac.uk/vbase).
- V-BASE is a comprehensive directory of all human antibody germline variable region sequences compiled from more than one thousand published sequences. It includes a version of the alignment software DNAPLOT (developed by Hans-Helmar Althaus and Werner Muller) that allows the assignment of rearranged antibody V genes to their closest germline gene segments.
- Antibodies Structure and Sequence(A. C. R. Martin, 2002; htto:https://www. bioinf.ora.uk/abs). This page summarizes useful information on antibody structure and sequence. It provides a query interface to the Kabat antibody sequence data, general information on antibodies, crystal structures, and links to other antibody-related information. It also distributes an automated summary of all antibody structures deposited in the Protein Databank (PDB). Of particular interest is a thorough description and comparison of the various numbering schemes for antibody variable regions.
- PDB Protein Databank
- AAAAA AHo's Amazing Atlas of Antibody Anatomy (A. Honegger, 2001;
- This resource includes tools for structural analysis, modeling, and engineering. It adopts a unifying scheme for comprehensive structural alignment of antibody and T- cell-receptor sequences, and includes Excel macros for antibody analysis and graphical representation.
- Therapeutic Antibody Human Homology Project which aims to correlate clinical efficacy and antiimmunoglobulin responses with variable region sequences of therapeutic antibodies.
- the Antibody Resource Page (The Antibody Resource Page, 2000;
- HapMap The International HapMap Consortium. 2003;
- the HapMap Project is an international project that aims to compare the genetic sequences of different individuals to identify chromosomal regions containing shared genetic variants.
- the HapMap www site provides tools to identify chromosomal regions and the variant therein, with options to drill down to population level frequency data.
- This resource provides complete genomic sequence for 2500 unidentified individuals from one of 25 distinct population groups, with the aim of identifying genomic variants of >1%.
- the site provides the ability to interrogate data utilizing online tools (e.g. 'Variation Pattern Finder') and to download variant data for individual population groups.
- a low- frequency immunoglobulin gene segment is classed as one with 'Minor Allele Frequency' (MAF) (cumulative frequency) of between 0.5% - 5%, rare variants are those classed as having a MAF of less than 0.5% in a particular human population.
- MAF 'Minor Allele Frequency'
- germline refers to the canonical germline gene segment sequence.
- the inventors have devised a collection of candidate polymorphic antibody gene segment variants, eg, human variant JH gene segments (eg, see Example 4), that can be built into the design of transgenic heavy chain loci in mice for expressing increasingly diverse and new, synthetic repertoires of human variable regions.
- candidate polymorphic antibody gene segment variants eg, human variant JH gene segments (eg, see Example 4)
- the invention provides the following embodiments.
- the present invention provides in a fourth configuration-
- Antibodies with long HCDR3 have been shown to neutralise a variety of pathogens effectively including HIV, Influenza virus, malaria and Africa trypanosomes. Reference is also made to naturally-occurring Camelid (eg, llama or camel) heavy chain-only antibodies which bear long HCDR3s for reaching relatively inaccessible epitopes (see, eg, EP0937140). Long HCDR3s can form unique stable subdomains with extended loop structure that towers above the antibody surface to confer fine specificity. In some cases, the long HCD 3 itself is sufficient for epitope binding and neutralization (Liu, L et al; Journal of Virology. 2011.
- the unique structure of the long HCDR3 allows it to bind to cognate epitopes within inaccessible structure or extensive glycosylation on a pathogen surface.
- human peripheral blood there is around 3.5% of naive B antibodies or 1.9% of memory B IgG antibodies containing the HCDR3s with lengths of more than 24 amino acids (PLoS One. 2012;7(5):e36750. Epub 2012 May 9; "Human peripheral blood antibodies with long HCDR3s are established primarily at original recombination using a limited subset of germline genes"; Briney BS e al, incorporated herein by reference) (Fig. 1).
- the inventors chose in this configuration of the invention to include a human JH6 gene segment as a mandatory human gene segment in their IgH locus design.
- a human JH6 gene segment as a mandatory human gene segment in their IgH locus design.
- Several different naturally- occurring human JH6 variants are known (eg, JH6*01 to *04 as well as others; I MGT nomenclature). The inventors considered this when deciding upon which human JH6 variant should be included in the transgenic IgH locus design.
- FIG. 7 An alignment of some human JH6 variants is shown in Figure 7 (from www.imgt.org: dashes indicate identical nucleotides; nucleotide changes versus the *01 variant are shown by underlined nucleotides and corresponding amino acid changes are shown by underlined amino acids; Genbank accession numbers (release 185.0) are shown prefixed by J, X, M or A).
- the inventors used sequencing of human genomic DNA samples, inspection of public IgH DNA databases as well as informed choices on the basis of variant sequences as means to arrive at a rational choice of which JH6 variant to use.
- the 1000 Genomes database uses human JH6*03 as the reference sequence, which would be a possible choice for the skilled person wishing to construct a transgenic IgH locus.
- position 6 in JH6*03 is a tyrosine (Y) encoded by a TAC codon
- Y tyrosine
- G glycine
- GGT codon the glycine being present as a YYG motif, forming part of a larger YYGXDX motif.
- YYG and YYGXDX motifs are conserved across many vertebrate species (see Figures 7 & 8). This suggested to the inventors, therefore, that preservation of this motif might be desirable, which could guide the choice of JH6 variant for use in the present invention.
- AID mutation hotspots the cytidine being the substrate of AID
- these hotspots being the underlined motifs in the previous sentence.
- the inventors considered the impact of this and in doing so they considered possible mutants created by AID activity at the cytidine.
- JH6*02 decided specifically to use human JH6*02 as the mandatory human JH6 for their IgH locus design.
- JH6*01 was rejected as the mandatory JH6 gene segment since the nucleotide sequence GGG CAA (encoding G and Q) contains a GGCA motif which is an AID recognition hotspot.
- the inventors realised that JH6*04 also contains such a motif due to the presence of the sequence GGC AAA encoding G and K (positions 11 and 12 respectively).
- the *02 variant has a C instead of a G that is in the *01 variant, the C desirably being a synonymous change (ie, not changing the encoded amino acid sequence around the CDR3/FW4 junction) and also this does not provide a GGCA AID hotspot motif.
- the inventors therefore, decided that the mandatory JH6 should have this C base and this too pointed them to using the human JH6*02 variant.
- the only JH6 species included in the locus or genome is human JH6*02.
- the inventors obtained 9 anonymised DNA samples from cheek swabs of 9 consenting human adults. Sequencing was performed on IgH locus DNA to confirm natural JH6 variant usage. It was found that the genome of all 9 humans contained a JH6*02 variant gene segment. In 7 out of the 9 humans, the genome was homozygous for JH6*02 (ie, each chromosome 14 had JH6*02 as its JH6 gene segment in the IgH locus). The inventors also inspected the publicly-available sequence information from the genomes of well-known scientists Craig Venter and Jim Watson. Both of these genomes contain JH6*02 too. This indicated to the inventors that this variant is common in humans.
- the inventors constructed transgenic JH6*02-containing IgH loci in ES cells, generated transgenic non-human vertebrates from the ES cells (both naive and immunised with a range of different target antigen types), isolated antibodies and heavy chain sequences based on JH6*02 as well as B-cells expressing these and made hybridomas expressing antigen-specific antibodies that are based on the chosen JH6*02 variant.
- the chosen variant was preferably used over other JH gene segments in all settings (naive, immunised and antigen-specific) for the production of HCD 3 of at least 20 amino acids.
- the present invention provides an IgH locus including human JH6*02 (IMGT nomenclature) as a mandatory JH gene segment.
- the locus comprises non-human vertebrate (eg, mouse or rat) constant region gene segments downstream (ie, 3' of) the human JH6*02; and one or more VH gene segments (eg, a plurality of human VH gene segments) and one or more D gene segments (eg, a plurality of human D gene segments) upstream of (ie, 5' of) the human JH6*02.
- the locus is comprised by a vector (eg, a DNA vector, eg, a yeast artificial chromosome (YAC), BAC or PAC).
- Such a vector eg, YAC
- a non-human vertebrate eg, mouse or rat
- standard techniques eg, pronuclear injection
- IgH chains comprising at least one chain whose variable domain is a product of the recombination of human JH6*02 with a VH and a D gene segment.
- the locus (eg, with a completely human, rat or mouse constant region, or a human/mouse chimaeric constant region) can be provided in the genome of a non-human vertebrate (eg, mouse or rat) cell.
- the cell is an ES cell or an antibody-producing cell (eg, an isolated B-cell, an iPS cell or a hybridoma).
- the invention provides a non-human vertebrate (eg, a mouse or a rat) comprising an IgH locus of the invention which comprises a human JH6*02 gene segment, wherein the locus can express an IgH chain whose variable domain is a product of the recombination of human JH6*02 with a VH and a D gene segment.
- a non-human vertebrate eg, a mouse or a rat
- the locus can express an IgH chain whose variable domain is a product of the recombination of human JH6*02 with a VH and a D gene segment.
- the inventors have successfully produced such mice which produce such IgH chains with VH domains based on human JH6*02.
- the inventors isolated and sequenced IgH chains from the mice before (naive) and after (immunised) exposure to a range of target antigens and confirmed by comparison to IMGT IgH gene segment sequences that the isolated chains (and antibodies containing these) were produced based on JH6*02. Such chains were found in naive mice, as well as in antigen-specific antibodies from immunised mice.
- B-cells were isolated from immunised mice, wherein the B-cells express antibodies based on JH6*02 and hybridomas were generated from the B-cells, the hybridomas expressing antigen-specific antibodies based on JH6*02.
- the inventors therefore, provided the locus, vertebrate, cell and hybridoma of the invention based on the use of human JH6*02 and showed that antibodies based on JH6*02 and B-cells expressing these can be successfully produced and isolated following immunisation of the vertebrates, corresponding hybridomas being a good source of antibodies whose VH domains are based on JH6*02, eg for administration to a patient, eg, for human medicine. Furthermore, it was found possible to produce and isolated antigen-specific antibodies whose VH domains are based on JH6*02 and which had a relatively long HCDR3 (eg, 20 amino acids).
- a non-human vertebrate (optionally a mouse or a rat) or vertebrate cell whose genome comprises an immunoglobulin heavy chain locus comprising human gene segment JH6*02, one or more VH gene segments and one or more D gene segments upstream of a constant region; wherein the gene segments in the heavy chain locus are operably linked to the constant region thereof so that the mouse is capable of producing an antibody heavy chain produced by recombination of the human JH6*02 with a D segment and a VH segment.
- the invention provides
- the locus comprises a human JH6, eg, JH6*02.
- the invention also provides a HCDR3, VH domain, antibody heavy chain or antibody having a HCDR3 size of at least 20 amino acids.
- the HCDR3 or VH domain (or VH domain of the heavy chain or antibody) comprises mouse AID-pattern somatic hypermutations and/or mouse dTd-pattern mutations. This can be provided, for example, wherein VH domain is produced in a mouse comprising mouse AID and/or mouse TdT (eg, endogenous AID or TdT). See also Annu. Rev. Biochem. 2007. 76:1-22; Javier M. Di noisya and Michael S.
- the vertebrate is naive. In another embodiment, the vertebrate instead is immunised with a target antigen.
- the vertebrate or cell mentioned below is capable of so producing an antibody heavy chain upon immunisation with a target antigen.
- the vertebrate is an immunised vertebrate that produces antibody heavy chains specific for a target antigen and wherein the variable domains of the heavy chains are the product of recombination between a VH, D and JH6*02.
- the D is selected from human D3-3, D2-15, D3-9; D4-17; D3-10; D2-2; D5-24; D6-19; D3-22; D6-13; D5-12; Dl-26; Dl-20; D5-18; D3-16; D2-21; Dl-14; D7-27; Dili D6-25; D2-14 and D4-23 (eg, selected from D3-9*01; D4-17*01; D3-10*01; D2-2*02; D5- 24*01; D6-19*01; D3-22*01; D6-13*01; D5-12*01; Dl-26*01; Dl-20*01; D5-18*01; D3-16*02; D2-21*02; Dl-14*01; D7-27*02; Dl-l*01; D6-25*01; D2-15*01; and D4-23*01).
- the D is human D3-9 or D3-10.
- the HCD 3 length is at least
- the genome comprises additional human JH gene segments (eg, JH2, 3, 4 and 5 gene segments).
- the genome comprises an immunoglobulin light chain locus comprising one or more human V gene segments and one or more human J gene segments upstream of a constant region (eg, a human or a mouse lambda or kappa constant region).
- a constant region eg, a human or a mouse lambda or kappa constant region
- the locus comprises control elements, such as an ⁇ and 5 ⁇ between the J gene segment(s) and the constant region as is known by the skilled person.
- control elements such as an ⁇ and 5 ⁇ between the J gene segment(s) and the constant region as is known by the skilled person.
- a mouse ⁇ and 5 ⁇ is included in the heavy chain locus between the JH6*02 and the constant region (ie, in 5' to 3' order the locus comprises the JH6*02, ⁇ and 5 ⁇ and constant region).
- the ⁇ and 5 ⁇ are ⁇ and 5 ⁇ of a mouse 129-derived genome (eg, a 129Sv-derived genome, eg, 129Sv/EV (such as 129S7Sv/Ev (such as from AB2.1 or AB2.2 cells obtainable from Baylor College of Medicine, Texas, USA) or 129S6Sv/Ev))); in another example, the ⁇ and 5 ⁇ are ⁇ and 5 ⁇ of a mouse C57BL/6 -derived genome.
- the locus can be constructed in the IgH locus of the genome of a cell selected from AB2.1, AB2.2, VGF1, CJ7 and FH14.
- VGF1 cells were established and described in Auerbach W, Dunmore JH, Fairchild-Huntress V, et al; Establishment and chimera analysis of 129/SvEv- and C57BL/6-derived mouse embryonic stem cell lines. Biotechniques 2000; 29:1024-8, 30, 32, incorporated herein by reference.
- the constant region (or at least a C ⁇ ; or C ⁇ and gamma constant regions thereof) is a constant region (or C ⁇ ; or C ⁇ and gamma constant regions thereof) is of a genome described in the paragraph immediately above.
- JH6*02 and other human DNA sequences will be readily apparent to the skilled person.
- a DNA sample from a consenting human donor (eg, a cheek swab sample as per the Example herein) from which can be obtained suitable DNA sequences for use in constructing a locus of the invention.
- Other sources of human DNA are commercially available, as will be known to the skilled person.
- the skilled person is able to construct gene segment sequence by referring to one or more databases of human Ig gene segment sequences disclosed herein.
- the immunised vertebrate produces an antibody heavy chain specific for a target antigen and wherein the variable domain of the heavy chain is the product of recombination between a VH, D and JH6*02 and wherein the HCDR3 length is at least 20 amino acids (eg, 20, 21, 23 or 24).
- a non-human vertebrate cell (optionally a mouse cell or a rat cell) whose genome comprises an immunoglobulin heavy chain locus comprising human gene segment JH6*02, one or more VH gene segments and one or more D gene segments upstream of a constant region; wherein the gene segments in the heavy chain locus are operably linked to the constant region thereof for producing (eg, in a subsequent progeny cell) an antibody heavy chain produced by recombination of the human JH6*02 with a D segment and a VH segment.
- the cell of clause 3 which is an ES cell capable of differentiation into a progeny antibody- producing cell that expresses said heavy chain.
- the heavy chain locus comprises a human JH6*02 recombination signal sequence (RSS) operably connected 5' to the JH6*02 gene segment.
- RSS recombination signal sequence
- the native RSS-JH6*02 sequence can be used to advantageously maintain the natural pairing between RSS and theis JH gene segment.
- the following sequence is used:- ggtttttgtggggteaggatggacattctgccattgtgattactactactactacggtatggacgtctggggccaagggaccacgg ⁇ tctcctcag (SEQ ID NO: 238)
- RSSs have a common architecture: 9mer (eg, first underlined sequence above) followed by a 22bp spacer and then a 7mer (eg, second underlined sequence above). Spacers are 23bp +/- 1 normally, while the 9 and 7mer are more conserved.
- JH6*02 is the only JH6-type gene segment in the genome.
- the locus comprises one, more or all human D gene segments D3-9; D4-17; D3-10; D2-2; D5-24; D6-19; D3-22; D6-13; D5-12; Dl-26; Dl-20; D5-18; D3-16; D2-21; Dl-14; D7-27; Dl-1; D6-25; D2-14; and D4-23.
- the locus comprises one, more or all of human D gene segments D3-9*01; D4- 17*01; D3-10*01; D2-2*02; D5-24*01; D6-19*01; D3-22*01; D6-13*01; D5-12*01; Dl-26*01; Dl-20*01; D5-18*01; D3-16*02; D2-21*02; Dl-14*01; D7-27*02; Dl-l*01; D6-25*01; D2-15*01; and D4-23*01.
- the vertebrate or cell of clause 10, wherein the locus comprises one, more or all human D gene segments D3-9, D3-10, D6-19, D4-17, D6-13, D3-22, D2-2, D2-25 and D3-3.
- the locus comprises one, more or all human D gene segments D3-9, D3-10, D6- 19, D4-17, D6-13 and D3-22 (for example one, more or all of D3-9*01, D3-10*01, D6-19*01, D4- 17*01, D6-13*01 and D3-22*01).
- D segments were found in naive repertoires to be productive in recombination with human JH6*02 to produce HCDR3s of at least 20 amino acids in length.
- the locus comprises one, more or all human D gene segments D3-10, D6-19 and Dl-26 (for example, one, more or all of D3-10*01, D6-19*01 and Dl-26*01). These D segments were found in immunised repertoires to be productive in recombination with human JH6*02 to produce HCDR3s of at least 20 amino acids in length.
- the locus comprises one, more or all human D gene segments D3-9 and D3-10 (for example, one, more or all of D3-9*01 and D3-10*01). These D segments were found in antigen-specific repertoires to be productive in recombination with human JH6*02 to produce HCDR3s of at least 20 amino acids in length.
- the 3'-most D gene segment is D7-27.
- the locus comprises all of human D gene segments from Dl-1 to D7-27 as present in a germline human IgH locus (eg, as shown in the IMGT database).
- the JH6*02 is in human germline configuration with respect to one, more or all of the ⁇ , 5 ⁇ and constant region (eg, C ⁇ ).
- the locus comprises one, more or all of IGHV gene segments selected from V3-21, V3-13, V3-7, V6-1, Vl-8, Vl-2, V7-4-1, Vl-3, Vl-18, V4-4, V3-9, V3-23, V3-11 and V3-20.
- the locus comprises one, more or all human IGHV gene segments V3-21, V3-13, V3-7, V6-1, Vl-8, Vl-2, V7-4-1, Vl-3, Vl-18, V4-4, V3-9, V3-23 (for example, one, more or all of V3-21*03, V3-13*01, V3-7*01, V6-l*01, Vl-8*01, Vl-2*02, V7-4-l*01, Vl-3*01, Vl-18*01, V4- 4*01, V3-9*01 and V3-23*04).
- These segments were found in naive repertoires to be productive in recombination with human JH6*02 to produce HCD 3s of at least 20 amino acids in length.
- the locus comprises one, more or all human IGHV gene segments V3-7, V3-11 and V4-4 (for example, one, more or all of V3-7*01, V3-ll*01 and V4-4*02). These segments were found in immunised repertoires to be productive in recombination with human JH6*02 to produce HCDR3s of at least 20 amino acids in length.
- the locus comprises one, more or all human IGHV gene segments V4-4, Vl-8, V3- 9, V3-11 and V3-20 (for example, one, more or all of V4-4*02, Vl-8*01, V3-9*01, V3-ll*01 and V3-20 (eg, *d01). These segments were found in antigen-specific repertoires to be productive in recombination with human JH6*02 to produce HCDR3s of at least 20 amino acids in length.
- the locus comprises one, more or all of human D3-9*01, D3-10*01, D6-19*01, D6-13*01, Dl-26*01, IGHV1-8*01, IGHV4-61*01, IGHV6- 1*01, IGHV4-4*02, IGHV1-3*01, IGHV3-66*03, IGHV3-7*01 and IGHV3-9*01.
- locus comprises one, more or all of human IGHV1-8*01, D3-9*01 and D3- 10*01. These gene segments were productive with JH6*02 to produce HCDR3s of at least 20 amino acids in more than 10 antibodies.
- An antibody-producing cell (eg, a B-cell) that is a progeny of the cell of any one of clauses 3 to 14, wherein the antibody-producing cell comprises a heavy chain locus comprising a rearranged variable region produced by recombination of human JH6*02 with a D segment and a VH segment (eg, JH6*02 with human VH3-11 (eg, VH3-11*01) and D3-9; VH3-20 (eg, VH3-20*01) and D3-10; VH4-4 (eg, VH4-4*02) and D3-10; VH3-9 (eg, VH3-9*01) and D3-10; or VH1-8 (eg, VH1-8*01) and D310).
- a heavy chain locus comprising a rearranged variable region produced by recombination of human JH6*02 with a D segment and a VH segment
- VH3-11 eg, VH3-11*01
- variable region would be the product of in vivo somatic hypermutation in a non-hman vertebrate or cell of the invention.
- a target antigen-specific antibody comprising a heavy chain that comprises a rearranged variable region produced by recombination of human JH6*02 with
- variable region would be the product of in vivo somatic hypermutation in a non-hman vertebrate or cell of the invention
- the HCDR3 length is at least 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 amino acids. Additionally, in one example the length is no more than 35, 34, 33, 32 or 31 amino acids. For example, the HCDR3 length is 20, 21, 22, 23 or 24 amino acids.
- a heavy chain (eg, comprised by an antibody) isolated from a vertebrate of any one of clauses 1, 2, 5 to 14 and 17 to 21 wherein the heavy chain comprises a HCD 3 of at least 20 amino acids.
- the heavy chain is chimaeric where the C region is non-human.
- the heavy chain is human where the C region is human.
- a heavy chain eg, comprised by an antibody whose VH variable domain is identical to the VH variable domain of the heavy chain of clause 22 or 23, and which comprises a human constant region or a human-mouse chimaeric constant region (eg, CHI is human and the other constant domains are mouse).
- a method for producing a heavy chain, VH domain or an antibody specific to a target antigen comprising immunizing a non-human vertebrate according to any one of clauses 1, 2, 5 to 14 and 17 to 21 with the antigen and isolating the heavy chain, VH domain or an antibody specific to a target antigen or a cell producing the heavy chain, VH domain or an antibody, wherein the heavy chain, VH domain or an antibody comprises a HCDR3 that is derived from the recombination of human JH6*02 with a VH gene segment and a D gene segment. 7.
- a method for producing a human heavy chain or antibody comprising carrying out the method of clause 26, wherein the constant region of the locus is a non-human vertebrate (eg, mouse or rat) constant region, and then replacing the non-human constant region of the isolated heavy chain or antibody with a human constant region (eg, by engineering of the nucleic acid encoding the antibody).
- the constant region of the locus is a non-human vertebrate (eg, mouse or rat) constant region, and then replacing the non-human constant region of the isolated heavy chain or antibody with a human constant region (eg, by engineering of the nucleic acid encoding the antibody).
- the HCD 3 length is at least 20 amino acids as herein described.
- a vector eg, a CHO cell or HEK293 cell vector comprising the nucleic acid of clause 30;
- a host cell eg, a CHO cell or HEK293 cell.
- a pharmaceutical composition comprising the antibody, heavy chain or VH domain (eg, comprised by an antibody) of any one of clauses 22 to 25 and 28, together with a
- pharmaceutically-acceptable excipient eg, a further antigen-specific variable domain, heavy chain or antibody.
- a medicament eg, a further antigen-specific variable domain, heavy chain or antibody.
- the antibody, heavy chain or VH domain eg, comprised by an antibody of any one of clauses 22 to 25 and 28 for use in medicine (eg, human medicine).
- the locus comprises the following human VH gene segments
- the locus comprises the following human VH gene segment
- the locus comprises the following human JH gene segment variants
- the locus comprises the following human D gene segments
- the present invention provides in a fifth confieuration:-
- Constant Regions Tailored to Human Use & Antibody Humanisation Additional rational design and bioinformatics has led the inventors to realise that specific human constant region variants are conserved across many diverse human populations. The inventors realised that this opens up the possibility of making a choice to humanise antibodies, chains and variable domains by using such specific constant regions in products, rather than arbitrarily choosing the human constant region (or a synthetic version of a human constant region). This aspect of the invention also enables one to tailor antibody-based drugs to specific human ethnic populations, thereby more closely matching drug to patient (and thus disease setting) than has hitherto been performed.
- antibodies are humanised with an arbitrary choice of human constant region (presumably derived from one (often unknown) ethnic population or non-naturally occurring) that does not function as well in patients of a different human ethnic population. This is important, since the constant region has the major role in providing antibody effector functions, eg, for antibody recycling, cellular and complement recruitment and for cell killing.
- human IgG sub-types IgGl, lgG2, gG3 and lgG4 exhibit differential capacity to recruit immune functions, such as antibody-dependent cellular cytotoxicity (ADCC, e.g., IgGl and lgG3), antibody-dependent cellular phagocytosis (ADCP, e.g., IgGl, lgG2, lgG3 and lgG4), and complement dependent cytotoxicity (CDC, e.g., IgGl, lgG3).
- ADCC antibody-dependent cellular cytotoxicity
- ADCP antibody-dependent cellular phagocytosis
- CDC complement dependent cytotoxicity
- Sub-type-specific engagement of such immune functions is based on selectivity for Fc receptors on distinct immune cells and the ability to bind Clq and activate the assembly of a membrane attack complex (MAC).
- MAC membrane attack complex
- FcYRI FcYRI
- FcYRIIa/b/c FcYRIIIa/b
- IgGl IgGl
- lgG2 restricted to the FcYRIIa 131H polymorphism
- lgG4 only has measurable affinity for FcYRI.
- the key contact residues for receptor binding have been mapped to the amino acid residues spanning the lower hinge and CH2 region.
- standard protein engineering techniques some success in enhancing or reducing the affinity of an antibody preparation for Fc receptors and the Clq component of complement has been achieved.
- lgG2 is least capable of binding the family of Fc receptors.
- lgG2 as the starting point, efforts have been made to find a mutant with diminished effector functions but which retains FcRn binding, prolonged stability, and low immunogenicity.
- Improved mutants of this nature may provide improved antibody therapeutics with retained safety.
- Human IgGl therapeutic antibodies that bind to cell surface targets are able to engage effector cells that may mediate cell lysis of the target cell by antibody-dependent cellular cytotoxicity (ADCC) or complement dependent cytotoxicity (CDC). These mechanisms occur through interaction of the CH2 region of the antibody Fc domain to Fcy receptors on immune effector cells or with Clq, the first component of the complement cascade.
- ADCC antibody-dependent cellular cytotoxicity
- CDC complement dependent cytotoxicity
- Table 19 shows the activities of different human gamma sub-types.
- the skilled person may choose accordingly to promote or dampen-down activity depending upon the disease setting in humans of interest.
- use of a human gamma-1 constant region is desirable when one wishes to isolated totally human heavy chains and antibodies that have relatively high complement activation activity by the classical pathway and FcYRl recognition in human patients. See also Mol Immunol. 2003 Dec;40(9):585-93; "Differential binding to human Fcgamma Rl la and Fcgamma Rllb receptors by human IgG wild type and mutant antibodies"; Armour KL et al, which is incorporated herein by reference.
- lgG2 constant regions are well suited to producing antibodies and heavy chains according to the invention for binding to cytokines or soluble targets in humans, since lgG2 is essentially FcYRl, Ill- silent, FcYRl la-active and has little Complement activity.
- IgGl constant regions have wide utility for human therapeutics, since IgGl antibodies and heavy chains are FcYRl, II, III- active and have complement activity. This can be enhanced by using a human gamma-1 constant region that has been activated by engineering as is known in the art.
- the work of the inventors has therefore identified a collection of human constant region of different isotypes from which an informed choice can be made when humanising chimaeric antibody chains (or conjugating V domains, such as dAbs or Camelid VHH, to constant regions).
- the collection was identified on the basis of bioinformatics analysis of the 1000 Genomes database, the inventors selecting constant region variants that are frequently occurring across several human ethnic populations, as well as those that appear with relatively high frequency within individual populations (as assessed by the number of individuals whose genomes comprise the variant).
- the inventors have provided a collection of human constant region variants that are naturally-occuring and which can be used when rationally designing antibodies, heavy chains and other antibody-based formats that bear a human constant region.
- this is useful when humanising chimaeric heavy chains to produce totally human chains in which both the variable and constant regions are human. This is useful for compatibility with human patients receiving antibody-based drugs.
- a method of producing an antibody heavy chain comprising
- an antigen-specific heavy chain variable domain eg, VH (such as a human VH or dAb) or VHH or a humanised heavy chain variable domain
- variable domain (b) combining the variable domain with a human heavy chain constant region to produce an antibody heavy chain comprising (in N- to C-terminal direction) the variable domain and the constant region;
- the human heavy chain constant region is an IGHAref, IGHAla, IGHA2a, IGHA2b, IGHGlref, IGHG2ref, IGHG2a, IGHG3ref, IGHG3a, IGHG3b, IGHG4ref, IGHG4a, IGHDref, IGHEref, IGHMref, IGHMa or IGHMb constant region.
- Step (b) can be carried out, eg, using recombinant DNA technology using the corresponding nucleotide sequences.
- genomic DNA or equivalent ie, having introns and exons and optionally also 5' UT sequences, eg, with native or a non-native leader sequence
- genomic DNA or equivalent ie, having introns and exons and optionally also 5' UT sequences, eg, with native or a non-native leader sequence
- an intronless sequence can be used, for example any of the "CDS" sequences disclosed as SEQ ID NO: 365 onwards herein (eg, with native or a non-native leader sequence).
- the human heavy chain constant region is an IGHAref constant region.
- the human heavy chain constant region is an IGHAla constant region.
- the human heavy chain constant region is an IGHA2a constant region.
- the human heavy chain constant region is an IGHA2b constant region.
- the human heavy chain constant region is IGHGlref constant region.
- the human heavy chain constant region is an IGHG2ref constant region.
- the human heavy chain constant region is an IGHG2a constant region.
- the human heavy chain constant region is an IGHG3ref constant region.
- the human heavy chain constant region is an IGHG3a constant region.
- the human heavy chain constant region is an IGHG3b constant region.
- the human heavy chain constant region is an IGHG4ref constant region.
- the human heavy chain constant region is an IGHG4a constant region.
- the human heavy chain constant region is an IGHDref constant region.
- the human heavy chain constant region is an IGHEref constant region.
- the human heavy chain constant region is an IGHMref constant region.
- the human heavy chain constant region is an IGHMa constant region.
- the human heavy chain constant region is an IGHMb constant region.
- a derivative eg, a mutant or conjugate
- a toxic payload can be conjugated (eg, for oncology applications).
- one or more mutations can be introduced, as is known in the art, to inactivate or enhance Fc effector function.
- variable domain is a human variable domain.
- a human variable domain is, for example, the product of recombination in a transgenic non- human vertebrate of human VH, D and JH gene segments.
- the variable domain is identified using in vitro display technology from a human VH library, eg, using phage display, ribosome display or yeast display, as is known in the art.
- the variable domain is a humanised variable domain, eg, comprising human frameworks with non-human (eg, mouse or rat) CD s). Humanisation technology is conventional in the art, and will be readily known to the skilled person.
- variable domain has previously been selected from a non-human vertebrate that has been immunised with the antigen.
- the vertebrate (such as a mouse or rat) genome comprises a chimaeric heavy chain locus comprising a human variable region (human V, D and JH gene segments) operably connected upstream of a non-human vertebrate constant region so that the locus is able to rearrange for the expression of heavy chains comprising human variable domains and non- human vertebrate constant regions.
- a human variable region human V, D and JH gene segments
- variable domain is selected using an in vitro technology such as phage display, ribosome display or yeast display.
- the variable domain may be displayed with or without an constant region, provided that it is later combined with a human constant region as per the invention.
- an expression vector (Eg, a mammalian expression vector, such as a CHO or HEK293 vector) comprising a nucleotide sequence encoding the constant region; inserting a nucleotide sequence encoding the variable domain into the vector 5' of the constant region sequence; inserting the vector into a host cell and expressing the heavy chain by the host cell; the method further comprising isolating a heavy chain (eg, as part of an antibody) comprising the variable domain and the human constant region.
- an expression vector Eg, a mammalian expression vector, such as a CHO or HEK293 vector
- the vector comprises regulatory elements sufficient to effect expression of the heavy chain when the vector is harboured by a host cell, eg, a CHO or HEK293 cell.
- An antibody comprising a human heavy chain, the heavy chain comprising a variable domain that is specific for an antigen and a constant region that is an IGHAref, IGHAla, IGHA2a, IGHA2b, IGHGlref, IGHG2ref, IGHG2a, IGHG3ref, IGHG3a, IGHG3b, IGHG4ref, IGHG4a, IGHDref, IGHEref, IGHMref, IGHMa or IGHMb constant region.
- a polypeptide comprising (in N- to C- terminal direction) a leader sequence, a human variable domain that is specific for an antigen and a human constant region that is an IGHAref, IGHAla, IGHA2a, IGHA2b, IGHGlref, IGHG2ref, IGHG2a, IGHG3ref, IGHG3a, IGHG3b, IGHG4ref, IGHG4a, IGHDref, IGHEref, IGHMref, IGHMa or IGHMb constant region; wherein (i) the leader sequence is not the native human variable domain leader sequence (eg, the leader sequence is another human leader sequence or a non-human leader sequence); and/or (ii) the variable domain comprises mouse AID-pattern somatic mutations or mouse terminal deoxynucleotidyl transferase (TdT)- pattern junctional mutations.
- TdT mouse terminal deoxynucleotidyl
- the promoter sequence is a human IGK 3-15 promoter.
- variable domain comprises mouse AID-pattern somatic mutations and/or mouse terminal deoxynucleotidyl transferase (TdT)- pattern junctional mutations.
- one way, in any aspect of this configuration of the invention, to provide mouse AID-pattern somatic mutations and/or mouse terminal deoxynucleotidyl transferase (TdT)- pattern junctional mutations is to select a variable domain from a non-human vertebrate or cell.
- a vertebrate or cell as disclosed herein.
- a vector eg, a CHO cell or HEK293 cell vector
- comprising the nucleic acid of aspect 8, 9 or 10; optionally wherein the vector is in a host cell eg, a CHO cell or HEK293 cell.
- a pharmaceutical composition comprising the antibody or polypeptide of any one of aspects 6, 7 and 10, together with a pharmaceutically-acceptable excipient, diluent or a medicament (eg, a further antigen-specific variable domain, antibody chain or antibody).
- a pharmaceutically-acceptable excipient e.g, a further antigen-specific variable domain, antibody chain or antibody.
- the antibody or polypeptide of any one of aspects 6, 7 and 10 for use in treating and/or preventing a medical condition in a human patient.
- IGHAla constant region and the human population is selected from any population number 1-14;
- IGHA2a constant region and the human population is selected from any population number 1-14;
- (iV) IGHG2a constant region and the human population is selected from any population number 1-9 and 11-13;
- IGHG3b constant region and the human population is selected from any population number 1-8 and 11-13;
- IGHG4a constant region and the human population is selected from any population number 1-9 and 11-13;
- IGHMa constant region and the human population is selected from any population number 1-14; or
- IGHMb constant region and the human population is selected from any population number 1-14; Wherein the populations are numbered as follows (population labels being according to 1000
- a vector (eg, a CHO cell or HEK293 cell vector) comprising a IGHGlref, IGHG2ref, IGHG2a,
- IGHG3ref IGHG3a, IGHG3b, IGHG4ref or IGHG4a constant region nucleotide sequence that is 3' of a cloning site for the insertion of a human antibody heavy chain variable domain nucleotide sequence, such that upon insertion of such a variable domain sequence the vector comprises (in 5' to 3' direction) a promoter, a leader sequence, the variable domain sequence and the constant region sequence so that the vector is capable of expressing a human antibody heavy chain when present in a host cell.
- the present invention provides in a Sixth confieuration:-
- the inventors' analysis has revealed groupings of naturally-occurring human antibody gene segment variants as set out in Table 13 and Table 14. This revealed the possibility of producing transgenic genomes in non-human vertebrates and cells wherein the genomes contain more than the natural human complement of specific human gene segments. In one example, this can be achieved by providing more than the natural human complement of a specific gene segment type on one or both of the respective Ig locus (eg, one or both chromosomes harbouring IgH in a mouse genome or mouse cell genome).
- this configuration of the invention provides the following (as set out in numbered paragraphs):-
- a non-human vertebrate eg, a mouse or rat
- a non-human vertebrate cell eg, an ES cell or a B-cell
- having a genome comprising at least 3 human variable region gene segments of the same type (eg, at least 3 human VH6-1 gene segments, at least 3 human J H6 gene segments, at least 3 human VK1-39 gene segments, at least 3 human D2-2 gene segments or at least 3 human JKI gene segments), wherein at least two of the human gene segments are variants that are not identical to each other.
- the genome comprises a variable region that comprises V, D and J gene segments (for the variable region of a heavy chain locus) or V and J gene segments (for the variable region of a light chain locus) upstream of a constant region for expression of heavy or light chains respectively.
- the skilled person can choose to provide more than the wild type human complement of a specific gene segment type by providing several copies of one variant type of the human gene segment.
- a non-human vertebrate eg, a mouse or rat
- a non-human vertebrate cell eg, an ES cell or a B-cell
- having a genome comprising at least 3 human variable region gene segments of the same type (eg, at least 3 human VH6-1 gene segments, at least 3 human J H6 gene segments, at least 3 human VK1-39 gene segments, at least 3 human D2-2 gene segments or at least 3 human JKI gene segments), wherein the human gene segments are identical variants.
- the genome comprises a variable region that comprises V, D and J gene segments (for the variable region of a heavy chain locus) or V and J gene segments (for the variable region of a light chain locus) upstream of a constant region for expression of heavy or light chains respectively.
- a non-human vertebrate eg, a mouse or rat
- a non-human vertebrate cell eg, an ES cell or a B-cell
- having a genome comprising at least 2 different non-endogenous variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 3 human JH6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments) cis at the same Ig locus.
- the skilled person can choose to provide more than the wild type human complement of a specific gene segment type by providing several copies of one variant type of the human gene segment.
- a non-human vertebrate eg, a mouse or rat
- a non-human vertebrate cell eg, an ES cell or a B-cell
- having a genome comprising at least 2 non-endogenous variable region gene segments of the same variant type (eg, at least 2 human JH6*02 gene segments) cis at the same Ig locus.
- a non-human vertebrate eg, a mouse or rat
- a non-human vertebrate cell eg, an ES cell or a B-cell
- having a genome comprising at least 2 different human variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human J H6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments) trans at the same Ig locus; and optionally a third human gene segment of the same type, wherein the third gene segment is cis with one of said 2 different gene segments.
- the skilled person can choose to provide more than the wild type human complement of a specific gene segment type by providing several copies of one variant type of the human gene segment.
- a non-human vertebrate eg, a mouse or rat
- a non-human vertebrate cell eg, an ES cell or a B-cell
- having a genome comprising at least 2 different human variable region gene segments of the same variant type (eg, at least 2 human JH6*02 gene segments) trans at the same Ig locus; and optionally a third human gene segment of the same variant type, wherein the third gene segment is cis with one of said 2 different gene segments.
- a population of non-human vertebrates comprising a repertoire of human variable region gene segments, wherein the plurality comprises at least 2 human variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human J H6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments), a first of said different gene segments is provided in the genome of a first vertebrate of the population, and a second of said different gene segments being provided in the genome of a second vertebrate of the population, wherein the genome of the first vertebrate does not comprise the second gene segment.
- the plurality comprises at least 2 human variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human J H6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments)
- a first of said different gene segments is provided in the genome of a first vertebrate
- a non-human vertebrate eg, a mouse or rat
- a non-human vertebrate cell eg, an ES cell or a B-cell
- having a genome comprising at least 2 different non-endogenous variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human JH6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments), wherein the gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
- a method of enhancing the human immunoglobulin gene diversity of a non-human vertebrate comprising providing the vertebrate with a genome comprising at least 3 human variable region gene segments of the same type (eg, at least 3 human VH6-1 gene segments, at least 3 human J H6 gene segments, at least 3 human VK1-39 gene segments, at least 3 human D2-2 gene segments or at least 3 human JKI gene segments), wherein at least two of the human gene segments are variants that are not identical to each other.
- a method of enhancing the immunoglobulin gene diversity of a non-human vertebrate comprising providing the vertebrate with a genome comprising at least 2 different non-endogenous variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human JH6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments) cis at the same Ig locus.
- a non-human vertebrate eg, a mouse or rat
- a method of enhancing the immunoglobulin gene diversity of a non-human vertebrate comprising providing the vertebrate with a genome comprising at least 2 different human variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human J H6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments) trans at the same Ig locus; and optionally a third human gene segment of the same type, wherein the third gene segment is cis with one of said 2 different gene segments.
- a non-human vertebrate eg, a mouse or rat
- a method of providing an enhanced human immunoglobulin variable region gene segment repertoire comprising providing a population of non-human vertebrates (eg, a mouse or rat) comprising a repertoire of human variable region gene segments, wherein the method comprises providing at least 2 different human variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human JH6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments), wherein a first of said different gene segments is provided in the genome of a first vertebrate of the population, and a second of said different gene segments is provided in the genome of a second vertebrate of the population, wherein the genome of the first vertebrate does not comprise the second gene segment.
- a population of non-human vertebrates eg, a mouse or rat
- the method comprises providing at least 2 different human variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human
- a method of enhancing the human immunoglobulin gene diversity of a non-human vertebrate comprising providing the vertebrate with a genome comprising at least 2 different non-endogenous variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human J H6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments), wherein the gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
- the gene segments are derived from the genome sequence of two or more different human individuals; optionally wherein the different human individuals are from different human populations.
- a method of enhancing the human immunoglobulin gene diversity of a non-human vertebrate comprising providing the vertebrate with a genome comprising at least 2 human variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human JH6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human J KI gene segments), wherein the gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations; optionally wherein at least 2 or 3 of said different gene segments are provided at the same Ig locus in said genome.
- a non-human vertebrate eg, a mouse or rat
- each of said gene segments occurs in 10 or more different human populations.
- each of said gene segments has a human frequency of 5% or greater (eg, 10, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, or 95% or greater).
- Frequency can, for example, be cumulative frequency in the 1000 Genomes database.
- each of said gene segments occurs in 10 or more different human populations.
- each of said gene segments occurs in the 1000 Genomes database in more than 50 individuals.
- each of said gene segments has a human frequency of 5% or greater (eg, 10, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, or 95% or greater); and (ii) occurs in 10 or more different human populations.
- Frequency can, for example, be cumulative frequency in the 1000 Genomes database.
- a non-human vertebrate eg, a mouse or rat
- a non-human vertebrate cell eg, an ES cell or a B-cell
- having a genome comprising first and second human Ig locus gene segments of the same type (eg, first and second human JH6 gene segments; or first and second lgG2 gene segments; or first and second human J ⁇ 7 gene segments), wherein the first gene segment is a gene segment selected from Table 14 (eg, IGHJ6-a) and the second gene segment is the corresponding reference sequence (eg, IGHJ6 ref; SEQ ID NO: 244).
- Table 14 lists commonly-occurring natural human variants. It can be seen that these occur across many human populations and thus usefully have wide applicability for human antibody- based drugs.
- the gene segments are provided as targeted insertions into an endogenous non- human vertebrate Ig locus.
- random integration eg, using YACs
- YACs YACs
- the genome comprises a variable region that comprises V, D and J gene segments (for the variable region of a heavy chain locus) or V and J gene segments (for the variable region of a light chain locus) upstream of a constant region for expression of heavy or light chains respectively.
- the invention enables the skilled person to select two or more different naturally-occurring human gene segment variants for combination into the genome of a non- human vertebrate or cell.
- a reference sequence need not be included. It may be desirable to use one or more rare gene segments to increase diversity of the repertoire. Additionally or alternatively, it may be desirable to include a mixture of frequent and rare variants of the same type to provide repertoire diversity. The variants may be chosen additionally or alternatively to tailor the gene segment inclusion to one or more specific human populations as indicated by the information provided in Table 13 or Table 14.
- a non-human vertebrate eg, a mouse or rat
- a non-human vertebrate cell eg, an ES cell or a B-cell
- having a genome comprising first and second human Ig locus gene segments of the same type (eg, first and second human JH6 gene segments; or first and second lgG2 gene segments; or first and second human J ⁇ 7 gene segments), wherein the gene segments are gene segments selected from Table 13 or Table 14; and optionally wherein one or more of the gene segments appears in Table 14 (eg, IGHJ6-a) or is a reference sequence (eg, IGHJ6 ref; SEQ. ID NO: 244).
- the gene segments are heavy chain gene segments and the non-human locus is an IgH locus.
- the gene segments are light chain (kappa or lambda) gene segments and the non-human locus is an IgL locus.
- the chromosomes are the same type (eg, both mouse chromosome 6 or rat chromosome 4).
- first gene segment is a gene segment selected from any one of Tables 1 to 7 and 9 to 14 (eg, selected from Table 13 or 14) and the second gene segment is the corresponding reference sequence.
- a population of non-human vertebrates comprising first and second human Ig locus gene segments of the same type (eg, first and second human JH6 gene segments; or first and second lgG2 gene segments; or first and second human J ⁇ 7 gene segments), wherein the first gene segment is a gene segment selected from any one of Tables 1 to 7 and 9 to 14 (eg, Table 13 or 14) (eg, IGHJ6-a) and the second gene segment is the corresponding reference sequence (eg, SEQ. ID NO: 7), wherein the first gene segment is provided in the genome of a first vertebrate of the population, and the second gene segment is provided in the genome of a second vertebrate of the population.
- the gene segments are heavy chain gene segments and the non-human locus is an IgH locus.
- the gene segments are light chain (kappa or lambda) gene segments and the non-human locus is an IgL locus.
- a method of enhancing the human immunoglobulin gene diversity of a non-human vertebrate comprising providing the vertebrate with a genome comprising first and second human Ig locus gene segments of the same type (eg, first and second human JH6 gene segments; or first and second lgG2 gene segments; or first and second human J ⁇ 7 gene segments), wherein the first gene segment is a gene segment selected from any one of Tables 1 to 7 and 9 to 14 (eg, Table 13 or 14) (eg, IGHJ6-a) and the second gene segment is the corresponding reference sequence (eg, SEQ. ID NO: 7).
- first and second human Ig locus gene segments of the same type eg, first and second human JH6 gene segments; or first and second lgG2 gene segments; or first and second human J ⁇ 7 gene segments
- the first gene segment is a gene segment selected from any one of Tables 1 to 7 and 9 to 14 (eg, Table 13 or 14) (eg, IGHJ6-a) and the second
- a method of providing an enhanced human immunogolobulin gene segment repertoire comprising providing a population according to any one of paragraphs 30 to 33.
- the inventors identified gene segment variants from their analysis that are relatively prevalent in a small number of human populations, and not across many populations.
- the inventors realized that inclusion of one or more of such gene segments in the configurations of the invention (eg, in transgenic Ig loci, vertebrates and cells) would be useful for producing antibodies, Ig chains and variable domains that can address antigens (eg, disease- causing antigens or pathogens) to which the small number of human populations may become exposed.
- antigens eg, disease- causing antigens or pathogens
- Such products would be useful for treating and/or preventing disease or medical conditions in members of such a population.
- This aspect could also be useful for addressing infectious disease pathogens that may have been common in the small number of populations, but which in the future or relatively recently in evolution has become a more prevalent disease-causing pathogen in other human populations (ie, those not listed in Table 13 against the gene segment variant(s) in question).
- the inventors From the 1000 Genomes database the inventors have identified the gene segment variants listed in Table 20.
- one, more or all of the gene segments used in the present invention can be a gene segment listed in Table 20A, 20B, 20C or 20D.
- a non-human vertebrate eg, a mouse or rat
- a non-human vertebrate cell eg, an ES cell or a B- cell
- having a genome comprising at least 3 human JH gene segments of the same type (JH1, JH2, JH3, JH4, JH5 or JH6), wherein at least two of the human JH gene segments are variants that are not identical to each other.
- any cell of the invention is an isolated cell.
- An "isolated" cell is one that has been identified, separated and/or recovered from a component of its production environment (eg, naturally or recombinantly).
- the isolated cell is free of association with all other components from its production environment, eg, so that the cell can produce an antibody to an FDA-approvable or approved standard.
- Contaminant components of its production environment such as that resulting from recombinant transfected cells, are materials that would typically interfere with research, diagnostic or therapeutic uses for the resultant antibody, and may include enzymes, hormones, and other proteinaceous or non-proteinaceous solutes.
- the polypeptide will be purified: (1) to greater than 95% by weight of antibody as determined by, for example, the Lowry method, and in some embodiments, to greater than 99% by weight; (2) to a degree sufficient to obtain at least 15 residues of N-terminal or internal amino acid sequence by use of a spinning cup sequenator, or (3) to homogeneity by SDS-PAGE under non- reducing or reducing conditions using Coomassie blue or, preferably, silver stain. Ordinarily, however, an isolated cell will be prepared by at least one purification step.
- a non-human vertebrate eg, a mouse or rat
- a non-human vertebrate cell eg, an ES cell or a B- cell
- having a genome comprising at least 2 different non-endogenous JH gene segments (eg, human gene segments) of the same type (JH1, JH2, JH3, JH4, JH5 or JH6) cis at the same Ig (eg, IgH, eg, endogenous IgH, eg, mouse or rat IgH) locus.
- the genome comprises a human VH, D and JH repertoire comprising said different JH gene segments.
- the non-endogenous JH gene segments are non-mouse or non-rat, eg, human JH gene segments.
- one or more or all of the non-endogenous gene segments are synthetic.
- a non-human vertebrate eg, a mouse or rat
- a non-human vertebrate cell eg, an ES cell or a B- cell
- having a genome comprising at least 2 different human JH gene segments of the same type (JH1, JH2, JH3, JH4, JH5 or JH6) trans at the same Ig (eg, IgH, eg, endogenous IgH, eg, mouse or rat IgH) locus; and optionally a third human JH gene segments of the same type, wherein the third JH is cis with one of said 2 different JH gene segments.
- a population of non-human vertebrates comprising a repertoire of human JH gene segments, wherein the plurality comprises at least 2 different human JH gene segments of the same type (JH1, JH2, JH3, JH4, JH5 or JH6), a first of said different JH gene segments is provided in the genome of a first vertebrate of the population, and a second of said different JH gene segments being provided in the genome of a second vertebrate of the population, wherein the genome of the first vertebrate does not comprise the second JH gene segment.
- non-human vertebrates eg, mice or rats
- the plurality comprises at least 2 different human JH gene segments of the same type (JH1, JH2, JH3, JH4, JH5 or JH6)
- a non-human vertebrate eg, a mouse or rat
- a non-human vertebrate cell eg, an ES cell or a B- cell
- having a genome comprising at least 2 different non-endogenous (eg, human) JH gene segments of the same type (JH1, JH2, JH3, JH4, JH5 or JH6), wherein the JH gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations (eg, 3, 4, 5 or 6 generations).
- the non-endogenous JH gene segments are human JH gene segments.
- one or more or all of the non-endogenous gene segments are synthetic.
- a method of enhancing the human immunoglobulin gene diversity of a non-human vertebrate comprising providing the vertebrate with a genome comprising at least 3 human JH gene segments of the same type (JH1, JH2, JH3, JH4, JH5 or JH6), wherein at least two of the human JH gene segments are variants that are not identical to each other.
- a method of enhancing the immunoglobulin gene diversity of a non-human vertebrate comprising providing the vertebrate with a genome comprising at least 2 different non-endogenous (eg, human) JH gene segments of the same type (JH1, JH2, JH3, JH4, JH5 or JH6) cis at the same Ig (eg, IgH, eg, endogenous IgH, eg, mouse or rat IgH) locus).
- the non-endogenous JH gene segments are non-mouse or non-rat, eg, human JH gene segments.
- one or more or all of the non-endogenous gene segments are synthetic.
- a method of enhancing the immunoglobulin gene diversity of a non-human vertebrate comprising providing the vertebrate with a genome comprising at least 2 different human JH gene segments of the same type (JH1, JH2, JH3, JH4, JH5 or JH6) trans at the same Ig (eg, IgH, eg, endogenous IgH, eg, mouse or rat IgH) locus; and optionally a third human JH gene segments of the same type, wherein the third JH is cis with one of said 2 different JH gene segments.
- JH1, JH2, JH3, JH4, JH5 or JH6 trans at the same Ig (eg, IgH, eg, endogenous IgH, eg, mouse or rat IgH) locus
- a third human JH gene segments of the same type wherein the third JH is cis with one of said 2 different JH gene segments.
- a method of providing an enhanced human immunoglobulin JH gene segment repertoire comprising providing a population of non-human vertebrates (eg, a mouse or rat) comprising a repertoire of human JH gene segments, wherein the method comprises providing at least 2 different human JH gene segments of the same type (JH1, JH2, JH3, JH4, JH5 or JH6), wherein a first of said different J H gene segments is provided in the genome of a first vertebrate of the population, and a second of said different JH gene segments is provided in the genome of a second vertebrate of the population, wherein the genome of the first vertebrate does not comprise the second JH gene segment.
- a method of enhancing the human immunoglobulin gene diversity of a non-human vertebrate comprising providing the vertebrate with a genome comprising at least 2 different non-endogenous (eg, human) JH gene segments of the same type (JH1, JH2, JH3, JH4, JH5 or JH6), wherein the JH gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations (eg, 3, 4, 5, or 6 generations).
- the non-endogenous JH gene segments are human JH gene segments.
- one or more or all of the non-endogenous gene segments are synthetic.
- At least 2 or 3 of said different gene segments are provided cis at the same Ig locus in said genome.
- the JH gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations (eg, 3, 4, 5, or 6 generations).
- the JH gene segments are derived from the genome sequence of two or more different human individuals; optionally wherein the different human individuals are from different human populations.
- the individuals are not genetically related (eg, going back 3, 4, 5, or 6 generations).
- At least one of the different JH segments is a synthetic mutant of a human germline JH gene segment.
- the invention also provides a method of enhancing the human immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising at least 2 human JH gene segments of the same type (JH1, JH2, J H3, JH4, JH5 or JH6), wherein the JH gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations (eg, 3, 4, 5, or 6 generations); optionally wherein at least 2 or 3 of said different gene segments are provided at the same IgH locus in said genome.
- a non-human vertebrate eg, a mouse or rat
- the genome comprises a substantially complete functional repertoire of human JH gene segment types supplemented with one, two or more human JH gene segments, wherein said substantially complete functional repertoire and the supplementary JH gene segments are not found together in the germline genome of a human individual.
- the population comprises a substantially complete functional repertoire of human JH gene segment types supplemented with one, two or more human JH gene segments, wherein said substantially complete functional repertoire and the supplementary JH gene segments are not found together in the germline genome of a human individual.
- a non-human vertebrate eg, a mouse or rat
- a non-human cell eg, an ES cell or a B-cell
- a population of non-human vertebrates comprising a substantially complete functional repertoire of human JH gene segment types supplemented with one, two or more human JH gene segments, wherein said substantially complete functional repertoire and the supplementary JH gene segments are not found together in the germline genome of a human individual.
- a population of non-human vertebrates eg, mice or rats
- comprising a substantially complete functional repertoire of human JH gene segment types supplemented with one, two or more human JH gene segments wherein said substantially complete functional repertoire and the supplementary JH gene segments are not found together in the germline genome of a human individual.
- At least one of said JH gene segments is SEQ ID NO: 1, 2, 3 or 4.
- at least one of said JH gene segments is SEQ ID NO: 1 and at least one, two or more of said supplementary JH gene segments is a variant according to any example above.
- at least one of said JH gene segments is SEQ ID NO: 2 and at least one, two or more of said supplementary JH gene segments is a variant according to any one of the examples above.
- at least one of said JH gene segments is SEQ ID NO: 2 and at least one, two or more of said supplementary JH gene segments is a variant according to any one of the examples above.
- the non-human vertebrate or vertebrate cell of the invention comprises a genome that comprises VH, D and JH gene repertoires comprising human gene segments, the JH gene repertoire (eg, a human JH gene segment repertoire) comprising a plurality of JH1 gene segments provided by at least 2 different JH1 gene segments in cis at the same Ig locus in said genome;
- the JH gene repertoire eg, a human JH gene segment repertoire
- JH gene segments are derived from the genome sequence of two or more different human individuals.
- said at least 2 different JH gene segments are human gene segments or synthetic gene segments derived from human gene segments.
- the Ig locus is a IgH locus, eg, an endogenous locus, eg, a mouse or rat IgH locus.
- the non-human vertebrate or vertebrate cell of the invention comprises a genome that comprises VH, D and JH gene repertoires comprising human gene segments, the JH gene repertoire (eg, a human JH gene segment repertoire) comprising
- JH gene segments are derived from the genome sequence of two or three different human individuals;
- said at least 3 different JH gene segments are human gene segments or synthetic gene segments derived from human gene segments.
- the Ig locus is a IgH locus, eg, an endogenous locus, eg, a mouse or rat IgH locus.
- the different human individuals are from different human populations.
- the individuals are not genetically related (eg, Going back 3, 4, 5 or 6generations).
- at least one of the different JH segments is a synthetic mutant of a human germline JH gene segment.
- the vertebrate or cell genome comprises human VH, D and JH gene repertoires, the JH gene repertoire (eg, a human JH gene repertoire) comprising
- JH1 gene segments provided by at least 2 different human JH1 gene segments, optionally in cis at the same Ig locus in said genome;
- JH2 gene segments provided by at least 2 different human JH2 gene segments, optionally in cis at the same Ig locus in said genome;
- JH3 gene segments provided by at least 2 different human JH3 gene segments, optionally in cis at the same Ig locus in said genome;
- JH4 gene segments provided by at least 2 different human JH4 gene segments, optionally in cis at the same Ig locus in said genome;
- JH5 gene segments provided by at least 2 different human JH5 gene segments, optionally in cis at the same Ig locus in said genome;
- JH6 gene segments provided by at least 2 different human JH6 gene segments, optionally in cis at the same Ig locus in said genome;
- JH gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations (eg, 3, 4, 5 or 6 generations).
- said at least 2 different JH gene segments are human gene segments or synthetic gene segments derived from human gene segments.
- the Ig locus is a IgH locus, eg, an endogenous locus, eg, a mouse or rat IgH locus.
- the human individuals are from different human populations.
- An embodiment provides a vertebrate, cell or population of the invention whose genome comprises a plurality of JH5 gene segments, wherein the plurality comprises a human JH5 gene variant of SEQ ID NO: 1, wherein the variant comprises a nucleotide mutation at one or more positions corresponding to positions
- the plurality comprises a human JH5 gene variant of SEQ ID NO: 1, wherein the variant comprises a guanine at a position corresponding to position 106,330,067 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
- the variant comprises additionally a mutation at a position corresponding to (i) position 106,330,071 on human chromosome 14 (optionally the additional mutation being a guanine); (ii) position 106,330,066 on human chromosome 14 (optionally the additional mutation being a guanine); and/or (iii) position 106,330,068 on human chromosome 14 (optionally the additional mutation being a thymine).
- the plurality comprises a human JH5 gene variant of SEQ ID NO: 1, wherein the variant comprises a guanine at a position corresponding to position 106,330,071 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
- the variant comprises additionally a mutation at a position corresponding to (i) position 106,330,063 on human chromosome 14 (optionally the additional mutation being an adenine); and/or (ii) position 106,330,067 on human chromosome 14 (optionally the additional mutation being a guanine).
- the plurality comprises a human JH5 gene variant of SEQ ID NO: 1, wherein the variant comprises a cytosine at a position corresponding to position 106,330,045 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
- the plurality comprises a human JH5 gene variant of SEQ ID NO: 1, wherein the variant comprises an adenine at a position corresponding to position 106,330,044 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
- the variant comprises additionally a mutation at a position corresponding to (i) position
- 106.330.066 on human chromosome 14 (optionally the additional mutation being a guanine); and/or (ii) position 106,330,068 on human chromosome 14 (optionally the additional mutation being a thymine).
- the plurality comprises a human JH5 gene variant of SEQ I D NO: 1, wherein the variant comprises a guanine at a position corresponding to position 106,330,066 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
- the variant comprises additionally a mutation at a position corresponding to (i) position
- 106.330.067 on human chromosome 14 (optionally the additional mutation being a guanine); and/or (ii) position 106,330,068 on human chromosome 14 (optionally the additional mutation being a thymine).
- the plurality comprises a human JH5 gene variant of SEQ ID NO: 1, wherein the variant comprises a thymine at a position corresponding to position 106,330,068 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
- the variant comprises additionally a mutation at a position corresponding to (i) position 106,330,067 on human chromosome 14 (optionally the additional mutation being a guanine); and/or (ii) position 106,330,066 on human chromosome 14 (optionally the additional mutation being a guanine).
- the plurality comprises a human JH5 gene variant of SEQ ID NO: 1, wherein the variant comprises a cytosine at a position corresponding to position 106,330,027 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
- the plurality comprises a human JH5 gene variant of SEQ ID NO: 1, wherein the variant comprises an adenine at a position corresponding to position 106,330,024 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
- the plurality comprises a human JH5 gene variant of SEQ ID NO: 1, wherein the variant comprises a thymine at a position corresponding to position 106,330,032 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
- the plurality comprises a human JH5 gene variant of SEQ ID NO: 1, wherein the variant comprises a thymine at a position corresponding to position 106,330,041 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
- the plurality comprises a human JH5 gene variant of SEQ ID NO: 1, wherein the variant comprises an adenine or thymine at a position corresponding to position 106,330,063 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
- the variant comprises additionally a mutation at a position corresponding to position 106,330,071 on human chromosome 14 (optionally the additional mutation being a guanine).
- the plurality comprises a human JH5 gene variant of SEQ ID NO: l,wherein the variant comprises a cytosine at a position corresponding to position 106,330,062 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
- the genome comprises SEQ ID NO:l; optionally in cis at the same Ig locus as one, two or more of the variants.
- An embodiment provides a vertebrate, cell or population of the invention whose genome comprises a plurality of JH6 gene segments, wherein the plurality comprises a human JH6 gene variant of SEQ ID NO: 2, wherein the variant comprises a nucleotide mutation at one or more positions corresponding to positions
- the genome of the vertebrate, cell or population comprises a plurality of JH6 gene segments, wherein the plurality comprises a human JH6 gene variant of SEQ ID NO: 2, wherein the variant comprises a guanine at a position corresponding to position 106,329,435 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 2.
- the variant comprises additionally a mutation at a position corresponding to (i) position 106,329,468 on human chromosome 14 (optionally the additional mutation being a guanine); (ii) position 106,329,419 on human chromosome 14 (optionally the additional mutation being an adenine); (iii) position 106,329,434 on human chromosome 14 (optionally the additional mutation being a cytosine) and/or position 106,329,414 on human chromosome 14 (optionally the additional mutation being a guanine); (iv) position 106,329,426 on human chromosome 14 (optionally the additional mutation being an adenine); (v) position 106,329,413 on human chromosome 14 (optionally the additional mutation being an adenine); (vi) position 106,329,417 on human chromosome 14 (optionally the additional mutation being a thymine); (vii) position 106,
- the variant comprises additionally mutations at positions corresponding to position
- the vertebrate, cell or population optionally comprises a plurality of JH6 gene segments, wherein the plurality comprises a human JH6 gene variant of SEQ ID NO: 2, wherein the variant comprises a guanine at a position corresponding to position 106,329,468 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 2.
- the variant comprises additionally a mutation at a position corresponding to position 106,329,435 on human chromosome 14 (optionally the additional mutation being a guanine).
- the vertebrate, cell or population comprises a plurality of JH6 gene segments, wherein the plurality comprises a human JH6 gene variant of SEQ ID NO: 2, wherein the variant comprises a thymine at a position corresponding to position 106,329,417 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 2.
- the variant comprises additionally a mutation at a position corresponding to position 106,329,435 on human chromosome 14 (optionally the additional mutation being a guanine).
- the vertebrate, cell or population comprises a plurality of JH6 gene segments, wherein the plurality comprises a human JH6 gene variant of SEQ ID NO: 2, wherein the variant comprises a cytosine at a position corresponding to position 106,329,434 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 2.
- the variant comprises additionally a mutation at a position corresponding to (i) position 106,329,414 on human chromosome 14 (optionally the additional mutation being a guanine); and/or (ii) position 106,329,435 on human chromosome 14 (optionally the additional mutation being a guanine).
- the vertebrate, cell or population comprises a plurality of JH6 gene segments, wherein the plurality comprises a human JH6 gene variant of SEQ ID NO: 2, wherein the variant comprises a thymine at a position corresponding to position 106,329,411 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 2.
- the variant comprises additionally a mutation at a position corresponding to position 106,329,435 on human chromosome 14 (optionally the additional mutation being a guanine).
- the vertebrate, cell or population comprises a plurality of JH6 gene segments, wherein the plurality comprises a human JH6 gene variant that is an antisense sequence of a variant described above.
- the genome comprises SEQ ID NO:2; optionally cis at the same Ig locus as one, two or more of the JH6 variants.
- An embodiment provides a vertebrate, cell or population of the invention whose genome comprises a plurality of JH2 gene segments, wherein the plurality comprises a human JH2 gene variant of SEQ ID NO: 3, wherein the variant comprises a nucleotide mutation at one or more positions
- the vertebrate, cell or population comprises said plurality of JH2 gene segments, wherein the plurality comprises a human JH2 gene variant of SEQ ID NO: 3, wherein the variant comprises a guanine at a position corresponding to position 106,331,455 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 3.
- the variant comprises additionally a mutation at a position corresponding to (i) position 106,331,453 on human chromosome 14 (optionally the additional mutation being an adenine); and/or (ii) position 106,331,409 on human chromosome 14 (optionally the additional mutation being an adenine); (iii) position 106,329,434 on human chromosome 14 (optionally the additional mutation being an adenine).
- the vertebrate, cell or population comprises a plurality of JH2 gene segments, wherein the plurality comprises a human JH2 gene variant of SEQ ID NO: 3, wherein the variant comprises an adenine at a position corresponding to position 106,331,453 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 3.
- the variant comprises additionally a mutation at a position corresponding to position 106,331,409 on human chromosome 14 (optionally the additional mutation being an adenine).
- the vertebrate, cell or population comprises a plurality of JH2 gene segments, wherein the plurality comprises a human JH2 gene variant of SEQ ID NO: 3, wherein the variant comprises an adenine at a position corresponding to position 106,331,409 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 3.
- the vertebrate, cell or population comprises a plurality of JH2 gene segments, wherein the plurality comprises a human JH2 gene variant that is an antisense sequence of a variant described above.
- the genome comprises SEQ ID NO:3; optionally cis at the same Ig locus as one, two or more of the JH2 variants.
- the vertebrate, cell or population genome comprises two or more different JH gene segments selected from SEQ ID NOs: 1 to 3 and variants described above; optionally wherein said JH gene segments are cis at the same immunoglobulin Ig locus.
- a non-human vertebrate eg, a mouse or rat
- a non-human vertebrate cell eg, an ES cell or a B-cell
- having a genome comprising at least 3 human D gene segments of the same type (eg, D2-2 gene segments), wherein at least two of the human D gene segments are variants that are not identical to each other (eg, D2-2ref and D2-2a).
- one or more or all of the variants are naturally-occurring human gene segments.
- one or more of the variants may be a synthetic variant of a human gene segment.
- a non-human vertebrate eg, a mouse or rat
- a non-human vertebrate cell eg, an ES cell or a B-cell
- having a genome comprising at least 2 different non-endogenous D gene segments of the same type type (eg, D2-2ref and D2-2a) cis at the same Ig locus.
- a non-human vertebrate eg, a mouse or rat
- a non-human vertebrate cell eg, an ES cell or a B-cell
- having a genome comprising at least 2 different human D gene segments of the same type (eg, D2-2ref and D2-2a) trans at the same Ig locus; and optionally a third human D gene segment (eg, (eg, D2-2ref, D2-2a or D2-2b) of the same type, wherein the third D is cis with one of said 2 different D gene segments.
- a population of non-human vertebrates comprising a repertoire of human D gene segments, wherein the plurality comprises at least 2 different human D gene segments of the same type (eg, D2-2 gene segments), a first of said different D gene segments (eg, D2-2ref) is provided in the genome of a first vertebrate of the population, and a second of said different D gene segment (eg, D2-2a) being provided in the genome of a second vertebrate of the population, wherein the genome of the first vertebrate does not comprise the second D gene segment.
- non-human vertebrates eg, mice or rats
- the plurality comprises at least 2 different human D gene segments of the same type (eg, D2-2 gene segments)
- a first of said different D gene segments eg, D2-2ref
- a second of said different D gene segment eg, D2-2a
- a non-human vertebrate eg, a mouse or rat
- a non-human vertebrate cell eg, an ES cell or a B-cell
- having a genome comprising at least 2 different non-endogenous D gene segments of the same type (eg, human D2-2 gene segments), wherein the D gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
- vertebrate eg, a mouse or rat
- the method comprising providing the vertebrate with a genome comprising at least 3 human D gene segments of the same type (eg, D2-2 gene segments), wherein at least two of the human D gene segments are variants that are not identical to each other (eg, D2-2ref and D2-2a).
- a method of enhancing the immunoglobulin gene diversity of a non-human vertebrate comprising providing the vertebrate with a genome comprising at least 2 different non-endogenous D gene segments of the same type (eg, human D2-2 gene segments) cis at the same Ig locus.
- a method of enhancing the immunoglobulin gene diversity of a non-human vertebrate comprising providing the vertebrate with a genome comprising at least 2 different human D gene segments of the same type (eg, D2-2ref and D2-2a) trans at the same Ig locus; and optionally a third human D gene segment (eg, D2-2ref, D2-2a or D2-2b) of the same type, wherein the third D is cis with one of said 2 different D gene segments.
- a method of providing an enhanced human immunoglobulin D gene segment repertoire comprising providing a population of non-human vertebrates (eg, a mouse or rat) comprising a repertoire of human D gene segments, wherein the method comprises providing at least 2 different human D gene segments of the same type (eg, D2-2ref and D2-2a), wherein a first of said different D gene segments is provided in the genome of a first vertebrate of the population, and a second of said different D gene segments is provided in the genome of a second vertebrate of the population, wherein the genome of the first vertebrate does not comprise the second D gene segment.
- non-human vertebrates eg, a mouse or rat
- the method comprises providing at least 2 different human D gene segments of the same type (eg, D2-2ref and D2-2a), wherein a first of said different D gene segments is provided in the genome of a first vertebrate of the population, and a second of said different D gene segments is provided in the genome of a second vertebrate of the population
- vertebrate eg, a mouse or rat
- the method comprising providing the vertebrate with a genome comprising at least 2 different non-endogenous D gene segments of the same type (eg, D2-2ref and D2-2a), wherein the D gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
- vertebrate eg, a mouse or rat
- the method comprising providing the vertebrate with a genome comprising at least 2 human D gene segments of the same type (eg, D2-2ref and D2-2a), wherein the D gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations; optionally wherein at least 2 or 3 of said different gene segments are provided at the same IgH locus in said genome. 170.
- a non-human vertebrate eg, a mouse or rat
- a non-human cell eg, an ES cell or a B-cell
- having a genome comprising a substantially complete functional repertoire of human D gene segment types supplemented with one, two or more variant human D gene segments, wherein said substantially complete functional repertoire and the supplementary D gene segments are not found together in the germline genome of a human individual.
- a population of non-human vertebrates comprising a substantially
- D6-13ref and D6-13a or D3-9ref and D3-9a; or
- first and/or second D gene segment is present in two or more copies.
- the vertebrate, cell or population comprises one or more D segments selected from human D3-3, D2-15, D3-9; D4-17; D3-10; D2-2; D5-24; D6-19; D3-22; D6-13; D5-12; Dl-26; Dl-20; D5-18; D3-16; D2-21; Dl-14; D7-27; Dl-1; D6-25; D2-14 and D4-23 (eg, selected from D3- 9*01; D4-17*01; D3-10*01; D2-2*02; D5-24*01; D6-19*01; D3-22*01; D6-13*01; D5-12*01; Dl- 26*01; Dl-20*01; D5-18*01; D3-16*02; D2-21*02; Dl-14*01; D7-27*02; Dl-l*01; D6-25*01; D2-15*01; and D4-23*01), together with the reference sequence(s) of said selected segment(s) of said
- a non-human vertebrate or vertebrate cell according to clause 155 comprising a genome that comprises VH, D and JH gene repertoires comprising human gene segments, the D gene repertoire comprising one or more of a plurality of D2-2 gene segments provided by at least 2 different D2-2 gene segments in cis at the same Ig locus in said genome;
- a non-human vertebrate or vertebrate cell according to clause 155 comprising a genome that comprises VH, D and JH gene repertoires comprising human gene segments, the D gene repertoire comprising one or more of a plurality of D2-2 gene segments provided by at least 2 different D2-2 gene segments in trans in said genome;
- D7-27 gene segments provided by at least 2 different D7-27 gene segments in trans in said genome; optionally wherein the D gene segments are derived from the genome sequence of two or more different human individuals.
- a non-human vertebrate or vertebrate cell (optionally an ES cell or B-cell), according to clause 154, comprising a genome that comprises VH, D and JH gene repertoires comprising human gene segments, the D gene repertoire comprising one or more of a plurality of D2-2 gene segments provided by at least 3 different D2-2 gene segments;
- D4-4 gene segments provided by at least 3 different D4-4 gene segments
- D7-27 gene segments provided by at least 3 different D7-27 gene segments
- the D gene segments are derived from the genome sequence of two or three different human individuals; optionally wherein at least 2 or 3 of said different gene segments are provided in cis at the same Ig locus in said genome.
- a non-human vertebrate or vertebrate cell (optionally an ES cell or B-cell) according to clause 158, comprising a genome comprising human VH, D and JH gene repertoires, the D gene repertoire comprising of one or more of a plurality of D2-2 gene segments provided by at least 2 different D2-2 gene ; optionally in cis in said genome;
- D3-16 gene segments provided by at least 2 different D3-16 gene ; optionally in cis in said genome;
- D3-9 gene segments provided by at least 2 different D3-9 gene ; optionally in cis in said genome;
- D7-27 gene segments provided by at least 2 different D7-27 gene ; optionally in cis in said genome; wherein the D gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
- one or more of the D gene segments is a variant of a human germline D gene segment, wherein the variant gene segment encodes an amino acid sequence that differs by 1, 2 or 3 amino acids from the corresponding amino acid sequence encoded by the human germline D gene segment, provided in that said amino acid sequence encoded by the variant does not include a stop codon when said corresponding amino acid sequence does not include a stop codon.
- variant and germline D gene segments encode the respective amino acid sequences in reading frame 2 (IMGT numbering). See Briney et al 2012.
- D segments are usable in all three reading frames.
- a variant of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or all of these human germline D gene segments is used.
- a human D2-2 gene segment ((optionally two copies and/or in homozygous state) comprising a thymine at a position corresponding to position 106,382,687 on human chromosome 14; and optionally no further mutation from the sequence of D2-2ref.
- a human D3-16 gene segment (optionally two copies and/or in homozygous state) comprising a cytosine at a position corresponding to position 106,361,515 on human chromosome 14; and optionally no further mutation from the sequence of D3-16a.
- the vertebrate, cell or population of clause 205 wherein the plurality comprises a human D6-13 gene segment (optionally two copies and/or in homozygous state) comprising a thymine at a position corresponding to position 106,367,013 on human chromosome 14; and optionally no further mutation from the sequence of D6-13ref. 207.
- a human D3-10 gene segment (optionally two copies and/or in homozygous state) comprising a thymine at a position corresponding to position 106,370,370 on human chromosome 14; and optionally no further mutation from the sequence of D3-10ref.
- a human D3-10 gene segment (optionally two copies and/or in homozygous state) comprising a cytosine at a position corresponding to position 106,370,370 on human chromosome 14; and optionally no further mutation from the sequence of D3-10a.
- a human D3-10 gene segment (optionally two copies and/or in homozygous state) comprising an adenine at a position corresponding to position 106,370,371 on human chromosome 14; and optionally no further mutation from the sequence of D3-10ref.
- a human D3-9 gene segment (optionally two copies and/or in homozygous state) comprising an adenine at a position corresponding to position 106,370,567 on human chromosome 14; and optionally no further mutation from the sequence of D3-9ref.
- a human D3-9 gene segment (optionally two copies and/or in homozygous state) comprising a thymine at a position corresponding to position 106,370,567 on human chromosome 14; and optionally no further mutation from the sequence of D3-9a.
- a human D2-8 gene segment (optionally two copies and/or in homozygous state) comprising a thymine at a position corresponding to position 106,373,085 on human chromosome 14; and optionally no further mutation from the sequence of D2-8b.
- a D4-4 gene segment (optionally two copies and/or in homozygous state) comprising a cytosine at a position corresponding to position 106,379,086 on human chromosome 14; and optionally no further mutation from the sequence of D4-4ref.
- a human D4-4 gene segment (optionally two copies and/or in homozygous state) comprising a cytosine at a position corresponding to position 106,379,089 on human chromosome 14; and optionally no further mutation from the sequence of D4-4ref or a cytosine at a position corresponding to position 106,379,086 on human chromosome 14.
- a D3-3 gene segment (optionally two copies and/or in homozygous state) comprising a thymine at a position corresponding to position 106,380,241 on human chromosome 14; and optionally no further mutation from the sequence of D3-3ref.
- a human D3-3 gene segment (optionally two copies and/or in homozygous state) comprising a cytosine at a position corresponding to position 106,380,241 on human chromosome 14; and optionally no further mutation from the sequence of D3-3a.
- a specific application of this configuration is the provision of multiple human JL gene segments ( and/or i ⁇ ) as follows (as set out in numbered paragraphs, starting at paragraph number 80).
- 80. A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) having a genome comprising at least 3 human JL gene segments of the same type (eg, JKI), wherein at least two of the human J L gene segments are variants that are not identical to each other.
- a non-human vertebrate eg, a mouse or rat
- a non-human vertebrate cell eg, an ES cell or a B-cell
- having a genome comprising at least 2 different non-endogenous JL gene segments of the same type (eg, JKI) cis at the same Ig locus.
- a non-human vertebrate eg, a mouse or rat
- a non-human vertebrate cell eg, an ES cell or a B-cell
- having a genome comprising at least 2 different human JL gene segments of the same type (eg, JKI) trans at the same Ig locus; and optionally a third human JL gene segment of the same type, wherein the third JL is cis with one of said 2 different JL gene segments.
- a population of non-human vertebrates comprising a repertoire of human JL gene segments, wherein the plurality comprises at least 2 different human JL gene segments of the same type (eg, JKI), a first of said different J L gene segments is provided in the genome of a first vertebrate of the population, and a second of said different JL gene segments being provided in the genome of a second vertebrate of the population, wherein the genome of the first vertebrate does not comprise the second JL gene segment.
- a non-human vertebrate eg, a mouse or rat
- a non-human vertebrate cell eg, an ES cell or a B-cell
- having a genome comprising at least 2 different non-endogenous JL gene segments of the same type (eg, JKI), wherein the JL gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
- a method of enhancing the human immunoglobulin gene diversity of a non-human vertebrate comprising providing the vertebrate with a genome comprising at least 3 human JL gene segments of the same type (eg, JKI), wherein at least two of the human JL gene segments are variants that are not identical to each other.
- a method of enhancing the immunoglobulin gene diversity of a non-human vertebrate comprising providing the vertebrate with a genome comprising at least 2 different non-endogenous JL gene segments of the same type (eg, JKI) cis at the same Ig locus.
- a method of enhancing the immunoglobulin gene diversity of a non-human vertebrate comprising providing the vertebrate with a genome comprising at least 2 different human JL gene segments of the same type(eg, JKI) trans at the same Ig locus; and optionally a third human JL gene segment of the same type, wherein the third JL is cis with one of said 2 different J L gene segments.
- a method of providing an enhanced human immunoglobulin JL gene segment repertoire comprising providing a population of non-human vertebrates (eg, a mouse or rat) comprising a repertoire of human JL gene segments, wherein the method comprises providing at least 2 different human JL gene segments of the same type (eg, JKI), wherein a first of said different JL gene segments is provided in the genome of a first vertebrate of the population, and a second of said different J L gene segments is provided in the genome of a second vertebrate of the population, wherein the genome of the first vertebrate does not comprise the second JL gene segment.
- non-human vertebrates eg, a mouse or rat
- JKI human JL gene segments of the same type
- a method of enhancing the human immunoglobulin gene diversity of a non-human vertebrate comprising providing the vertebrate with a genome comprising at least 2 different non-endogenous JL gene segments of the same type (eg, JKI), wherein the JL gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
- JL gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
- JL gene segments are derived from the genome sequence of two or more different human individuals; optionally wherein the different human individuals are from different human populations.
- a method of enhancing the human immunoglobulin gene diversity of a non-human vertebrate comprising providing the vertebrate with a genome comprising at least 2 human J L gene segments of the same type (eg, JKI), wherein the J L gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations; optionally wherein at least 2 or 3 of said different gene segments are provided at the same IgL locus in said genome.
- the population of paragraph 83 wherein the population comprises a substantially complete functional repertoire of human J L gene segment types supplemented with one, two or more human JK and/or iX gene segments respectively, wherein said substantially complete functional repertoire and the supplementary gene segments are not found together in the germline genome of a human individual.
- a non-human vertebrate eg, a mouse or rat
- a non-human cell eg, an ES cell or a B-cell
- having a genome comprising a substantially complete functional repertoire of human JK and/or iX gene segment types supplemented with one, two or more human JK and/or iX gene segments respectively, wherein said substantially complete functional repertoire and the supplementary gene segments are not found together in the germline genome of a human individual.
- a population of non-human vertebrates comprising a substantially complete functional repertoire of human JK and/or iX gene segment types supplemented with one, two or more human JK and/or iX gene segments respectively, wherein said substantially complete functional repertoire and the supplementary gene segments are not found together in the germline genome of a human individual.
- a non-human vertebrate or vertebrate cell according to paragraph 81 comprising a genome that comprises VL and J L gene repertoires comprising human gene segments, the J L gene repertoire comprising a plurality of human JKI gene segments provided by at least 2 different human JKI gene segments in cis at the same Ig locus in said genome;
- a non-human vertebrate or vertebrate cell (optionally an ES cell or B-cell), according to paragraph 80, comprising a genome that comprises VL and J L gene repertoires comprising human gene segments, the J L gene repertoire comprising a plurality of human JKI gene segments provided by at least 3 (eg, 3, 4, 5, 6, or 7) different human JKI gene segments;
- a plurality of human JK2 gene segments provided by at least 3 (eg, 3, 4, 5, 6, or 7) different human JKI gene segments;
- a plurality of human JK3 gene segments provided by at least 3 (eg, 3, 4, 5, 6, or 7) different human JKI gene segments;
- a plurality of human JK4 gene segments provided by at least 3 (eg, 3, 4, 5, 6, or 7) different human JKI gene segments;
- a plurality of human JK5 gene segments provided by at least 3 (eg, 3, 4, 5, 6, or 7) different human JKI gene segments;
- a plurality of human J ⁇ l gene segments provided by at least 3 (eg, 3, 4, 5, 6, or 7) different human J ⁇ l gene segments;
- a plurality of human J ⁇ 2 gene segments provided by at least 3 (eg, 3, 4, 5, 6, or 7) different human J ⁇ 2 gene segments;
- a plurality of human J ⁇ 3 gene segments provided by at least 3 (eg, 3, 4, 5, 6, or 7) different human J ⁇ 3 gene segments;
- a plurality of human J ⁇ 4 gene segments provided by at least 3 (eg, 3, 4, 5, 6, or 7) different human J ⁇ 4 gene segments;
- a plurality of human J ⁇ 5 gene segments provided by at least 3 (eg, 3, 4, 5, 6, or 7) different human J ⁇ 5 gene segments;
- a plurality of human J ⁇ 6 gene segments provided by at least 3 (eg, 3, 4, 5, 6, or 7) different human J ⁇ 6 gene segments; or
- J ⁇ 7 gene segments provided by at least 3 (eg, 3, 4, 5, 6, or 7) different human J ⁇ 7 gene segments; optionally wherein the J L gene segments are derived from the genome sequence of two or three different human individuals; optionally wherein at least 2 or 3 of said different gene segments are provided in cis at the same Ig locus in said genome.
- a non-human vertebrate or vertebrate cell (optionally an ES cell or B-cell) according to paragraph 84, comprising a genome comprising human VL and J L gene repertoires, the J L gene repertoire comprising a plurality of human JKI gene segments provided by at least 2 different human JKI gene segments, optionally in cis at the same Ig locus in said genome;
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Abstract
The invention relates to the provision of antibody therapeutics and prophylactics that are tailored specifically for human use. The present invention provides libraries, vertebrates and cells, such as transgenic mice or rats or transgenic mouse or rat cells. Furthermore, the invention relates to methods of using the vertebrates to isolate antibodies or nucleotide sequences encoding antibodies. Antibodies, heavy chains, polypeptides, nucleotide sequences, pharmaceutical compositions and uses are also provided by the invention.
Description
ANTIBODIES. VARIABLE DOMAINS & CHAINS TAILORED FOR HUMAN USE
FIELD OF THE INVENTION
The present invention relates to the provision of antibody therapeutics and prophylactics that are tailored specifically for human use.
The present invention provides libraries, vertebrates and cells, such as transgenic mice or rats or transgenic mouse or rat cells. Furthermore, the invention relates to methods of using the vertebrates to isolate antibodies or nucleotide sequences encoding antibodies. Antibodies, heavy chains, polypeptides, nucleotide sequences, pharmaceutical compositions and uses are also provided by the invention.
BACKGROUND
The state of the art provides non-human vertebrates (eg, mice and rats) and cells comprising transgenic immunoglobulin loci, such loci comprising human variable (V), diversity (D) and/or joining (J) segments, and optionally human constant regions. Alternatively, endogenous constant regions of the host vertebrate (eg, mouse or rat constant regions) are provided in the transgenic loci. Methods of constructing such transgenic vertebrates and use of these to generate antibodies and nucleic acids thereof following antigen immunisation are known in the art, eg, see US7501552 (Medarex), US5939598 (Abgenix), US6130364 (Abgenix), WO02/066630 ( egeneron), WO2011004192 (Genome Research Limited), WO2009076464, WO2009143472 and WO2010039900 (Ablexis), the disclosures of which are explicitly incorporated herein. Such transgenic loci in the art include varying amounts of the human V(D) J repertoire. Existing transgenic immunoglobulin loci are based on a single human DNA source. The potential diversity of human antibody variable regions in non-human vertebrates bearing such transgenic loci is thus confined.
The inventors considered that it would be desirable to tailor the genomes of these transgenic non- human vertebrates (and thus antibody and antibody chain products of these) to address the variability - and commonality - in the natural antibody gene usage of humans. The inventors wanted to do this in order to better address human use of antibody-based therapeutic and prophylactic drugs.
It would be desirable also to provide for novel and potentially expanded repertoire and diversity of human variable regions in transgenic immunoglobulin loci and non-human vertebrates harbouring these, as well as in antibodies produced following immunisation of such animals.
SUMMARY OF THE INVENTION
The present invention has been developed from extensive bioinformatics analysis of natural antibody gene segment distributions across a myriad of different human populations and across more than two thousand samples from human individuals. The inventors have undertaken this huge task to more thoroughly understand and design non-human vertebrate systems and resultant antibodies to better address human medical therapeutics as a whole, as well as to enable rational design to address specific ethnic populations of humans. Using such rational design, the inventors have constructed transgenic non-human vertebrates and isolated antibodies, antibody chains and cells expressing these in a way that yields products that utilise gene segments that have been purposely included on the basis of the human bioinformatics analysis. The examples illustrate worked experiments where the inventors isolated many cells and antibodies to this effect.
The invention also relates to synthetically-extended & ethnically-diverse superhuman
immunoglobulin gene repertoires. The present invention thus provides for novel and potentially expanded synthetic immunoglobulin diversities, thus providing a pool of diversity from which human antibody therapeutic leads can be selected. This expanded pool is useful when seeking to find antibodies with desirable characteristics, such as relatively high affinity to target antigen without the need for further affinity maturation (eg, using laborious in vitro techniques such as phage or ribosome display), or improved biophysical characteristics, or to address targets and new epitopes that have previously been difficult to address with antibodies are not reached by prior antibody binding sites.
The invention also provides for diversity that is potentially biased towards variable gene usage common to members of a specific human population, which is useful for generating antibodies for treating and/or preventing diseases or conditions within such population. This ability to bias the
antibody repertoire allows one to tailor antibody therapeutics with the aim of more effectively treating and/or preventing disease or medical conditions in specific human populations.
The present inventors realised the possibility of providing immunoglobulin gene segments from disparate sources in transgenic loci, in order to provide for novel and potentially-expanded antibody diversities from which antibody therapeutics (and antibody tool reagents) could be generated. This- opens up the potential of transgenic human-mouse/rat technologies to the possibility of interrogating different and possibly larger antibody sequence-spaces than has hitherto been possible.
In rationally designing transgenic antibody loci, as well as antibodies and antibody chains, the inventors also realised that a relatively long HCDR3 length (at least 20 amino acids) is often desirable to address epitopes. For example, naturally-occurring antibodies have been isolated from humans infected with infectious disease pathogens, such antibodies having a long HCDR3 length.
Neutralising antibodies have been found in this respect. A long HCDR3 length would be desirable to address other antigens (eg, receptor clefts or enzyme active sites), not just limited to infectious disease pathogens, and thus the inventors realised the general desirability of the possibility of engineering transgenic loci to be able to produce long HCDR3 antibodies and heavy chains. The inventors, through laborious execution of bioinformatics on in excess of 2000 human DNA samples via the 1000 Genomes project together with rational sequence choices, identified that the inclusion of the specific human gene segment variant JH6*02 is desirable for producing long HCDR3 antibodies and chains.
Additional rational design and bioinformatics has led the inventors to realise that specific human constant region variants are conserved across many diverse human populations. The inventors realised that this opens up the possibility of making a choice to humanise antibodies, chains and variable domains by using such specific constant regions in products, rather than arbitrarily choosing the human constant region (or a synthetic version of a human constant region). This aspect of the invention also enables one to tailor antibody-based drugs to specific human ethnic populations, thereby more closely matching drug to patient (and thus disease setting) than has hitherto been performed. It can be a problem in the state of the art that antibodies are humanised with an arbitrary choice of human constant region (presumably derived from one (often unknown) ethnic
population or non-naturally occurring) that does not function as well in patients of a different human ethnic population. This is important, since the constant region has the major role in providing antibody effector functions, eg, for antibody recycling, cellular and complement recruitment and for cell killing.
To this end, in a first configuration of the invention, there is provided
First Configuration
A non-human vertebrate or vertebrate cell (optionally an ES cell or antibody-producing cell) comprising a genome having a superhuman immunoglobulin heavy chain human VH and/or D and/or J gene repertoire.
A non-human vertebrate or vertebrate cell (optionally an ES cell or antibody-producing cell) comprising a genome having a superhuman immunoglobulin light chain human VL gene repertoire; optionally wherein the vertebrate or cell is according to the first configuration.
A non-human vertebrate or vertebrate cell (optionally an ES cell or antibody-producing cell) whose genome comprises a transgenic immunoglobulin locus (eg, a heavy chain locus or a light chain locus), said locus comprising immunoglobulin gene segments according to the first and second human immunoglobulin gene segments (optionally V segments) as mentioned below operably connected upstream of an immunoglobulin constant region; optionally wherein the genome is homozygous for said transgenic immunoglobulin locus;
optionally wherein the immunoglobulin locus comprises more than the natural human complement of functional V gene segments; and/or
optionally wherein the immunoglobulin locus comprises more than the natural human complement of functional D gene segments; and/or
optionally wherein the immunoglobulin locus comprises more than the natural human complement of functional J gene segments.
A transgenic non-human vertebrate (eg, a mouse or rat) or vertebrate cell (optionally an ES cell or antibody-producing cell) whose genome comprises a transgenic immunoglobulin locus comprising a plurality of human immunoglobulin gene segments operably connected upstream of a non-human vertebrate constant region for the production of a repertoire of chimaeric antibodies, or chimaeric light or heavy chains, having a non-human vertebrate constant region and a human variable region; wherein the transgenic locus comprises one or more human immunoglobulin V gene segments, one or more human J gene segments and optionally one or more human D gene segments, a first (optionally a V segment) of said gene segments and a second (optionally a V segment) of said gene segments being different and derived from the genomes of first and second human individuals respectively, wherein the individuals are different; and optionally not related;
optionally wherein the immunoglobulin locus comprises more than the natural human complement of functional V gene segments; and/or
optionally wherein the immunoglobulin locus comprises more than the natural human complement of functional D gene segments; and/or
optionally wherein the immunoglobulin locus comprises more than the natural human complement of functional J gene segments.
A transgenic non-human vertebrate (eg, a mouse or rat) or vertebrate cell (optionally an ES cell or antibody-producing cell) whose genome comprises first and second transgenic immunoglobulin loci, each locus comprising a plurality of human immunoglobulin gene segments operably connected upstream of a non-human vertebrate constant region for the production of a repertoire of chimaeric antibodies, or chimaeric light or heavy chains, having a non-human vertebrate constant region and a human variable region; wherein (i) the first transgenic locus comprises one or more human immunoglobulin V gene segments, one or more human J gene segments and optionally one or more human D gene segments, (ii) the second transgenic locus comprises one or more human immunoglobulin V gene segments, one or more human J gene segments and optionally one or more human D gene segments; and (iii) wherein a first (optionally a V) gene segment of said first locus and a second (optionally a V) gene segment of said second gene locus are different and derived from the genomes of first and second human individuals respectively, wherein the individuals are different; and optionally not related;
optionally wherein the first and second loci are on different chromosomes (optionally chromosomes with the same chromosome number) in said genome; optionally wherein each immunoglobulin locus comprises more than the natural human
complement of functional V gene segments; and/or optionally wherein each immunoglobulin locus comprises more than the natural human
complement of functional D gene segments; and/or optionally wherein each immunoglobulin locus comprises more than the natural human
complement of functional J gene segments.
A method of constructing a cell (eg, an ES cell) according to the invention, the method comprising
(a) identifying functional V and J (and optionally D) gene segments of the genome sequence of a (or said) first human individual;
(b) identifying one or more functional V and/or D and/or J gene segments of the genome sequence of a (or said) second human individual, wherein these additional gene segments are not found in the genome sequence of the first individual;
(c) and constructing a transgenic immunoglobulin locus in the cell, wherein the gene segments of (a) and (b) are provided in the locus operably connected upstream of a constant region.
In one embodiment, the gene segment(s) in step (b) are identified from an immunoglobulin gene database selected from the 1000 Genomes, Ensembl, Genbank and IMGT databases.
Throughout this text, Genbank is a reference to Genbank release number 185.0 or 191.0; the 1000 Genomes database is Phase 1, release v3, 16th March 2012; the Ensembl database is assembly GRCh37.p8 (10/04/2012); the IMGT database is available at www.imgt.org .
In one embodiment, the first and second human individuals are members of first and second ethnic populations respectively, wherein the populations are different, optionally wherein the human
immunoglobulin gene segment derived from the genome sequence of the second individual is low- frequency (optionally rare) within the second ethnic population.
This configuration of the invention also provides a method of making a transgenic non-human vertebrate (eg, a mouse or rat), the method comprising
(a) constructing an ES cell (eg, a mouse C57BL/6N, C57BL/6J, 129S5 or 129Sv strain ES cell) by carrying out the method above;
(b) injecting the ES cell into a donor non-human vertebrate blastocyst (eg, a mouse C57BL/6N, C57BL/6J, 129S5 or 129Sv strain blastocyst);
(c) implanting the blastocyst into a foster non-human vertebrate mother (eg, a C57BL/6N, C57BL/6J, 129S5 or 129Sv strain mouse); and
(d) obtaining a child from said mother, wherein the child genome comprises a transgenic immunoglobulin locus.
In one embodiment, the invention provides a method of isolating an antibody that binds a predetermined antigen (eg, a bacterial or viral pathogen antigen), the method comprising immunising a non-human vertebrate according to the invention.
Second Configuration
A library of antibody-producing transgenic cells whose genomes collectively encode a repertoire of antibodies, wherein
(a) a first transgenic cell expresses a first antibody having a chain encoded by a first immunoglobulin gene, the gene comprising a first variable domain nucleotide sequence produced following recombination of a first human unrearranged immunoglobulin gene segment;
(b) a second transgenic cell expresses a second antibody having a chain encoded by a second immunoglobulin gene, the second gene comprising a second variable domain nucleotide sequence produced following recombination of a second human unrearranged immunoglobulin gene segment, the first and second antibodies being non-identical;
(c) the first and second gene segments are different and derived from the genome sequences of first and second human individuals respectively, wherein the individuals are different; and optionally not related;
(d) wherein the cells are non-human vertebrate (eg, mouse or rat) cells.
In one embodiment, the first and second human individuals are members of first and second ethnic populations respectively, wherein the populations are different; optionally wherein the ethnic populations are selected from those identified in the 1000 Genomes database.
In another embodiment, the second human immunoglobulin gene segment is a polymorphic variant of the first human immunoglobulin gene segment; optionally wherein the second gene segment is selected from the group consisting of a gene segment in any of Tables 1 to 7 and 9 to 14 below (eg, selected from Table 13 or Table 14), eg, the second gene segment is a polymorphic variant of VH1- 69.
Third Configuration
An isolated antibody having
(a) a heavy chain encoded by a nucleotide sequence produced following recombination in a transgenic non-human vertebrate cell of an unrearranged human immunoglobulin V gene segment with a human D and human J segment, optionally with affinity maturation in said cell, wherein one of the gene segments is derived from the genome of an individual from a first human ethnic population; and the other two gene segments are derived from the genome of an individual from a second, different, human ethnic population, and wherein the antibody comprises heavy chain constant regions of said non-human vertebrate (eg, rodent, mouse or rat heavy chain constant regions); and/or
(b) a light chain encoded by a nucleotide sequence produced following recombination in a transgenic non-human vertebrate cell of an unrearranged human immunoglobulin V gene segment with a human J segment, optionally with affinity maturation in said cell, wherein one of the gene segments is derived from the genome of an individual from a first human ethnic population (optionally the same as the first population in (a)); and the other gene segment is derived from the genome of an individual from a second, different, human ethnic population (optionally the same as the second population in (a)), and wherein the antibody comprises light chain constant regions of said non-human vertebrate (eg, rodent, mouse or rat heavy light constant regions);
Optionally wherein each variable domain of the antibody is a human variable domain. Optionally wherein the heavy chain constant regions are gamma-type constant regions.
The invention also provides an isolated nucleotide sequence encoding the antibody, optionally wherein the sequence is provided in an antibody expression vector, optionally in a host cell.
The invention also provides a method of producing a human antibody, the method comprising replacing the non-human vertebrate constant regions of the antibody of the third configuration with human antibody constant regions.
The invention also provides a pharmaceutical composition comprising an antibody according to the third configuration, or an antibody produced according to the method above and a diluent, excipient or carrier; optionally wherein the composition is provided in a container connected to an IV needle or syringe or in an IV bag.
The invention also provides an antibody-producing cell that expresses the second antibody recited in any one of the configurations.
In an alternative configuration, the invention contemplates the combination of nucleotide sequences of first and second immunoglobulin gene segments (eg, two or more polymorphic variants of a particular human germline VH or VL gene segment) to provide a synthetic gene segment. Such synthetic gene segment is used, in one embodiment, to build a transgenic immunoglobulin locus, wherein the synthetic gene segment is provided in combination with one or more human variable and J regions (and optionally one or more human D regions) operably connected upstream of a constant region. When provided in the genome of a non-human vertebrate or cell (eg, mouse or rat cell, eg, ES cell), the invention provides for superhuman gene segment diversity. The sequences to be combined can be selected from gene segments that have been observed to be commonly used in human antibodies raised against a particular antigen (eg, a flu antigen, such as haemaglutinin). By combining the sequences, the synthetic gene segment may
recombine in vivo to produce an antibody that is well suited to the treatment and/or prevention of a disease or condition (eg, influenza) mediated by said antigen.
Fourth Configuration
A non-human vertebrate (optionally a mouse or a rat) or vertebrate cell whose genome comprises an immunoglobulin heavy chain locus comprising human gene segment JH6*02, one or more VH gene segments and one or more D gene segments upstream of a constant region; wherein the gene segments in the heavy chain locus are operably linked to the constant region thereof so that the mouse is capable of producing an antibody heavy chain produced by recombination of the human JH6*02 with a D segment and a VH segment.
A non-human vertebrate cell (optionally a mouse cell or a rat cell) whose genome comprises an immunoglobulin heavy chain locus comprising human gene segment JH6*02, one or more VH gene segments and one or more D gene segments upstream of a constant region; wherein the gene segments in the heavy chain locus are operably linked to the constant region thereof for producing (eg, in a subsequent progeny cell) an antibody heavy chain produced by recombination of the human JH6*02 with a D segment and a VH segment.
A heavy chain (eg, comprised by an antibody) isolated from a vertebrate of the invention wherein the heavy chain comprises a HCD 3 of at least 20 amino acids.
A method for producing a heavy chain, VH domain or an antibody specific to a target antigen, the method comprising immunizing a non-human vertebrate according to the invention with the antigen and isolating the heavy chain, VH domain or an antibody specific to a target antigen or a cell producing the heavy chain, VH domain or an antibody, wherein the heavy chain, VH domain or an antibody comprises a HCDR3 that is derived from the recombination of human JH6*02 with a VH gene segment and a D gene segment.
A heavy chain, VH domain or an antibody produced by the method.
A B-cell or hybridoma expressing a heavy chain VH domain that is identical to the VH domain of the heavy chain.
A nucleic acid encoding the VH domain of the heavy chain of claim 22, 23 or 28, or encoding the heavy chain.
A vector (eg, a CHO cell or HEK293 cell vector) comprising the nucleic acid; optionally wherein the vector is in a host cell (eg, a CHO cell or HEK293 cell).
A pharmaceutical composition comprising the antibody, heavy chain or VH domain (eg, comprised by an antibody), together with a pharmaceutically-acceptable excipient, diluent or a medicament (eg, a further antigen-specific variable domain, heavy chain or antibody).
The antibody, heavy chain or VH domain (eg, comprised by an antibody) as above for use in medicine.
The use of an antibody, heavy chain or VH domain (eg, comprised by an antibody) as above in the manufacture of a medicament for treating and/or preventing a medical condition in a human.
Fifth Configuration
A method of producing an antibody heavy chain, the method comprising
(a) providing an antigen-specific heavy chain variable domain; and
(b) combining the variable domain with a human heavy chain constant region to produce an antibody heavy chain comprising (in N- to C-terminal direction) the variable domain and the constant region;
wherein
the human heavy chain constant region is an IGHGlref, IGHG2ref, IGHG2a, IGHG3ref, IGHG3a, IGHG3b, IGHG4ref or IGHG4a constant region.
An antibody comprising a human heavy chain, the heavy chain comprising a variable domain that is specific for an antigen and a constant region that is an IGHGlref, IGHG2ref, IGHG2a, IGHG3ref, IGHG3a, IGHG3b, IGHG4ref or IGHG4a constant region . Optionally, the variable domain comprises mouse-pattern AID somatic mutations.
A polypeptide comprising (in N- to C- terminal direction) a leader sequence, a human variable domain that is specific for an antigen and a human constant region that is an IGHGlref, IGHG2ref, IGHG2a, IGHG3ref, IGHG3a, IGHG3b, IGHG4ref or IGHG4a constant region wherein (i) the leader sequence is not the native human variable domain leader sequence; and/or (ii) the variable domain comprises mouse AID-pattern somatic mutations and/or mouse Terminal deoxynucleotidyl transferase (TdT)- pattern junctional mutations.
A nucleotide sequence encoding (in 5' to 3' direction) a leader sequence and a human antibody heavy chain, the heavy chain comprising a variable domain that is specific for an antigen and a constant region that is an IGHGlref, IGHG2ref, IGHG2a, IGHG3ref, IGHG3a, IGHG3b, IGHG4ref or IGHG4a constant region; and the leader sequence being operable for expression of the heavy chain and wherein the leader sequence is not the native human variable domain leader sequence.
A nucleotide sequence encoding (in 5' to 3' direction) a promoter and a human antibody heavy chain, the heavy chain comprising a variable domain that is specific for an antigen and a constant region that is an IGHGlref, IGHG2ref, IGHG2a, IGHG3ref, IGHG3a, IGHG3b, IGHG4ref or IGHG4a constant region ; and the promoter being operable for expression of the heavy chain and wherein the promoter is not the native human promoter.
A vector (eg, a CHO cell or HEK293 cell vector) comprising a IGHGlref, IGHG2ref, IGHG2a, IGHG3ref, IGHG3a, IGHG3b, IGHG4ref or IGHG4a constant region nucleotide sequence that is 3' of a cloning site for the insertion of a human antibody heavy chain variable domain nucleotide sequence, such
that upon insertion of such a variable domain sequence the vector comprises (in 5' to 3' direction) a promoter, a leader sequence, the variable domain sequence and the constant region sequence so that the vector is capable of expressing a human antibody heavy chain when present in a host cell.
Sixth Configuration
A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B- cell) having a genome comprising at least 3 human variable region gene segments of the same type (eg, at least 3 human VH6-1 gene segments, at least 3 human JH6 gene segments, at least 3 human VK1-39 gene segments, at least 3 human D2-2 gene segments or at least 3 human JKI gene segments), wherein at least two of the human gene segments are variants that are not identical to each other.
A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B- cell) having a genome comprising at least 2 different non-endogenous variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 3 human JH6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments) cis at the same Ig locus.
A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B- cell) having a genome comprising at least 2 different human variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human JH6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments) trans at the same Ig locus; and optionally a third human gene segment of the same type, wherein the third gene segment is cis with one of said 2 different gene segments.
A population of non-human vertebrates (eg, mice or rats) comprising a repertoire of human variable region gene segments, wherein the plurality comprises at least 2 human variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human JH6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments), a first of said different gene segments is provided in the genome of a
first vertebrate of the population, and a second of said different gene segments being provided in the genome of a second vertebrate of the population, wherein the genome of the first vertebrate does not comprise the second gene segment.
A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B- cell) having a genome comprising at least 2 different non-endogenous variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human J H6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments), wherein the gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
A method of enhancing the human immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising at least 3 human variable region gene segments of the same type (eg, at least 3 human VH6-1 gene segments, at least 3 human J H6 gene segments, at least 3 human VK1-39 gene segments, at least 3 human D2-2 gene segments or at least 3 human JKI gene segments), wherein at least two of the human gene segments are variants that are not identical to each other.
A method of enhancing the immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising at least 2 different non-endogenous variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human J H6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments) cis at the same Ig locus.
A method of enhancing the immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising at least 2 different human variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human JH6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments) trans at the same Ig locus; and
optionally a third human gene segment of the same type, wherein the third gene segment is cis with one of said 2 different gene segments.
A method of providing an enhanced human immunoglobulin variable region gene segment repertoire, the method comprising providing a population of non-human vertebrates (eg, a mouse or rat) comprising a repertoire of human variable region gene segments, wherein the method comprises providing at least 2 different human variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human JH6 gene segments, at least 2 human VKI- 39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments), wherein a first of said different gene segments is provided in the genome of a first vertebrate of the population, and a second of said different gene segments is provided in the genome of a second vertebrate of the population, wherein the genome of the first vertebrate does not comprise the second gene segment.
A method of enhancing the human immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising at least 2 different non-endogenous variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human J H6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments), wherein the gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
A method of enhancing the human immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising at least 2 human variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human J H6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments), wherein the gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations; optionally wherein at least 2 or 3 of said different gene segments are provided at the same Ig locus in said genome.
A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B- cell) having a genome comprising first and second human Ig locus gene segments of the same type (eg, first and second human JH6 gene segments; or first and second lgG2 gene segments; or first and second human J\7 gene segments), wherein the first gene segment is a gene segment selected from any one of Tables 1 and 9 to 14 (eg, selected from Table 13 or Table 14) (eg, IGHJ6-a) and the second gene segment is the corresponding reference sequence.
A population of non-human vertebrates (eg, mice or rats) comprising first and second human Ig locus gene segments of the same type (eg, first and second human JH6 gene segments; or first and second lgG2 gene segments; or first and second human J\7 gene segments), wherein the first gene segment is a gene segment selected from any one of Tables 1 and 9 to 14 (eg, selected from Table 13 or Table 14) (eg, IGHJ6-a) and the second gene segment is the corresponding reference sequence, wherein the first gene segment is provided in the genome of a first vertebrate of the population, and the second gene segment is provided in the genome of a second vertebrate of the population.
A method of enhancing the human immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising first and second human Ig locus gene segments of the same type (eg, first and second human JH6 gene segments; or first and second lgG2 gene segments; or first and second human J\7 gene segments), wherein the first gene segment is a gene segment selected from any one of Tables 1 and 9 to 14 (eg, selected from Table 13 or Table 14) (eg, IGHJ6-a) and the second gene segment is the corresponding reference sequence.
In one aspect of this configuration, the invention relates to human D gene segment variants as described further below.
In one aspect of this configuration, the invention relates to human V gene segment variants as described further below.
In one aspect of this configuration, the invention relates to human J gene segment variants as described further below.
BRIEF DESCRIPTION OF THE FIGURES
Figures 1 to 3: Schematic illustrating a protocol for producing recombineered BAC vectors to add V gene segments into a mouse genome;
Figure 4: Schematic illustrating a protocol for adding V gene segments to a mouse genome using sequential recombinase mediated cassette exchange (s MCE); and
Figure 5 (in 4 parts): Alignment of 13 IGHVl-69 variants showing the variable (V) coding region only. Nucleotides that differ from VH1-69 variant *01 are indicated at the appropriate position whereas identical nucleotides are marked with a dash. Where nucleotide changes result in amino acid differences, the encoded amino acid is shown above the corresponding triplet. Boxed regions correspond to CDR1, CDR2 and CDR3 as indicated.
Figure 6 is a schematic illustrating gene segment diversity and the effect of including variant variants in cis according to the invention:-
(a) Situation in a normal person: Recombination on the same chromosome limits combinations of variants, for instance the antibody gene V4-4 can only be recombined within variant 1 to form for instance for instance V4-4-D-J6 or V4-4-D-J2A. Similarly the variant V4-4A can't be recombined with either J6 or J2A from variant 1 and can only be joined with J-genes from variant 2 to form V4-4A-D-J6A and V4-4A-D-J2. V4-4-J2/J6 complexity = 4.
(b) Situation in a transgenic mouse: Only one variant is provided so the genome is limited. V4- 4-J6/J2 complexity = 2.
(c) Supra mouse of the invention: The variants are added in cis and thus can be recombined in every combination, expanding the repertoire. For instance V4-4 can be combined with J6A, J6, J2A or J2 and similarly V4-4A can be recombined with these same J-genes. The V4-4-J6/J2 complexity = 8, which in this simple example is double that of a person and 4X that of a mouse with a single variant.
Figure 7: Alignment of human JH6*02 variants. Nucleotides that differ from JH6 *01 are indicated at the appropriate position whereas identical nucleotides are marked with a dash. Where nucleotide changes result in amino acid differences, the encoded amino acid is shown above. Accession numbers (eg, J00256) are shown to the left of the IMGT variant name.
Figure 8: Alignment of JH sequences from various species.
Figure 9: Codon Table
Figure 10: BAC database extract
BRIEF DESCRIPTION OF THE TABLES
Table 1: Human IgH V Polymorphic Variants
Table 2: Human IgH D Polymorphic Variants
Table 3: Human IgH J Polymorphic Variants
Table 4: Human Ig Vk Polymorphic Variants
Table 5: Human Ig V\ Polymorphic Variants
Table 6: Human IgH Jk Polymorphic Variants
Table 7: Human IgH i\ Polymorphic Variants
Table 8: 1000 Genomes Project Human Populations
Table 9: Immunoglobulin Gene Usage in Human Antibody Responses to Infectious Disease
Pathogens
Table 10A: Human IgH JH5 Variant Occurrences
Table 10B: Non-Synonymous Human IgH JH5 Variants
Table 11A: Human IgH JH6 Variant Occurrences
Table 11B: Non-Synonymous Human IgH JH6 Variants
Table 12A: Human IgH JH2 Variant Occurrences
Table 12B: Non-Synonymous Human IgH JH2 Variants
Table 13: Variant Frequency Analyses & Human Population Distributions
Table 14: Frequent Human Variant Distributions
Table 15: Human Gene Segment Usage: Heavy Chain Repertoires From Naive Non-Human
Vertebrates
Table 16: Human Gene Segment Usage: Heavy Chain Repertoires From Immunised Non- Human Vertebrates
Table 17: Human Gene Segment Usage: Heavy Chain Repertoires From Antigen-Specific
Hybridomas
Table 18: Sequence Correlation Table
Table 19: Summary Of Function Correlated With Human Gamma Constant Region Sub-Type
Table 20: Gene Segments Prevalent In Few Human Populations
Table 21: Genomic and sequence information
DETAILED DESCRIPTION OF THE INVENTION
A suitable source of JH6*02 and other human DNA sequences for use in the invention will be readily apparent to the skilled person. For example, it is possible to collect a DNA sample from a consenting human donor (eg, a cheek swab sample as per the Example herein) from which can be obtained suitable DNA sequences for use in constructing a locus of the invention. Other sources of human DNA are commercially available, as will be known to the skilled person. Alternatively, the skilled person is able to construct gene segment sequence by referring to one or more databases of human Ig gene segment sequences disclosed herein.
An example source for human V, D and J gene segments according to the invention are Bacterial Artificial Chromosomes (RPCI-11 BACs) obtained from Roswell Park Cancer Institute
(RPCI)/lnvitrogen. See https://bacpac.chori.org/hmalell.htm. which describes the BACs as follows:-
- 11 Human Male BAC Library
The RPCI-11 Human Male BAC Library (Osoegawa et ai, 2001) was constructed using improved cloning technigues (Osoegawa et ai, 1998) developed by Kazutoyo Osoegawa. The library was generated by Kazutoyo Osoegawa. Construction was funded by a grant from the National Human Genome Research Institute (NHGRI, NIH) (#lR01RG01165-03). This library was generated according to the new NHGRI/DOE "Guidance on Human Subjects in Large-Scale DNA
Seguencing...
"Male blood was obtained via a double-blind selection protocol. Male blood DNA was isolated from one randomly chosen donor (out of 10 male donors)".
• Osoegawa K, Mammoser AG, Wu C, Frengen E, Zeng C, Catanese JJ, de Jong PJ; Genome Res.
2001 Mar;ll(3):483-96; "A bacterial artificial chromosome library for sequencing the complete human genome";
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Superhuman Immunoglobulin Gene Repertoires
The invention relates to synthetically-extended & ethnically-diverse superhuman immunoglobulin gene repertoires. The human immunoglobulin repertoires are beyond those found in nature (ie, "Superhuman"), for example, they are more diverse than a natural human repertoire or they comprise combinations of human immunoglobulin gene segments from disparate sources in a way that is non-natural. Thus, the repertoires of the invention are "superhuman" immunoglobulin repertoires, and the invention relates to the application of these in transgenic cells and non-human vertebrates for utility in producing chimaeric antibodies (with the possibility of converting these into fully-human, isolated antibodies using recombinant DNA technology). The present invention thus provides for novel and potentially expanded synthetic immunoglobulin diversities, which provides for a pool of diversity from which antibody therapeutic leads (antibody therapeutics and antibody tool reagents) can be selected. This opens up the potential of transgenic human-mouse/rat technologies to the possibility of interrogating different and possibly larger antibody sequence- spaces than has hitherto been possible. To this end, in one embodiment, the invention provides a SUPERHUMAN MOUSE™ (aka SUPRA-MOUSE™) and a SUPERHUMAN RAT™ (aka SUPRA-RAT™)
In developing this thinking, the present inventors have realised the possibility of mining the huge genetics resources now available to the skilled person thanks to efforts such as the HapMap Project, 1000 Genomes Project and sundry other immunoglobulin gene databases (see below for more details). Thus, in some embodiments, the inventors realised the application of these genome sequencing developments in the present invention to generate synthetically-produced and ethnically-diverse artificial immunoglobulin gene repertoires. In one aspect, the inventors realised that such repertoires are useful for the production of antibodies having improved affinity and/or biophysical characteristics, and/or wherein the range of epitope specificities produced by means of such repertoire is novel, provides for antibodies to epitopes that have hitherto been intractable by prior transgenic immunoglobulin loci or difficult to address.
The present invention provides libraries, vertebrates and cells, such as transgenic mice or rats or transgenic mouse or rat cells. Furthermore, the invention relates to methods of using the vertebrates to isolate antibodies or nucleotide sequences encoding antibodies. Antibodies, nucleotide sequences, pharmaceutical compositions and uses are also provided by the invention.
Variation Analysis
The present inventors have realized methods and antibody loci designs that harness the power of genetic variation analysis. The reference human genome provides a foundation for experimental work and genetic analysis of human samples. The reference human is a compilation of the genomes from a small number of individuals and for any one segment of the genome a high quality single reference genome for one of the two chromosomes is available. Because the reference genome was assembled from a series of very large insert clones, the identity of these clones is known.
Accordingly, experimental work with human genomic DNA is usually conducted on the clones from which the reference sequence was derived.
Individual humans differ in their sequence and recently several individuals have had their genomes sequenced, for instance James Watson and Craig Venter. Comparison of the genome sequence of these individuals has revealed differences between their sequences and the reference genome in both coding and non-coding parts of the genome, approximately 1 in 1000 bases are different. Some variants will be significant and contribute to differences between individuals. In extreme cases
these will result in genetic disease. Variation can be implicated in differing responses to drugs administered to human patients, eg, yielding an undesirable lowering of patient response to treatment.
The 1000-Genomes Project has the objective of identifying the most frequent variations in the human genome. This public domain project involved sequencing the genomes of more than 1000 individuals from diverse ethnic groups, comparing these sequences to the reference and assembling a catalogue of variants. This has enabled the annotation of variants in coding regions, but because this sequence wasn't derived from large clones of DNA, the analysis of the sequence from diploid individuals can't discriminate the distribution of the variation between the maternal and paternally inherited chromosomes. Where more than one variant is identified in a protein coding gene, it is not possible to illuminate the distribution of the pattern of variants in each version of the protein. For example, if two variants are detected in different positions of the same protein in an individual, this could have resulted from one copy with two variants and none in the other or each copy could have just one variant. To illuminate the sequence of real proteins, the 1000-Genome Project has sequenced mother-father-child trios. This allows one to "phase" the sequence variants, in other words identify blocks of sequence that are inherited from one or other parent and deconvolute the variants.
To further understand the variation within the 1000-genome set a tool has been developed that can identify the significant variants (defined as non-synonymous amino acid changes) from a region of DNA from the phased data in the 1000-genome data set. This tool has been made available online https://www.100Qgenomes.org/variation-pattern-finder. This tool allows an investigator to download non-synonymous variation delimited between specific coordinates. The downloaded files are configured as individual genotypes, but the data is phased so the haplotype information and the frequencies of specific halotypes in different populations can be extracted.
The inventors' analysis of the 1000-genome data for the individual human coding segments of the C, V D and J genes from the heavy and light chains reveals that there is significant variation in these segments. Individuals will usually have two different heavy chain alleles and also different light chain alleles at both kappa and lambda loci. The repertoire of antibodies that can be generated
from each allele will be different. This variation will contribute to a better or differing immune response to certain antigens.
Humanized mice that have hitherto been generated with immunoglobulin heavy and light chain loci contain just one type of immunoglobulin locus. Even if these mice contain a full human heavy chain locus, the variation will be less than contained in a typical human because only one set of C, V, D and J genes are available, while a typical human would have two sets.
The inventors have devised ways to improve on this limitation when constructing transgenic non- human vertebrates and cells for human antibody and variable region production in vivo.
Mice can be generated with two different loci, each engineered to have a different repertoire of V, D and J segments. This could be in a single mouse or two or more separate mouse strains and would be analogous to or beyond the repertoire found in a normal human. The engineering of such a mouse would go beyond the repertoire described in humanized mice to date which only have one set of alleles.
However, the inventors also realized that this also has limitations, because the different loci would not normally interact to shuffle V, D and J variants between loci. This same limitation is also inherent in a human, thus this system does not utilize the advantage of recombining variants in all combinations.
To go beyond the normal repertoire in humans and take advantage of combinations of C, V, D and J variants the inventors decided, in one embodiment, to provide these on the same chromosome in cis. See figure 6. These loci would be characterized by having more than the normal number of J, D or V genes. For example n=6 for the J genes, but including one J6 variant and one J2 variant would increase this to n=8. This could be combined with additional variants for the D and V genes, for example. By detailed analysis of the 1000- Genomes database, the inventors have devised a collection of candidate polymorphic human variant gene segments, eg, JH gene segments (eg, see the examples), that can be built into the design of transgenic heavy and light chain loci in mice for
expressing increasingly diverse and new, synthetic repertoires of human variable regions. Moreover, by utilizing naturally-occurring human variant gene segments, as per embodiments of the invention, this addresses compatibility with human patients since the inventor's analysis has drawn out candidate variants that are naturally conserved and sometimes very prevalent amongst human ethnic populations. Additionally this enables one to tailor the configurations of the invention to provide for antibody-based drugs that better address specific human ethnic populations.
In an example according to any configuration of the invention, loci (and cells and vertebrates comprising these) are provided in which gene segments from different human populations are used. This is desirable to increase antibody gene diversity to better address more diverse human patients. In an example, the gene segments are from first and second different human populations respectively, and thus the second gene segment is found in the second human population, but not so (or rarely) in the first human population. Rarely means, for example, that the gene segment is found in 5, 4, 3, 2, or 1 or zero individuals in the first population in the 1000 Genomes database. For example, the first gene segment may be shown as present in a first population by reference to Table 13 or 14 herein, the second gene segment may be shown as present in the second population by reference to Table 13 and not in the first population. Optionally, the first gene segment may also be shown as being present in the second population by reference to Table 13 or 14.
In any configuration or aspect of the invention, where a V gene segment is used, this may be used optionally with the native leader sequence. For example, use of genomic DNA (eg, from BACs as in the examples) will mean that the native leader will be used for each V gene segment incorporated into the locus and genomes of the invention. In an alternative, the skilled person may wish to inert a non-native leader sequence together with one or more of the V gene segments. Similarly, in any configuration or aspect of the invention, where a V gene segment is used, this may be used optionally with the native 5' UTR sequence. For example, use of genomic DNA (eg, from BACs as in the examples) will mean that the native 5' UTR sequence will be used for each V gene segment incorporated into the locus and genomes of the invention. In an alternative, the skilled person may wish to exclude the native 5' UTR sequence.
The present invention provides, in a first configuration
(a) Superhuman heavy chain gene repertoires
A non-human vertebrate or vertebrate cell (optionally an ES cell or antibody-producing cell) comprising a genome having a superhuman immunoglobulin heavy chain human VH and/or D and/or J gene repertoire.
In one aspect the cell of the invention is an embryonic stem cell. For example, the ES cell is derived from the mouse C57BL/6N, C57BL/6J, 129S5 or 129Sv strain. In one aspect the non-human vertebrate is a rodent, suitably a mouse, and cells of the invention, are rodent cells or ES cells, suitably mouse ES cells. The ES cells of the present invention can be used to generate animals using techniques well known in the art, which comprise injection of the ES cell into a blastocyst followed by implantation of chimaeric blastocystys into females to produce offspring which can be bred and selected for homozygous recombinants having the required insertion. In one aspect the invention relates to a transgenic animal comprised of ES cell-derived tissue and host embryo derived tissue. In one aspect the invention relates to genetically-altered subsequent generation animals, which include animals having a homozygous recombinants for the VDJ and/or VJ regions.
The natural human immunoglobulin gene segment repertoire consists of (see eg, www.imgt.org ¾:-
VH: total-125 ; functional-41 DH: total-27; functional-23 JH: total-8; functional-6
Vk: total-77; functional-38 Jk: total-5; functional-5
V lambda: total-75; functional-31
J lambda: total-7; functional-5
In one embodiment, the vertebrate or cell genome comprises a transgenic immunoglobulin heavy chain locus comprising a plurality of human immunoglobulin VH gene segments, one or more human D gene segments and one or more human J gene segments, wherein the plurality of VH gene segments consists of more than the natural human repertoire of functional VH gene segments; optionally wherein the genome is homozygous for said transgenic heavy chain locus.
In one embodiment of the vertebrate or cell, the VH gene repertoire consists of a plurality of VH gene segments derived from the genome sequence of a first human individual, supplemented with one or more different VH gene segments derived from the genome sequence of a second, different human individual. Optionally the D and J segments are derived from the genome sequence of the first human individual. Optionally the VH gene segments from the genome sequence of the second individual are selected from the VH gene segments listed in Table 1, 13 or 14. In this way, the locus provides a superhuman repertoire of D gene segments.
Optionally the individuals are not related. Individuals are "not related" in the context of any configuration or aspect of the invention, for example, if one of the individuals does not appear in a family tree of the other individual in the same generation or going back one, two, three or four generations. Alternatively, are not related, for example, if they do not share a common ancestor in the present generation or going back one, two, three or four generations.
In one embodiment of the vertebrate or cell, the transgenic locus comprises more than 41 functional human VH gene segment species, and thus more than the natural human functional repertoire. Optionally the locus comprises at least 42, 43, 44, 45, 46, 47, 48, 49 or 50 functional human VH gene segment species (eg, wherein the locus comprises the full functional VH repertoire of said first individual supplemented with one or more VH gene segments derived from the genome sequence of the second human individual and optionally with one or more VH gene segments derived from the genome sequence of a third human individual). In this way, the locus provides a superhuman repertoire of VH gene segments that is useful for generating a novel gene and antibody diversity for
use in therapeutic and tool antibody selection.
In one embodiment of the vertebrate or cell, the transgenic locus comprises a first VH gene segment derived from the genome sequence of the first individual and a second VH gene segment derived from the genome sequence of the second individual, wherein the second VH gene segment is a polymorphic variant of the first VH gene segment. For example, the VH gene segments are polymorphic variants of VHl-69 as illustrated in the examples below. Optionally the locus comprises a further polymorphic variant of the first VH gene segment (eg, a variant derived from the genome sequence of a third human individual). In this way, the locus provides a superhuman repertoire of VH gene segments.
In one embodiment of the vertebrate or cell, the genome (alternatively or additionally to the superhuman VH diversity) comprises a transgenic immunoglobulin heavy chain locus comprising a plurality of human immunoglobulin VH gene segments, a plurality of human D gene segments and one or more human J gene segments, wherein the plurality of D gene segments consists of more than the natural human repertoire of functional D gene segments. Optionally the genome is homozygous for said transgenic heavy chain locus.
In one embodiment of the vertebrate or cell, the D gene repertoire consists of a plurality of D gene segments derived from the genome sequence of a (or said) first human individual, supplemented with one or more different D gene segments derived from the genome sequence of a (or said) second, different human individual. Optionally the individuals are not related. Optionally the J segments are derived from the genome sequence of the first human individual. Optionally the D gene segments from the genome sequence of the second individual are selected from the D gene segments listed in Table 2, 13 or 14. In this way, the locus provides a superhuman repertoire of D gene segments.
In one embodiment of the vertebrate or cell, the transgenic locus comprises more than 23 functional human D gene segment species; optionally wherein the locus comprises at least 24, 25, 26, 27, 28, 29, 30 or 31 functional human D gene segment species (eg, wherein the locus comprises the full functional D repertoire of said first individual supplemented with one or more D gene segments derived from the genome sequence of the second human individual and optionally with one or more
D gene segments derived from the genome sequence of a third human individual). In this way, the locus provides a superhuman repertoire of D gene segments.
In one embodiment of the vertebrate or cell, the transgenic locus comprises a first D gene segment derived from the genome sequence of the first individual and a second D gene segment derived from the genome sequence of the second individual, wherein the second D gene segment is a polymorphic variant of the first D gene segment. Optionally the locus comprises a further polymorphic variant of the first D gene segment (eg, a variant derived from the genome sequence of a third human individual). In this way, the locus provides a superhuman repertoire of D gene segments.
In one embodiment of the vertebrate or cell (alternatively or additionally to the superhuman VH and/or JH diversity), the genome comprises a (or said) transgenic immunoglobulin heavy chain locus comprising a plurality of human immunoglobulin VH gene segments, one or more human D gene segments and a plurality of human JH gene segments, wherein the plurality of J gene segments consists of more than the natural human repertoire of functional J gene segments; optionally wherein the genome is homozygous for said transgenic heavy chain locus.
In one embodiment of the vertebrate or cell, the JH gene repertoire consists of a plurality of J gene segments derived from the genome sequence of a (or said) first human individual, supplemented with one or more different J gene segments derived from the genome sequence of a (or said) second, different human individual. Optionally the individuals are not related. Optionally D segments are derived from the genome sequence of the first human individual. Optionally the J gene segments from the genome sequence of the second individual are selected from the J gene segments listed in Table 3 13 or 14. In this way, the locus provides a superhuman repertoire of JH gene segments.
In one embodiment of the vertebrate or cell, the transgenic locus comprises more than 6 functional human JH gene segment segments. Optionally the locus comprises at least 7, 8, 9, 10, 11, 12, 13, 14, 15, or 16 functional human JH gene segments (eg, wherein the locus comprises the full functional JH repertoire of said first individual supplemented with one or more J H gene segments derived from
the genome sequence of the second human individual and optionally with one or more J H gene segments derived from the genome sequence of a third human individual). In this way, the locus provides a superhuman repertoire of JH gene segments.
In one embodiment of the vertebrate or cell, the transgenic locus comprises a first J H gene segment derived from the genome sequence of the first individual and a second JH gene segment derived from the genome sequence of the second individual, wherein the second J H gene segment is a polymorphic variant of the first JH gene segment. Optionally the locus comprises a further polymorphic variant of the first JH gene segment (eg, a variant derived from the genome sequence of a third human individual). In this way, the locus provides a superhuman repertoire of JH gene segments.
(b) Superhuman light chain gene repertoires
The first configuration of the invention also provides:-
A non-human vertebrate or vertebrate cell (optionally an ES cell or antibody-producing cell) comprising a genome having a superhuman immunoglobulin light chain human VL gene repertoire. Optionally the vertebrate or cell comprises a heavy chain transgene according to aspect (a) of the first configuration. Thus, superhuman diversity is provided in both the heavy and light chain immunoglobulin gene segments in the cell and vertebrate. For example, the genome of the cell or vertebrate is homozygous for the heavy and light chain transgenes and endogenous antibody expression is inactivated. Such a vertebrate is useful for immunisation with a predetermined antigen to produce one or more selected antibodies that bind the antigen and have human variable regions resulting from recombination within the superhuman gene segment repertoire. This provides potentially for a novel antibody and gene sequence space from which to select therapeutic, prophylactic and tool antibodies.
In one embodiment of aspect (b) of the first configuration, the vertebrate or cell genome comprises a transgenic immunoglobulin kappa light chain locus comprising a plurality of human
immunoglobulin VK gene segments and one or more human J gene segments, wherein the plurality of VK gene segments consists of more than the natural human repertoire of functional VK gene segments; optionally wherein the genome is homozygous for said transgenic kappa light chain locus; and/or
(ii) a transgenic immunoglobulin lambda light chain locus comprising a plurality of human immunoglobulin V\ gene segments and one or more human J gene segments, wherein the plurality of V\ gene segments consists of more than the natural human repertoire of functional V\ gene segments; optionally wherein the genome is homozygous for said transgenic lambda light chain locus.
In this way, the locus provides a superhuman repertoire of VL gene segments.
In one embodiment of the vertebrate or cell,
(i) the VK gene repertoire consists of a plurality of VK gene segments derived from the genome sequence of a first human individual, supplemented with one or more VK gene segments derived from the genome sequence of a second, different human individual; optionally wherein the individuals are not related; optionally wherein the J segments are derived from the genome sequence of the first human individual; and optionally wherein the VK gene segments from the genome sequence of the second individual are selected from the VK gene segments listed in Table 4, 13 or 14; and
(i) the V\ gene repertoire consists of a plurality of V\ gene segments derived from the genome sequence of a first human individual, supplemented with one or more V\ gene segments derived from the genome sequence of a second, different human individual; optionally wherein the individuals are not related; optionally wherein the J segments are derived from the genome sequence of the first human individual; and optionally wherein the V\ gene segments from the genome sequence of the second individual are selected from the V\ gene segments listed in Table 5, 13 or 14.
In this way, the locus provides a superhuman repertoire of VL gene segments.
In one embodiment of the vertebrate or cell,
-the kappa light transgenic locus comprises more than 38 functional human VK gene segment species; optionally wherein the locus comprises at least 39, 40, 41, 42, 43, 44, 45, 46, 47 or 48 functional human VK gene segment species (eg, wherein the locus comprises the full functional VK repertoire of said first individual supplemented with one or more VK gene segments derived from the genome sequence of the second human individual and optionally with one or more VK gene segments derived from the genome sequence of a third human individual); and
-the lambda light transgenic locus comprises more than 31 functional human V\ gene segment species; optionally wherein the locus comprises at least 32, 33, 34, 35, 36, 37, 38, 39, 40 or 41 functional human V\ gene segment species (eg, wherein the locus comprises the full functional V\ repertoire of said first individual supplemented with one or more V\ gene segments derived from the genome sequence of the second human individual and optionally with one or more V\ gene segments derived from the genome sequence of a third human individual).
In this way, the locus provides a superhuman repertoire of VL gene segments.
In one embodiment of the vertebrate or cell,
-the kappa light transgenic locus comprises a first VK gene segment derived from the genome sequence of the first individual and a second VK gene segment derived from the genome sequence of the second individual, wherein the second VK gene segment is a polymorphic variant of the first VK gene segment; optionally wherein the locus comprises a further polymorphic variant of the first VK gene segment (eg, a variant derived from the genome sequence of a third human individual); and
-the lambda light transgenic locus comprises a first V\ gene segment derived from the genome sequence of the first individual and a second V\ gene segment derived from the genome sequence of the second individual, wherein the second V\ gene segment is a polymorphic variant of the first V\ gene segment; optionally wherein the locus comprises a further polymorphic variant of the first VX gene segment (eg, a variant derived from the genome sequence of a third human individual).
In this way, the locus provides a superhuman repertoire of VL gene segments.
In one embodiment of the vertebrate or cell, the genome comprises a (or said) transgenic immunoglobulin light chain locus comprising a plurality of human immunoglobulin VL gene segments and a plurality of human JL gene segments, wherein the plurality of J gene segments consists of more than the natural human repertoire of functional J gene segments; optionally wherein the genome is homozygous for said transgenic heavy chain locus.
In one embodiment of the vertebrate or cell,
(i) the JK gene repertoire consists of a plurality of JK gene segments derived from the genome sequence of a (or said) first human individual, supplemented with one or more J K gene segments derived from the genome sequence of a (or said) second, different human individual; optionally wherein the individuals are not related; optionally wherein the VK segments are derived from the genome sequence of the first human individual; optionally wherein the J K gene segments from the genome sequence of the second individual are selected from the J K gene segments listed in Table 6, 13 or 14; and
(ii) the JK gene repertoire consists of a plurality of iX gene segments derived from the genome sequence of a (or said) first human individual, supplemented with one or more iX gene segments derived from the genome sequence of a (or said) second, different human individual; optionally wherein the individuals are not related; optionally wherein the V\ segments are derived from the genome sequence of the first human individual; optionally wherein the iX gene segments from the genome sequence of the second individual are selected from the iX gene segments listed in Table 7, 13 or 14.
In this way, the locus provides a superhuman repertoire of J L gene segments.
In one embodiment of the vertebrate or cell,
(i) the transgenic light chain locus comprises more than 5 functional human J K gene segment species; optionally wherein the locus comprises at least 6, 7, 8, 9, 10, 11, 12, 13, 14 or 15 functional human JK gene segment species (eg, wherein the locus comprises the full functional J K repertoire of said first individual supplemented with one or more JK gene segments derived from the genome sequence of the second human individual and optionally with one or more J K gene segments derived
from the genome sequence of a third human individual); and/or
(i) the transgenic light chain locus comprises more than 5 functional human iX gene segment species; optionally wherein the locus comprises at least 6, 7, 8, 9, 10, 11, 12, 13, 14 or 15 functional human iX gene segment species (eg, wherein the locus comprises the full functional iX repertoire of said first individual supplemented with one or more iX gene segments derived from the genome sequence of the second human individual and optionally with one or more iX gene segments derived from the genome sequence of a third human individual).
In this way, the locus provides a superhuman repertoire of J L gene segments.
In one embodiment of the vertebrate or cell,
(i) the kappa light transgenic locus comprises a first JK gene segment derived from the genome sequence of the first individual and a second JK gene segment derived from the genome sequence of the second individual, wherein the second JK gene segment is a polymorphic variant of the first J K gene segment; optionally wherein the locus comprises a further polymorphic variant of the first J κ gene segment (eg, a variant derived from the genome sequence of a third human individual); and
(ii) the lambda light transgenic locus comprises a first iX gene segment derived from the genome sequence of the first individual and a second iX gene segment derived from the genome sequence of the second individual, wherein the second JK gene segment is a polymorphic variant of the first iX gene segment; optionally wherein the locus comprises a further polymorphic variant of the first iX gene segment (eg, a variant derived from the genome sequence of a third human individual).
In this way, the locus provides a superhuman repertoire of J L gene segments.
Further aspects of the first configuration are described below.
The present invention provides, in a second configuration
A library of antibody-producing transgenic cells whose genomes collectively encode a repertoire of antibodies, wherein
(a) a first transgenic cell expresses a first antibody having a chain (eg, heavy chain) encoded by a first immunoglobulin gene, the gene comprising a first variable domain nucleotide sequence produced following recombination of a first human unrearranged immunoglobulin gene segment (eg, a VH);
(b) a second transgenic cell expresses a second antibody having a chain (eg, a heavy chain) encoded by a second immunoglobulin gene, the second gene comprising a second variable domain nucleotide sequence produced following recombination of a second human unrearranged immunoglobulin gene segment (eg, a VH), the first and second antibodies being non-identical;
(c) the first and second gene segments are different and derived from the genome sequences of first and second human individuals respectively, wherein the individuals are different; and optionally not related;
(d) wherein the cells are non-human vertebrate (eg, mouse or rat) cells (eg, B-cells or hybridomas).
In one embodiment, the library is provided in vitro. In another embodiment, the library is provided in vivo by one or a plurality of transgenic non-human vertebrates. For example, the or each vertebrate is according to any aspect of the first configuration of the invention.
In one embodiment, the library encodes an antibody repertoire of from 10 to 109 antibodies, for example, 10, 20, 30, 40, 50, 100 or 1000 to 10s; or 10, 20, 30, 40, 50, 100 or 1000 to 107; or 10, 20, 30, 40, 50, 100 or 1000 to 10s; or 10, 20, 30, 40, 50, 100 or 1000 to 10s; or 10, 20, 30, 40, 50, 100 or 1000 to 104 antibodies. In an example, library encodes an antibody repertoire of at least 103, 104, 10s, 10s, 107, 10s, 109' or 1010 antibodies.
The first variable domain nucleotide sequence is produced following recombination of the first human unrearranged immunoglobulin gene segment with one or more other immunoglobulin gene segments (for example, human immunoglobulin gene segments). For example, where the first gene segment is a VH, the first variable domain nucleotide sequence (a VH domain) is produced following recombination of the VH with a human D and JH segments in vivo, optionally with somatic hypermutation, in the first transgenic cell or an ancestor thereof. For example, where the first gene segment is a VL, the first variable domain nucleotide sequence (a VL domain) is produced following recombination of the VL with a human JL segment in vivo, optionally with somatic hypermutation, in
e first transgenic cell or an ancestor thereof.
The second variable domain nucleotide sequence is produced following recombination of the second human unrearranged immunoglobulin gene segment with one or more other immunoglobulin gene segments (for example, human immunoglobulin gene segments). For example, where the second gene segment is a VH, the second variable domain nucleotide sequence (a VH domain) is produced following recombination of the VH with a human D and JH segments in vivo, optionally with somatic hypermutation, in the second transgenic cell or an ancestor thereof. For example, where the second gene segment is a VL, the second variable domain nucleotide sequence (a VL domain) is produced following recombination of the VL with a human JL segment in vivo, optionally with somatic hypermutation, in the second transgenic cell or an ancestor thereof.
The first and second gene segments are respectively derived from genome sequences of first and second human individuals. In one example, such a gene segment is isolated or cloned from a sample cell taken from said individual using standard molecular biology techniques as know to the skilled person. The sequence of the gene segment may be mutated (eg, by the introduction of up to 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 or 15 nucleotide changes) prior to use in the present invention. In another example, a gene segment is derived by identifying a candidate human immunoglobulin gene segment in a database (see guidance below) and a nucleotide sequence encoding a gene segment for use in the present invention is made by reference (eg, to be identical or a mutant with up to 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 or 15 nucleotide changes to the reference sequence) to the database sequence. The skilled person will be aware of methods of obtaining nucleotide sequences by reference to databases or by obtaining from cellular samples.
In one embodiment of the vertebrate, cell or library of any configuration of the invention, the first and second human individuals are members of first and second ethnic populations respectively, wherein the populations are different. This, therefore, provides for superhuman gene diversity in transgenic loci, cells and vertebrates as per the invention.
Human Populations
Optionally the ethnic populations are selected from those identified in the 1000 Genomes Project of database. In this respect, see Table 8 which provides details of the ethnic populations on which the 1000 Genomes database is based.
N A Rosenberg et al (Science 20 December 2002: vol. 298 no. 5602 2342-2343) studied the genetic structure of human populations of differing geographical ancestry. In total, 52 populations were sampled, these being populations with:
African ancestry
(Mbuti Pygmies, Biaka Pygmies, San peoples, and speakers of Niger-Kordofanian languages (Bantu, Yoruba or Mandenka populations),
Eurasian ancestry
(European ancestry (Orcadian, Adygei, Basque, French, Russians, Italians, Sardinian, Tuscan), Middle Eastern ancestry (Mozabite, Bedouin, Druze, Palestinians),
Central/South Asian ancestry (Balochl, Brahul, Makrani, Sindhi, Pathan, Burusho, Hazara, Uygur, Kalash)),
East Asian ancestry
(Han, Dal, Daur, Hezhen, Lahu, Miao, Oroqen, She, Tujia, Tu, Xibo, Yi, Mongola, Naxi, Cambodian, Japanese, Yakut), Oceanic ancestry (Melanesian, Papuan); or
Americas ancestry
(Karitiana, Surui, Colombian, Maya, Pima).
The International HapMap Project, Nature, 2003 Dec 18;426(6968):789-96, discloses that goal of the HapMap Project: to determine the common patterns of DNA sequence variation in the human genome by determining the genotypes of one million or more sequence variants, their frequencies and the degree of association between them in DNA samples from populations with ancestry from parts of Africa, Asia and Europe. The relevant human populations of differing geographical ancestry include Yoruba, Japanese, Chinese, Northern European and Western European populations. More specifically:-
Utah population with Northern or Western European ancestry (samples collected in 1980 by the
Centre d'Etude du Polymorphisme Humain (CEPH));
population with ancestry of Yoruba people from Ibadan, Nigeria;
population with Japanese ancestry; and
population with ancestry of Han Chinese from China.
The authors, citing earlier publications, suggest that ancestral geography is a reasonable basis for sampling human populations.
A suitable sample of human populations from which the populations used in the present invention are selected is as follows:-
(a) European ancestry
(b) Northern European ancestry; Western European ancestry; Toscani ancestry; British ancestry, Finnish ancestry or Iberian ancestry.
(c) More specifically, population of Utah residents with Northern and/or Western European ancestry; Toscani population in Italia; British population in England and/or Scotland; Finnish population in Finland; or Iberian population in Spain.
(a) East Asian ancestry
(b) Japanese ancestry; Chinese ancestry or Vietnamese ancestry.
(c) More specifically, Japanese population in Toyko, Japan; Han Chinese population in Beijing, China; Chinese Dai population in Xishuangbanna; Kinh population in Ho Chi Minh City, Vietnam; or Chinese population in Denver, Colorado, USA.
(a) West African ancestry
(b) Yoruba ancestry; Luhya ancestry; Gambian ancestry; or Malawian ancestry.
(c) More specifically, Yoruba population in Ibadan, Nigeria; Luhya population in Webuye, Kenya; Gambian population in Western Division, The Gambia; or Malawian population in Blantyre, Malawi.
(a) Population of The Americas
(b) Native American ancestry; Afro-Caribbean ancestry; Mexican ancestry; Puerto ican
ancestry; Columbian ancestry; or Peruvian ancestry.
(c) More specifically, population of African Ancestry in Southwest US; population of African American in Jackson, MS; population of African Caribbean in Barbados; population of Mexican Ancestry in Los Angeles, CA; population of Puerto Rican in Puerto Rico; population of Colombian in Medellin, Colombia; or population of Peruvian in Lima, Peru.
(a) South Asian ancestry
(b) Ahom ancestry; Kayadtha ancestry; Reddy ancestry; Maratha; or Punjabi ancestry.
(c) More specifically, Ahom population in the State of Assam, India; Kayadtha population in Calcutta, India; Reddy population in Hyderabad, India; Maratha population in Bombay, India; or Punjabi population in Lahore, Pakistan.
In any configuration of the invention, in one embodiment, each human population is selected from a population marked "(a)" above.
In any configuration of the invention, in another embodiment, each human population is selected from a population marked "(b)" above.
In any configuration of the invention, in another embodiment, each human population is selected from a population marked "(c)" above.
In one embodiment of the library of the vertebrate, cell or library of the invention, the first and second ethnic populations are selected from the group consisting of an ethnic population with
European ancestry, an ethnic population with East Asian, an ethnic population with West African ancestry, an ethnic population with Americas ancestry and an ethnic population with South Asian ancestry.
In one embodiment of the library of the vertebrate, cell or library of the invention, the first and second ethnic populations are selected from the group consisting of an ethnic population with Northern European ancestry; or an ethnic population with Western European ancestry; or an ethnic population with Toscani ancestry; or an ethnic population with British ancestry; or an ethnic population with Icelandic ancestry; or an ethnic population with Finnish ancestry; or an ethnic population with Iberian ancestry; or an ethnic population with Japanese ancestry; or an ethnic population with Chinese ancestry; or an ethnic population Vietnamese ancestry; or an ethnic population with Yoruba ancestry; or an ethnic population with Luhya ancestry; or an ethnic population with Gambian ancestry; or an ethnic population with Malawian ancestry; or an ethnic population with Native American ancestry; or an ethnic population with Afro-Caribbean ancestry; or an ethnic population with Mexican ancestry; or an ethnic population with Puerto ican ancestry; or an ethnic population with Columbian ancestry; or an ethnic population with Peruvian ancestry; or an ethnic population with Ahom ancestry; or an ethnic population with Kayadtha ancestry; or an ethnic population with Reddy ancestry; or an ethnic population with Maratha; or an ethnic population with Punjabi ancestry.
In one embodiment of any configuration of the vertebrate, cell or library of the invention, the human immunoglobulin gene segment derived from the genome sequence of the second individual is low-frequency (optionally rare) within the second ethnic population. Optionally human immunoglobulin gene segment has a Minor Allele Frequency (MAF) (cumulative frequency) of between 0.5% - 5%, optionally less than 0.5%, in the second human population, eg, as in the 1000 Genomes database.
In one embodiment of any configuration of the vertebrate, cell or library of the invention, the first variable region nucleotide sequence is produced by recombination of the first human
immunoglobulin gene segment with a first J gene segment and optionally a first D gene segment, wherein the first human immunoglobulin gene segment is a V gene segment and the V, D and J segments are derived from the first human population, optionally from the genome of one individual
the first human populati
In one embodiment of the library of the vertebrate, cell or library of the invention, the second variable region nucleotide sequence is produced by recombination of the second human immunoglobulin gene segment with a second J gene segment and optionally a second D gene segment, wherein the second human immunoglobulin gene segment is a V gene segment derived from the second population and the D and/or J segments are derived from the first human population, optionally the D and J gene segments being from the genome of one individual of the first human population.
In one embodiment of the library of the vertebrate, cell or library of the invention, all of the D and J segments that have been recombined with the first and second V gene segments are D and J segments derived from the first human population, optionally the D and J gene segments being from the genome of one individual of the first human population.
In one embodiment of the library, the second human immunoglobulin gene segment is a polymorphic variant of the first human immunoglobulin gene segment; optionally wherein the second gene segment is selected from the group consisting of a gene segment in any of Tables 1 to 7 and 9 to 14 (eg, selected from Table 13 or 14).
In one embodiment of the library, the first and second human immunoglobulin gene segments are both (i) VH gene segments; (ii) D segments; (iii) J segments (optionally both JH segments, both JK segments or both ϋλ segments); (iv) constant regions (optionally both a gamma constant region, optionally both a C gamma-1 constant region); (v) CHI regions; (vi) CH2 regions; or (vii) CH3 regions.
The library is, for example, a naive and optionally has a library size of from 10 or 102 to 109 cells. For example, from 10, 20, 30, 40, 50, 100 or 1000 to 10s; or 10, 20, 30, 40, 50, 100 or 1000 to 107; or 10, 20, 30, 40, 50, 100 or 1000 to 10s; or 10, 20, 30, 40, 50, 100 or 1000 to 10s; or 10, 20, 30, 40, 50, 100 or 1000 to 104 cells.
The library has, for example, been selected against a predetermined antigen and optionally has a library size of from 10 or 102 to 109 cells. For example, from 10, 20, 30, 40, 50, 100 or 1000 to 10s; or 10, 20, 30, 40, 50, 100 or 1000 to 107; or 10, 20, 30, 40, 50, 100 or 1000 to 10s; or 10, 20, 30, 40, 50, 100 or 1000 to 10s; or 10, 20, 30, 40, 50, 100 or 1000 to 104 cells.
In one embodiment of the library of the invention, said first and second cells are progeny of first and second ancestor non-human vertebrate cells respectively, wherein the first ancestor cell comprises a genome comprising said first human immunoglobulin gene segment; and the second ancestor cell comprises a genome comprising said second human immunoglobulin gene segment.
The invention further provides a library of antibody-producing transgenic cells whose genomes collectively encode a repertoire of antibodies, wherein the library comprises the first and second ancestor cells described above.
The invention further provides a library of hybridoma cells produced by fusion of the library of the invention (eg, a B-cell library) with fusion partner cells and optionally has a library size of from 10 or 102 to 109 cells. For example, from 10, 20, 30, 40, 50, 100 or 1000 to 10s; or 10, 20, 30, 40, 50, 100 or 1000 to 107; or 10, 20, 30, 40, 50, 100 or 1000 to 10s; or 10, 20, 30, 40, 50, 100 or 1000 to 10s; or 10, 20, 30, 40, 50, 100 or 1000 to 104 cells. Production of hybridomas is well known to the skilled person. Examples of fusion partners are SP2/0-gl4 (obtainable from ECACC), P3X63-Ag8.653 (obtainable from LGC Standards; C L-1580), NS1 and NS0 cells. PEG fusion or electrofusion can be carried out, as is conventional.
The invention provides, in a third confieuration:- An isolated antibody having
(a) a heavy chain encoded by a nucleotide sequence produced following recombination in a transgenic non-human vertebrate cell of an unrearranged human immunoglobulin V gene segment with a human D and human J segment, optionally with affinity maturation in said cell, wherein one of the gene segments (eg, VH) is derived from the genome of an individual from a first human ethnic population; and the other two gene segments (eg, D and JH) are derived from the genome of an individual from a second (eg, a second and third respectively), different, human ethnic population,
and wherein the antibody comprises heavy chain constant regions (eg, C gamma) of said non-human vertebrate (eg, rodent, mouse or rat heavy chain constant regions); and/or
(b) a light chain encoded by a nucleotide sequence produced following recombination in a transgenic non-human vertebrate cell of an unrearranged human immunoglobulin V gene segment with a human J segment, optionally with affinity maturation in said cell, wherein one of the gene segments (eg, VL) is derived from the genome of an individual from a first human ethnic population (optionally the same as the first population in (a)); and the other gene segment (eg, JL) is derived from the genome of an individual from a second, different, human ethnic population (optionally the same as the second population in (a)), and wherein the antibody comprises light chain constant regions of said non-human vertebrate (eg, rodent, mouse or rat heavy light constant regions);
(c) Optionally wherein each variable domain of the antibody is a human variable domain.
(d) Optionally wherein the heavy chain constant regions are mu- or gamma-type constant regions.
The invention also provides an isolated nucleotide sequence encoding the antibody of the third configuration, optionally wherein the sequence is provided in an antibody expression vector, optionally in a host cell. Suitable vectors are mammalian expression vectors (eg, CHO cell vectors or HEK293 cell vectors), yeast vectors (eg, a vector for expression in Picchia pastoris, or a bacterial expression vector, eg, a vector for E. coli expression.
The invention also provides a method of producing a human antibody, the method comprising replacing the non-human vertebrate constant regions of the antibody of the third configuration with human antibody constant regions (eg, a C variant disclosed in table 13 or 18). The skilled person will be aware of standard molecular biology techniques to do this. For example, see Harlow, E. & Lane, D. 1998, 5th edition, Antibodies: A Laboratory Manual, Cold Spring Harbor Lab. Press, Plainview, NY; and Pasqualini and Arap, Proceedings of the National Academy of Sciences (2004) 101:257-259 for standard immunisation. Joining of the variable regions of an antibody to a human constant region can be effected by techniques readily available in the art, such as using conventional recombinant DNA and NA technology as will be apparent to the skilled person. See e.g. Sambrook, J and Russell, D. (2001, 3'd edition) Molecular Cloning: A Laboratory Manual (Cold Spring Harbor Lab. Press, Plainview, NY).
In one embodiment, the method comprises further making a mutant or derivative of the antibody.
The invention also provides a pharmaceutical composition comprising an antibody according to the third configuration, or a human antibody of the invention and a diluent, excipient or carrier;
optionally wherein the composition is provided in a container connected to an IV needle or syringe or in an IV bag.
The invention also provides an antibody-producing cell (eg, a mammalian cell, eg, CHO or HEK293; a yeast cell, eg, P pastoris; a bacterial cell, eg, E coli; a B-cell; or a hybridoma) that expresses the second antibody of the third configuration or the isolated antibody of the invention.
The first configuration of the invention also provides:-
A non-human vertebrate or vertebrate cell (optionally an ES cell or antibody-producing cell) whose genome comprises a transgenic immunoglobulin locus (eg, a heavy chain locus or a light chain locus), said locus comprising immunoglobulin gene segments according to the first and second human immunoglobulin gene segments (optionally V segments) described above in connection with the third configuration. The gene segments are operably connected upstream of an immunoglobulin constant region; optionally wherein the genome is homozygous for said transgenic immunoglobulin locus.
Optionally the immunoglobulin locus comprises more than the natural human complement of functional V gene segments; and/or
Optionally wherein the immunoglobulin locus comprises more than the natural human complement of functional D gene segments; and/or
Optionally wherein the immunoglobulin locus comprises more than the natural human complement of functional J gene segments.
In this way, a superhuman immunoglobulin gene repertoire is provided in a transgenic non-human vertebrate or vertebrate cell according to the invention.
The first configuration also provides:-
A transgenic non-human vertebrate (eg, a mouse or rat) or vertebrate cell (optionally an ES cell or antibody-producing cell) whose genome comprises a transgenic immunoglobulin locus comprising a plurality of human immunoglobulin gene segments operably connected upstream of a non-human vertebrate constant region for the production of a repertoire of chimaeric antibodies, or chimaeric light or heavy chains, having a non-human vertebrate constant region and a human variable region; wherein the transgenic locus comprises one or more human immunoglobulin V gene segments, one or more human J gene segments and optionally one or more human D gene segments, a first (optionally a V segment) of said gene segments and a second (optionally a V segment) of said gene segments being different and derived from the genomes of first and second human individuals respectively, wherein the individuals are different; and optionally not related; optionally wherein the immunoglobulin locus comprises more than the natural human complement of functional V gene segments; and/or optionally wherein the immunoglobulin locus comprises more than the natural human complement of functional D gene segments; and/or optionally wherein the immunoglobulin locus comprises more than the natural human complement of functional J gene segments.
In this way, a superhuman immunoglobulin gene repertoire is provided in a transgenic non-human vertebrate or vertebrate cell according to the invention.
The first configuration also provides:-
A transgenic non-human vertebrate (eg, a mouse or rat) or vertebrate cell (optionally an ES cell or antibody-producing cell) whose genome comprises first and second transgenic immunoglobulin loci, each locus comprising a plurality of human immunoglobulin gene segments operably connected upstream of a non-human vertebrate constant region for the production of a repertoire of chimaeric antibodies, or chimaeric light or heavy chains, having a non-human vertebrate constant region and a human variable region;
wherein (i) the first transgenic locus comprises one or more human immunoglobulin V gene segments, one or more human J gene segments and optionally one or more human D gene segments, (ii) the second transgenic locus comprises one or more human immunoglobulin V gene segments, one or more human J gene segments and optionally one or more human D gene segments; and (iii) wherein a first (optionally a V) gene segment of said first locus and a second (optionally a V) gene segment of said second gene locus are different and derived from the genomes of first and second human individuals respectively, wherein the individuals are different; and optionally not related; optionally wherein the first and second loci are on different chromosomes (optionally chromosomes with the same chromosome number) in said genome; optionally wherein each immunoglobulin locus comprises more than the natural human
complement of functional V gene segments; and/or optionally wherein each immunoglobulin locus comprises more than the natural human
complement of functional D gene segments; and/or optionally wherein each immunoglobulin locus comprises more than the natural human
complement of functional J gene segments.
In this way, a superhuman immunoglobulin gene repertoire is provided in a transgenic non-human vertebrate or vertebrate cell according to the invention.
In these embodiments of the first configuration, the immunoglobulin gene segments are optionally as described for the third configuration.
In these embodiments of the first configuration, the genome optionally comprises a third immunoglobulin gene segment (optionally a V segment), the third gene segment being derived from a human individual that is different from the individual from which the first (and optionally also the second) gene segment is derived; optionally wherein the first, second and third gene segments are polymorphic variants of a human immunoglobulin gene segment (eg, VH1-69 - see the examples for
further description).
In these embodiments of the first configuration, the genome of the vertebrate or cell is optionally homozygous for the first, second and optional third gene segment, wherein a copy of the first, second and optional third gene segments are provided together on the same chromosome operably connected upstream of a common non-human vertebrate constant region.
For example, each first, second and optional third gene segment is a V gene segment.
In one example, the library of the invention is provided by a collection of non-human vertebrates (optionally a collection of rodents, mice or rats); optionally, wherein a first member of said collection produces said first antibody but not said second antibody, and a second member of the collection produces said second antibody (but optionally not said first antibody). It is therefore contemplated to make non-human vertebrates where different human genomes have been used as a source for building the transgenic loci in the vertebrates. For example, a first vertebrate comprises a transgenic heavy chain locus having gene segments only from a first (and optionally a second) human population or individual; a second vertebrate comprises a transgenic heavy chain locus having gene segments only from a third (and optionally a fourth) human population or individual; and optionally third and more vertebrates can be built similarly based on unique or overlapping human population genomes. However, when provided as a mixed population of transgenic vertebrates, the mixed population provides a collective pool of human immunoglobulin genes that is greater than found in a natural human repertoire. This is useful to extend the antibody and gene sequence space beyond those possible with prior transgenic mice and rats bearing human immunoglobulin loci. As explained above, these have been based on a single human genome.
In one embodiment, the collection of non-human vertebrates bear human immunoglobulin genes confined to human populations that are together grouped under the same population genus "(a)" mentioned above. This provides for a gene repertoire that is biased to producing human antibody variable regions prevalent in the population genus (a) and thus useful for generating antibody therapeutics/prophylactics for members of said population. Alternatively, where gene segments from different human populations are provided in a single transgene according to the invention (not necessarily in a collection of vertebrates), the different human populations are for example together
grouped under the same population genus "(a)" mentioned above.
The invention also provides a repertoire of antibodies expressed from a library of cells according to the invention.
In the non-human vertebrate or cell of any configuration of the invention, the constant region of the transgenic locus is, in one example, an endogenous constant region of said vertebrate (eg, endogenous mouse or rat constant region, eg, from the same strain of mouse or rat as the non- human vertebrate itself).
The invention also provides a method of constructing a cell (eg, an ES cell) according to the invention, the method comprising
(a) identifying functional V and J (and optionally D) gene segments of the genome sequence of a (or said) first human individual;
(b) identifying one or more functional V and/or D and/or J gene segments of the genome sequence of a (or said) second human individual, wherein these additional gene segments are not found in the genome sequence of the first individual;
(c) and constructing a transgenic immunoglobulin locus in the cell, wherein the gene segments of (a) and (b) are provided in the locus operably connected upstream of a constant region.
Optionally the cell comprises a heavy chain locus constructed according to steps (a) to (c) and/or a light chain locus (kappa and/or lambda loci) constructed according to steps (a) to (c).
Optionally the cell is homozygous for the or each transgenic locus; optionally wherein antibody expression from loci endogenous to said cell has been inactivated. This is useful for confining the functional antibody gene repertoire, and thus antibody production, to antibodies bearing human variable regions.
Optionally the gene segment(s) in step (b) are identified from an immunoglobulin gene database selected from the 1000 Genomes, Ensembl, Genbank and IMGT databases.
Optionally the first and second human individuals are members of first and second ethnic populations respectively, wherein the populations are different, optionally wherein the human immunoglobulin gene segment derived from the genome sequence of the second individual is low- frequency (optionally rare) within the second ethnic population.
The invention also provides a method of making a transgenic non-human vertebrate (eg, a mouse or rat), the method comprising
(a) constructing an ES cell (eg, a mouse C57BL/6N, C57BL/6J, 129S5 or 129Sv strain ES cell) by carrying out the method above;
(b) injecting the ES cell into a donor non-human vertebrate blastocyst (eg, a mouse C57BL/6N, C57BL/6J, 129S5 or 129Sv strain blastocyst);
(c) implanting the blastocyst into a foster non-human vertebrate mother (eg, a C57BL/6N, C57BL/6J, 129S5 or 129Sv strain mouse); and
(d) obtaining a child from said mother, wherein the child genome comprises a transgenic immunoglobulin locus.
The invention provides a transgenic non-human vertebrate (eg, a mouse or rat) made by the method or a progeny thereof. The invention also provides a population of such non-human vertebrates.
Microinjection of ES cells into blastocysts and generation of transgenic mice therafter are conventional practices in the state of the art, and the skilled person is aware of techniques useful to effect this. C57BL/6N, C57BL/6J, 129S5 or 129Sv mouse strains and ES cells are readily and publicly available.
The invention also provides a method of isolating an antibody that binds a predetermined antigen (eg, a bacterial or viral pathogen antigen), the method comprising
(a) providing a vertebrate (optionally a mouse or rat) according to the invention;
(b) immunising (eg, using a standard prime-boost method) said vertebrate with said antigen (optionally wherein the antigen is an antigen of an infectious disease pathogen);
(c) removing B lymphocytes from the vertebrate and selecting one or more B lymphocytes expressing antibodies that bind to the antigen;
(d) optionally immortalising said selected B lymphocytes or progeny thereof, optionally by
producing hybridomas therefrom; and
(e) isolating an antibody (eg, and IgG-type antibody) expressed by the B lymphocytes; and
(f) optionally producing a derivative or variant of the antibody.
This method optionally further comprises after step (e) the step of isolating from said B lymphocytes nucleic acid encoding said antibody that binds said antigen; optionally exchanging the heavy chain constant region nucleotide sequence of the antibody with a nucleotide sequence encoding a human or humanised heavy chain constant region and optionally affinity maturing the variable region of said antibody; and optionally inserting said nucleic acid into an expression vector and optionally a host.
Bioinformatics Analysis & Selection of Immunoglobulin Gene Segments
See also the discussion on variation analysis above.
The skilled person will know of sources of human antibody gene sequences, such as IMGT
(www.imgt.org). GenBank (www.ncbi.nlm.nih.gov/genbank) Bioinformatics tools for database manipulation are also readily available and known to the skilled person, eg, as publicly available from the 1000 Genomes Project/EBI (www.100Qgenomes.org)
As a source of antibody gene segment sequences, the skilled person will also be aware of the following available databases and resources (including updates thereof):-
1.1. The Kabat Database (G. Johnson and T. T.Wu, 2002; https://www.kabatdatabase.com). Created by E. A. Kabat and T. T. Wu in 1966, the Kabat database publishes aligned sequences of antibodies, T-cell receptors, major histocompatibility complex (MHC) class I and II molecules, and other proteins of immunological interest. A searchable interface is provided by the Seqhuntll tool, and a range of utilities is available for sequence alignment, sequence subgroup classification, and the generation of variability plots. See also Kabat, E. A.,Wu, T. T., Perry, H., Gottesman, K., and Foeller, C. (1991) Sequences of Proteins of Immunological Interest, 5th ed., NIH Publication No. 91-
3242,Bethesda, MD, which is incorporated herein by reference, in particular with reference to human gene segments for use in the present invention.
1.2. KabatMan (A. C. R. Martin, 2002; https://www.bioinf.org.uk/abs/simkab.html ¾. This is a web interface to make simple queries to the Kabat sequence database.
1.3. IMGT, the International ImMunoGeneTics Information System9; M.-P. Lefranc, 2002;
h tto:https://im t. cin es. fr). IMGT is an integrated information system that specializes in antibodies, T cell receptors, and MHC molecules of all vertebrate species. It provides a common portal to standardized data that include nucleotide and protein sequences, oligonucleotide primers, gene maps, genetic polymorphisms, specificities, and two-dimensional (2D) and three-dimensional (3D) structures. IMGT includes three sequence databases (IMGT/LIGM-DB, IMGT/MHC-DB, IMGT/PRIMERDB), one genome database (IMGT/GENE-DB), one 3D structure database (IMGT/3Dstructure-DB), and a range of web resources ("/MGf Marie-Paule page") and interactive tools.
1.4. V-BASE (I. M. Tomlinson, 2002;https://www.mrc-cpe.cam. ac.uk/vbase). V-BASE is a comprehensive directory of all human antibody germline variable region sequences compiled from more than one thousand published sequences. It includes a version of the alignment software DNAPLOT (developed by Hans-Helmar Althaus and Werner Muller) that allows the assignment of rearranged antibody V genes to their closest germline gene segments.
1.5. Antibodies— Structure and Sequence(A. C. R. Martin, 2002; htto:https://www. bioinf.ora.uk/abs). This page summarizes useful information on antibody structure and sequence. It provides a query interface to the Kabat antibody sequence data, general information on antibodies, crystal structures, and links to other antibody-related information. It also distributes an automated summary of all antibody structures deposited in the Protein Databank (PDB). Of particular interest is a thorough description and comparison of the various numbering schemes for antibody variable regions.
1.6. AAAAA—AHo's Amazing Atlas of Antibody Anatomy (A. Honegger, 2001;
htto:https://www. unizh.ch/~antibodv). This resource includes tools for structural analysis, modeling, and engineering. It adopts a unifying scheme for comprehensive structural alignment of antibody and T-
cell-receptor sequences, and includes Excel macros for antibody analysis and graphical representation.
1.7. WAM— Web Antibody Modeling (N. Whitelegg and A. R. Rees, 2001;
https://antibodv.bath.ac.uk). Hosted by the Centre for Protein Analysis and Design at the University of Bath, United Kingdom. Based on the AbM package (formerly marketed by Oxford Molecular) to construct 3D models of antibody Fv sequences using a combination of established theoretical methods, this site also includes the latest antibody structural information.
1.8. Mike's Immunoglobulin Structure/Function Page (M. R. Clark, 2001;
https://www.oath. cam.ac.uk/~mrc7/mikeimaaes. html) These pages provide educational materials on immunoglobulin structure and function, and are illustrated by many colour images, models, and animations. Additional information is available on antibody humanization and Mike Clark's
Therapeutic Antibody Human Homology Project, which aims to correlate clinical efficacy and antiimmunoglobulin responses with variable region sequences of therapeutic antibodies.
1.9. The Antibody Resource Page (The Antibody Resource Page, 2000;
https://www.antibodvresource.com). This site describes itself as the "complete guide to antibody research and suppliers." Links to amino acid sequencing tools, nucleotide antibody sequencing tools, and hybridoma/cell-culture databases are provided.
1.9. Humanization bY Design (J. Saldanha. 2000: https://peoole.crvst.bbk.ac.uk/~ubca07s). This resource provides an overview on antibody humanization technology. The most useful feature is a searchable database (by sequence and text) of more than 40 published humanized antibodies including information on design issues, framework choice, framework back-mutations, and binding affinity of the humanized constructs.
See also Antibody Engineering Methods and Protocols, Ed. Benny K C Lo, Methods in Molecular Biology™, Human Press. Also at https://www.blogsua.com/pdf/antibodv-engineering-methods-and- protocolsantibodv-engineering-methods-and-protocols.pdf
As a source of genomic sequence variation data, the skilled person will also be aware of the following available databases and resources (including updates thereof):-
1. HapMap (The International HapMap Consortium. 2003;
https://hapmap.ncbi.nlm.nih.gov/index.html.en). The HapMap Project is an international project that aims to compare the genetic sequences of different individuals to identify chromosomal regions containing shared genetic variants. The HapMap www site provides tools to identify chromosomal regions and the variant therein, with options to drill down to population level frequency data.
2. 1000 Genomes (The 1000 Genomes Project Consortium 2010: https://www.1000genomes.org/).
This resource provides complete genomic sequence for 2500 unidentified individuals from one of 25 distinct population groups, with the aim of identifying genomic variants of >1%. The site provides the ability to interrogate data utilizing online tools (e.g. 'Variation Pattern Finder') and to download variant data for individual population groups.
3. Japanese SNP Database (H.Haga et al. 2002: https://snp.ims.u-tokvo.ac.ip/index.html). Based on a study identifying 190,562 human genetic variants this site catalogues genomic variants with useful features for searching and summarizing data.
It is possible to identify variants in immunoglobulin genes classed as low-frequency or rare variants that segregate with specific human ethnic populations. For the purpose of this analysis, a low- frequency immunoglobulin gene segment is classed as one with 'Minor Allele Frequency' (MAF) (cumulative frequency) of between 0.5% - 5%, rare variants are those classed as having a MAF of less than 0.5% in a particular human population.
The following bioinformatics protocol is envisaged to indentify human immunoglobulin gene segments for use in the present invention:
(a) Identify one or more genomic regions containing gene segments of interest ('target genomic regions') and calculate the genomic coordinates, using coordinates that match the sequence assembly build used by either the 1000 Genomes project or International HapMap project (or another selected human gene database of choice).
(b) Identify genomic variants mapped to the genomic regions previously identified in (a).
Retrieve variant frequencies for variants for each super population and preferably sub- population where such data is available. Tools readily available on the HapMap WWW site and the VWC tools for the lOOOGenomes Project are useful for this step.
(c) Filter list of genomic variants from target genomic regions to contain only variants classed as either 'Non-synonymous' single nucleotide polymorphisms (SNPs) or genomic 'insertions or delections' (indels). Filter further to include those that are present in exonic sequences only.
(d) Correlate population frequency data for each of the identified variants for each of the super populations (for example 'European Ancestry', 'East Asian ancestry', 'West African ancestry', 'Americas', and 'South Asian ancestry') to identify those variants that segregate with less than two super-populations. Further correlate all identified variants with each of the sub- populations (for example, 'European ancestry' super-population might be subdivided into groups such as 'CEU - Utah residents with Northern or Western European ancestry', 'TSI Toscani in Italia' and 'British from England and Scotland') and produce a second score for rarity of variants in within a super-population.
(e) Collect one or more gene segments that show segregation to specific sub-populations for construction of synthetic loci according to the invention.
In one embodiment throughout the present text, "germline" refers to the canonical germline gene segment sequence.
By detailed analysis of the 1000 Genomes database, the inventors have devised a collection of candidate polymorphic antibody gene segment variants, eg, human variant JH gene segments (eg, see Example 4), that can be built into the design of transgenic heavy chain loci in mice for expressing increasingly diverse and new, synthetic repertoires of human variable regions. To this end, the invention provides the following embodiments.
The present invention provides in a fourth configuration-
Selection of Human JH6*02 Variant
Transgenic IgH Loci. Non-Human Vertebrates. Cells & Antibodies Based on Human JH6*02
As explained above, in designing transgenic Ig heavy chain loci the present inventors have considered the huge amount of data available from the 1000 Genomes project (see
www.100Qgenomes.org) that analyses gene distributions amongst many human populations, and in particular data on Ig gene segments. The inventors were also aware of human gene segments disclosed in the IMGT database (see www.imgt.org) and in Ensembl (see www.ensembl.org). The inventors needed to make choices about which human gene segments to include amongst the large number of human gene segments presented in these databases and the other sources of human Ig gene segment information known in the art, including those other databases disclosed herein. When choosing human JH gene segments, the inventors were aware that human JH6 encodes a relatively long amino acid sequence, and thus the inventors thought it desirable to include this for increasing the chances of producing IgH chains with relatively long HCDR3 regions. Antibodies with long HCDR3 (at least 20 amino acids according to IMGT nomenclature) have been shown to neutralise a variety of pathogens effectively including HIV, Influenza virus, malaria and Africa trypanosomes. Reference is also made to naturally-occurring Camelid (eg, llama or camel) heavy chain-only antibodies which bear long HCDR3s for reaching relatively inaccessible epitopes (see, eg, EP0937140). Long HCDR3s can form unique stable subdomains with extended loop structure that towers above the antibody
surface to confer fine specificity. In some cases, the long HCD 3 itself is sufficient for epitope binding and neutralization (Liu, L et al; Journal of Virology. 2011. 85: 8467-8476, incorporated herein by reference). The unique structure of the long HCDR3 allows it to bind to cognate epitopes within inaccessible structure or extensive glycosylation on a pathogen surface. In human peripheral blood, there is around 3.5% of naive B antibodies or 1.9% of memory B IgG antibodies containing the HCDR3s with lengths of more than 24 amino acids (PLoS One. 2012;7(5):e36750. Epub 2012 May 9; "Human peripheral blood antibodies with long HCDR3s are established primarily at original recombination using a limited subset of germline genes"; Briney BS e al, incorporated herein by reference) (Fig. 1). The usage analysis indicates that these antibodies have the preference to use human JH6 with human D2-2, D3-3 or D2-15 (Brinley, BS et al, Figs. 2-5). See also PLoS One. 2011 Mar 30;6(3):el6857; Comparison of antibody repertoires produced by HIV-1 infection, other chronic and acute infections, and systemic autoimmune disease"; Breden F et al, incorporated herein by reference. Around 20% of all HCDR3 of antibodies use JH6. However, in those antibodies with HCDR3 of more than 24 amino acids, 70% use JH6 (Brinley, BS et al, Fig.2).
There is a need in the art for genetically modified non-human vertebrates and cells that can make antibodies and heavy chains that have long human HCDR3s, as well as antibodies, chains and VH domains that can be selected from such vertebrates and cells wherein these can address target epitopes better accessed by long HCDR3s.
The inventors, therefore, chose in this configuration of the invention to include a human JH6 gene segment as a mandatory human gene segment in their IgH locus design. Several different naturally- occurring human JH6 variants are known (eg, JH6*01 to *04 as well as others; I MGT nomenclature). The inventors considered this when deciding upon which human JH6 variant should be included in the transgenic IgH locus design. An alignment of some human JH6 variants is shown in Figure 7 (from www.imgt.org: dashes indicate identical nucleotides; nucleotide changes versus the *01 variant are shown by underlined nucleotides and corresponding amino acid changes are shown by underlined amino acids; Genbank accession numbers (release 185.0) are shown prefixed by J, X, M or A). The inventors used sequencing of human genomic DNA samples, inspection of public IgH DNA databases as well as informed choices on the basis of variant sequences as means to arrive at a rational choice of which JH6 variant to use.
The 1000 Genomes database uses human JH6*03 as the reference sequence, which would be a possible choice for the skilled person wishing to construct a transgenic IgH locus. The inventors noticed (eg, Figure 7 herein) that position 6 in JH6*03 is a tyrosine (Y) encoded by a TAC codon, whereas some other naturally-occurring human variants have a glycine (G) encoded by a GGT codon (the glycine being present as a YYG motif, forming part of a larger YYGXDX motif). To understand the potential significance of this, the inventors carried out analysis of JH sequences from other vertebrate species. The inventors surprisingly noticed that YYG and YYGXDX motifs are conserved across many vertebrate species (see Figures 7 & 8). This suggested to the inventors, therefore, that preservation of this motif might be desirable, which could guide the choice of JH6 variant for use in the present invention.
Another pointer arose when the inventors considered the TAC codon versus the GGT codon encoding Y or G respectively. The inventors considered the impact of these nucleotide sequences on the action of activation-induced cytidine deaminase (AID). The inventors knew that activation- induced cytidine deaminase (AID) is believed to initiate Ig somatic hypermutation (SHM) in a multi- step mechanism and they addressed this activity when rationally designing the locus. AID catalyses the deamination of C to U in DNA, generating mutations at C bases. Cytidines located within hotspot motifs are preferentially deaminated. Certain motifs are hotspots for AID acitivity (DGYW, W C. WRCY. WRCH. RGYW, AGY, TAC, WGCW, wherein W=A or T, Y=C or T, D=A, G or T, H=A or C or T, and R=A or G). The presence of a TAC codon encoding Y at position 6 in JH6*03 creates AID mutation hotspots (the cytidine being the substrate of AID), these hotspots being the underlined motifs in the previous sentence. The inventors considered the impact of this and in doing so they considered possible mutants created by AID activity at the cytidine. Reference is made to Figure 9. The inventors noticed that a mutation at the third base of the TAC codon would yield 3 possible outcomes: Y, stop or stop. Thus, out of the three stop codons possible in the genetic code (the other being encoded by TGA - see Figure 9), two of them would be provided by mutation of the cytidine in the TAC codon encoding position 6 in JH6*03. The inventors, therefore, considered that this might increase the chances of non-productive IgH variable region production in transgenic loci based on JH6*03. Moreover, the inventors noticed that provision of a GGT codon instead (as per the other human JH6 variants) seemed preferable since mutation of the third base would never yield a stop codon (see Figure 9), and furthermore would retain coding, and thus conservation, of glycine at position 6, which the inventors also noticed was is in the YYG and YYGXDX motifs conserved across species.
Having decided against using JH6*03, the inventors needed to make a choice from other possible human variants. The MDV motif is at the C-terminus of HCD 3 based on human JH6, the adjacent framework 4 (FW4) starting with the WGQ motif (with reference to the sequence shown encoded by JH6*01; Figure 7). In making their choices for locus design, the inventors wished to maximise conservation of this HCDR3/FW4 junction in product IgH chains and antibodies including these. The inventors believed this to be desirable for heavy chain variable domain functionality and
conformation. The inventors thought that this might in some cases be desirable to minimise immunogenicity (suitable for human pharmaceutical use). Consistent with these considerations, the inventors wanted to make a choice that would minimise mutation around the HCDR3/FW4 junction as a result of SHM in vivo to conserve junction configuration. See Rogozin & Diaz; "Cutting Edge: DGYW/WRCH Is a Better Predictor of Mutability at G:C Bases in Ig Hypermutation Than the Widely Accepted RGYW/WRCY Motif and Probably Reflects a Two-Step Activation-Induced Cytidine Deaminase-Triggered Process"; Journal of Immunology; March 15, 2004 vol. 172 no. 6 3382-3384. An example of a DGYW motif is GGCA. The inventors had this in mind when analysing the variant sequences.
With these considerations in mind, the inventors decided specifically to use human JH6*02 as the mandatory human JH6 for their IgH locus design. JH6*01 was rejected as the mandatory JH6 gene segment since the nucleotide sequence GGG CAA (encoding G and Q) contains a GGCA motif which is an AID recognition hotspot. The inventors realised that JH6*04 also contains such a motif due to the presence of the sequence GGC AAA encoding G and K (positions 11 and 12 respectively). The inventors also realised that the *02 variant has a C instead of a G that is in the *01 variant, the C desirably being a synonymous change (ie, not changing the encoded amino acid sequence around the CDR3/FW4 junction) and also this does not provide a GGCA AID hotspot motif. The inventors, therefore, decided that the mandatory JH6 should have this C base and this too pointed them to using the human JH6*02 variant.
In one example of any configuration of the invention herein, the only JH6 species included in the locus or genome is human JH6*02.
The inventors obtained 9 anonymised DNA samples from cheek swabs of 9 consenting human adults. Sequencing was performed on IgH locus DNA to confirm natural JH6 variant usage. It was found that the genome of all 9 humans contained a JH6*02 variant gene segment. In 7 out of the 9 humans, the genome was homozygous for JH6*02 (ie, each chromosome 14 had JH6*02 as its JH6 gene segment in the IgH locus). The inventors also inspected the publicly-available sequence information from the genomes of well-known scientists Craig Venter and Jim Watson. Both of these genomes contain JH6*02 too. This indicated to the inventors that this variant is common in humans.
So, the inventors made a choice of human JH6*02 on the basis of
(i) Containing the YYG and YYGXDX motifs that is conserved across several vertebrate species;
(ii) Provision of one less TAC codon (an AID hotspot that risks stop codons) and a choice instead of a codon that preserves the YYG and YYGXDX motifs;
(iii) Avoidance of a GGCA AID hotspot in the region of the HCDR3/FW4 junction; and
(iv) Common occurrence (and thus conservation and acceptability) in humans of the JH6*02 variant.
This rationale was tested by the inventors in laboratory examples, in order to see if human JH6*02 could desirably participate in antibody gene segment recombination and heavy chain production in a foreign (non-human vertebrate) setting, and moreover to assess if long HCDFGs based on human JH6*02 could be produced in vivo (in naive and immunised settings) in such non-human systems. It was noted that in some non-human settings, such as a mouse, the YYG and YYGXDX motifs are not conserved, and thus the inventors decided that it was important to test whether or not JH6*02 (having the YYG and YYGXDX motifs) could function properly in such a foreign setting to participate in VDJ recombination and selection against antigen.
Thus, as explained further in the examples, the inventors constructed transgenic JH6*02-containing IgH loci in ES cells, generated transgenic non-human vertebrates from the ES cells (both naive and immunised with a range of different target antigen types), isolated antibodies and heavy chain sequences based on JH6*02 as well as B-cells expressing these and made hybridomas expressing antigen-specific antibodies that are based on the chosen JH6*02 variant. The inventors found that the JH6*02 variant was extensively used and could contribute to the production of HCDR3 of at least
20 amino acids in many different heavy chains (including antigen-specific heavy chains). The chosen variant was preferably used over other JH gene segments in all settings (naive, immunised and antigen-specific) for the production of HCD 3 of at least 20 amino acids.
Thus, the present invention provides an IgH locus including human JH6*02 (IMGT nomenclature) as a mandatory JH gene segment. In one embodiment, the locus comprises non-human vertebrate (eg, mouse or rat) constant region gene segments downstream (ie, 3' of) the human JH6*02; and one or more VH gene segments (eg, a plurality of human VH gene segments) and one or more D gene segments (eg, a plurality of human D gene segments) upstream of (ie, 5' of) the human JH6*02. For example, the locus is comprised by a vector (eg, a DNA vector, eg, a yeast artificial chromosome (YAC), BAC or PAC). Such a vector (eg, YAC) can be introduced into a non-human vertebrate (eg, mouse or rat) cell using standard techniques (eg, pronuclear injection) so that the locus is integrated into the cell genome for expression of IgH chains comprising at least one chain whose variable domain is a product of the recombination of human JH6*02 with a VH and a D gene segment.
In another example, the locus (eg, with a completely human, rat or mouse constant region, or a human/mouse chimaeric constant region) can be provided in the genome of a non-human vertebrate (eg, mouse or rat) cell. For example, the cell is an ES cell or an antibody-producing cell (eg, an isolated B-cell, an iPS cell or a hybridoma).
In another example, the invention provides a non-human vertebrate (eg, a mouse or a rat) comprising an IgH locus of the invention which comprises a human JH6*02 gene segment, wherein the locus can express an IgH chain whose variable domain is a product of the recombination of human JH6*02 with a VH and a D gene segment. As shown in the examples, the inventors have successfully produced such mice which produce such IgH chains with VH domains based on human JH6*02. The inventors isolated and sequenced IgH chains from the mice before (naive) and after (immunised) exposure to a range of target antigens and confirmed by comparison to IMGT IgH gene segment sequences that the isolated chains (and antibodies containing these) were produced based on JH6*02. Such chains were found in naive mice, as well as in antigen-specific antibodies from immunised mice. B-cells were isolated from immunised mice, wherein the B-cells express antibodies based on JH6*02 and hybridomas were generated from the B-cells, the hybridomas expressing antigen-specific antibodies based on JH6*02. The inventors, therefore, provided the locus,
vertebrate, cell and hybridoma of the invention based on the use of human JH6*02 and showed that antibodies based on JH6*02 and B-cells expressing these can be successfully produced and isolated following immunisation of the vertebrates, corresponding hybridomas being a good source of antibodies whose VH domains are based on JH6*02, eg for administration to a patient, eg, for human medicine. Furthermore, it was found possible to produce and isolated antigen-specific antibodies whose VH domains are based on JH6*02 and which had a relatively long HCDR3 (eg, 20 amino acids).
us, the present invention provides embodiments as in the following clauses:-
A non-human vertebrate (optionally a mouse or a rat) or vertebrate cell whose genome comprises an immunoglobulin heavy chain locus comprising human gene segment JH6*02, one or more VH gene segments and one or more D gene segments upstream of a constant region; wherein the gene segments in the heavy chain locus are operably linked to the constant region thereof so that the mouse is capable of producing an antibody heavy chain produced by recombination of the human JH6*02 with a D segment and a VH segment.
In another example, the invention provides
A non-human vertebrate (optionally a mouse or a rat) or vertebrate cell whose genome comprises an immunoglobulin heavy chain locus comprising one, more or all of human IGHV gene segments selected from V3-21, V3-13, V3-7, V6-1, Vl-8, Vl-2, V7-4-1, Vl-3, Vl-18, V4-4, V3-9, V3-23, V3-11 and V3-20 (eg, one, more or all of V3-21*03, V3-13*01, V3-7*01, V6-l*01, Vl-8*01, Vl-2*02, V7-4-l*01, Vl-3*01, Vl-18*01, V4-4*01, V3-9*01 and V3-23*04). These segments were found in naive repertoires to be productive to produce HCDR3s of at least 20 amino acids in length. In an embodiment, the locus comprises a human JH6, eg, JH6*02.
The invention also provides a HCDR3, VH domain, antibody heavy chain or antibody having a HCDR3 size of at least 20 amino acids. Optionally, the HCDR3 or VH domain (or VH domain of the heavy chain or antibody) comprises mouse AID-pattern somatic hypermutations and/or mouse dTd-pattern mutations. This can be provided, for example, wherein VH domain is produced in a mouse comprising mouse AID and/or mouse TdT (eg, endogenous AID or TdT). See also Annu. Rev. Biochem. 2007. 76:1-22; Javier M. Di Noia and Michael S. Neuberger, "Molecular Mechanisms of Antibody Somatic Hypermutation" (in particular figure 1 and
associated discussion on AID hotspots in mouse); and Curr Opin Immunol. 1995 Apr;7(2):248-54, "Somatic hypermutation", Neuberger MS and Milstein C (in particular, discussion on hotspots in mouse), the disclosures of which are incorporated herein by reference.
These segments were found in naive repertoires to be productive in recombination with human JH6*02 to produce HCDFGs of at least 20 amino acids in length.
In an example, the vertebrate is naive. In another embodiment, the vertebrate instead is immunised with a target antigen.
In an example, the vertebrate or cell mentioned below is capable of so producing an antibody heavy chain upon immunisation with a target antigen. In an example, the vertebrate is an immunised vertebrate that produces antibody heavy chains specific for a target antigen and wherein the variable domains of the heavy chains are the product of recombination between a VH, D and JH6*02. For example, the D is selected from human D3-3, D2-15, D3-9; D4-17; D3-10; D2-2; D5-24; D6-19; D3-22; D6-13; D5-12; Dl-26; Dl-20; D5-18; D3-16; D2-21; Dl-14; D7-27; Dili D6-25; D2-14 and D4-23 (eg, selected from D3-9*01; D4-17*01; D3-10*01; D2-2*02; D5- 24*01; D6-19*01; D3-22*01; D6-13*01; D5-12*01; Dl-26*01; Dl-20*01; D5-18*01; D3-16*02; D2-21*02; Dl-14*01; D7-27*02; Dl-l*01; D6-25*01; D2-15*01; and D4-23*01). For example, the D is human D3-9 or D3-10. In an example, the HCD 3 length is at least 20 amino acids (eg, 20, 21, 23 or 24).
In an example of the vertebrate or cell, the genome comprises additional human JH gene segments (eg, JH2, 3, 4 and 5 gene segments).
In an example of the vertebrate or cell, the genome comprises an immunoglobulin light chain locus comprising one or more human V gene segments and one or more human J gene segments upstream of a constant region (eg, a human or a mouse lambda or kappa constant region).
For rearrangement and expression of heavy chains, the locus comprises control elements, such as an Εμ and 5μ between the J gene segment(s) and the constant region as is known by the skilled person. In one example, a mouse Εμ and 5μ is included in the heavy chain locus between the JH6*02 and the constant region (ie, in 5' to 3' order the locus comprises the JH6*02, Εμ and 5μ and constant region). In an example, the Εμ and 5μ are Εμ and 5μ of a mouse 129-derived
genome (eg, a 129Sv-derived genome, eg, 129Sv/EV (such as 129S7Sv/Ev (such as from AB2.1 or AB2.2 cells obtainable from Baylor College of Medicine, Texas, USA) or 129S6Sv/Ev))); in another example, the Εμ and 5μ are Εμ and 5μ of a mouse C57BL/6 -derived genome. In this respect, the locus can be constructed in the IgH locus of the genome of a cell selected from AB2.1, AB2.2, VGF1, CJ7 and FH14. VGF1 cells were established and described in Auerbach W, Dunmore JH, Fairchild-Huntress V, et al; Establishment and chimera analysis of 129/SvEv- and C57BL/6-derived mouse embryonic stem cell lines. Biotechniques 2000; 29:1024-8, 30, 32, incorporated herein by reference.
Additionally or alternatively, the constant region (or at least a Cμ; or Cμ and gamma constant regions thereof) is a constant region (or Cμ; or Cμ and gamma constant regions thereof) is of a genome described in the paragraph immediately above.
A suitable source of JH6*02 and other human DNA sequences will be readily apparent to the skilled person. For example, it is possible to collect a DNA sample from a consenting human donor (eg, a cheek swab sample as per the Example herein) from which can be obtained suitable DNA sequences for use in constructing a locus of the invention. Other sources of human DNA are commercially available, as will be known to the skilled person. Alternatively, the skilled person is able to construct gene segment sequence by referring to one or more databases of human Ig gene segment sequences disclosed herein. The vertebrate of clause 1, wherein the vertebrate has been immunised with a target antigen and wherein the variable domain of the heavy chain is the product of recombination between a VH, D and JH6*02 and wherein the HCD 3 length is at least 20 amino acids (eg, 20, 21, 23 or 24).
Optionally, the immunised vertebrate produces an antibody heavy chain specific for a target antigen and wherein the variable domain of the heavy chain is the product of recombination between a VH, D and JH6*02 and wherein the HCDR3 length is at least 20 amino acids (eg, 20, 21, 23 or 24). A non-human vertebrate cell (optionally a mouse cell or a rat cell) whose genome comprises an immunoglobulin heavy chain locus comprising human gene segment JH6*02, one or more VH gene segments and one or more D gene segments upstream of a constant region; wherein the gene segments in the heavy chain locus are operably linked to the constant region thereof for
producing (eg, in a subsequent progeny cell) an antibody heavy chain produced by recombination of the human JH6*02 with a D segment and a VH segment.
The cell of clause 3, which is an ES cell capable of differentiation into a progeny antibody- producing cell that expresses said heavy chain.
The vertebrate or cell of any preceding clause, wherein the heavy chain locus comprises a human JH6*02 recombination signal sequence (RSS) operably connected 5' to the JH6*02 gene segment.
For example, the native RSS-JH6*02 sequence can be used to advantageously maintain the natural pairing between RSS and theis JH gene segment. In this respect, the following sequence is used:- ggtttttgtggggteaggatggacattctgccattgtgattactactactactacggtatggacgtctggggccaagggaccacgg^ tctcctcag (SEQ ID NO: 238)
RSSs have a common architecture: 9mer (eg, first underlined sequence above) followed by a 22bp spacer and then a 7mer (eg, second underlined sequence above). Spacers are 23bp +/- 1 normally, while the 9 and 7mer are more conserved.
6. The vertebrate or cell of clause 5, wherein the RSS is SEQ ID NO: 238 or a sequence having an identical 9mer and 7mer sequence flanking a sequence that is at least 70% identical to the 22mer sequence of SEQ ID NO: 238.
7. The vertebrate or cell of clause 6, wherein the RSS and JH6*02 are provided as SEQ ID NO: 237.
8. The vertebrate or cell of any preceding clause, wherein the JH6*02 is the only JH6-type gene segment in the genome.
9. The vertebrate or cell of any preceding clause, wherein the JH6*02 is the closest JH gene
segment to the constant region in the locus.
The vertebrate or cell of any preceding clause, wherein the locus comprises one, more or all human D gene segments D3-9; D4-17; D3-10; D2-2; D5-24; D6-19; D3-22; D6-13; D5-12; Dl-26; Dl-20; D5-18; D3-16; D2-21; Dl-14; D7-27; Dl-1; D6-25; D2-14; and D4-23.
For example, the locus comprises one, more or all of human D gene segments D3-9*01; D4- 17*01; D3-10*01; D2-2*02; D5-24*01; D6-19*01; D3-22*01; D6-13*01; D5-12*01; Dl-26*01; Dl-20*01; D5-18*01; D3-16*02; D2-21*02; Dl-14*01; D7-27*02; Dl-l*01; D6-25*01; D2-15*01; and D4-23*01. The vertebrate or cell of clause 10, wherein the locus comprises one, more or all human D gene segments D3-9, D3-10, D6-19, D4-17, D6-13, D3-22, D2-2, D2-25 and D3-3.
These D segments were found to be productive in recombination with human JH6*02 to produce HCD 3s of at least 20 amino acids in length.
In an example, the locus comprises one, more or all human D gene segments D3-9, D3-10, D6- 19, D4-17, D6-13 and D3-22 (for example one, more or all of D3-9*01, D3-10*01, D6-19*01, D4- 17*01, D6-13*01 and D3-22*01). These D segments were found in naive repertoires to be productive in recombination with human JH6*02 to produce HCDR3s of at least 20 amino acids in length.
In an example, the locus comprises one, more or all human D gene segments D3-10, D6-19 and Dl-26 (for example, one, more or all of D3-10*01, D6-19*01 and Dl-26*01). These D segments were found in immunised repertoires to be productive in recombination with human JH6*02 to produce HCDR3s of at least 20 amino acids in length.
In an example, the locus comprises one, more or all human D gene segments D3-9 and D3-10 (for example, one, more or all of D3-9*01 and D3-10*01). These D segments were found in antigen-specific repertoires to be productive in recombination with human JH6*02 to produce HCDR3s of at least 20 amino acids in length. The vertebrate or cell of any preceding clause, wherein the locus comprises a plurality of human D gene segments and the JH6*02 is in human germline configuration with respect to the 3'-most human D gene segment (or all of the human D segments comprised by the locus).
In an example, the 3'-most D gene segment is D7-27. In an example, the locus comprises all of human D gene segments from Dl-1 to D7-27 as present in a germline human IgH locus (eg, as shown in the IMGT database).
Alternatively or additionally, the JH6*02 is in human germline configuration with respect to one, more or all of the Εμ, 5μ and constant region (eg, Cμ). The vertebrate or cell of any preceding clause, wherein the locus comprises one, more or all of IGHV gene segments selected from V3-21, V3-13, V3-7, V6-1, Vl-8, Vl-2, V7-4-1, Vl-3, Vl-18, V4-4, V3-9, V3-23, V3-11 and V3-20.
In an example, the locus comprises one, more or all human IGHV gene segments V3-21, V3-13, V3-7, V6-1, Vl-8, Vl-2, V7-4-1, Vl-3, Vl-18, V4-4, V3-9, V3-23 (for example, one, more or all of V3-21*03, V3-13*01, V3-7*01, V6-l*01, Vl-8*01, Vl-2*02, V7-4-l*01, Vl-3*01, Vl-18*01, V4- 4*01, V3-9*01 and V3-23*04). These segments were found in naive repertoires to be productive in recombination with human JH6*02 to produce HCD 3s of at least 20 amino acids in length.
In an example, the locus comprises one, more or all human IGHV gene segments V3-7, V3-11 and V4-4 (for example, one, more or all of V3-7*01, V3-ll*01 and V4-4*02). These segments were found in immunised repertoires to be productive in recombination with human JH6*02 to produce HCDR3s of at least 20 amino acids in length.
In an example, the locus comprises one, more or all human IGHV gene segments V4-4, Vl-8, V3- 9, V3-11 and V3-20 (for example, one, more or all of V4-4*02, Vl-8*01, V3-9*01, V3-ll*01 and V3-20 (eg, *d01). These segments were found in antigen-specific repertoires to be productive in recombination with human JH6*02 to produce HCDR3s of at least 20 amino acids in length. The vertebrate or cell of any preceding clause, wherein the locus comprises one, more or all of human D3-9*01, D3-10*01, D6-19*01, D6-13*01, Dl-26*01, IGHV1-8*01, IGHV4-61*01, IGHV6- 1*01, IGHV4-4*02, IGHV1-3*01, IGHV3-66*03, IGHV3-7*01 and IGHV3-9*01.
These are gene segments that very frequently combine with JH6*02 to produce productive heavy chains and antibodies.
For example, the locus comprises one, more or all of human IGHV1-8*01, D3-9*01 and D3- 10*01. These gene segments were productive with JH6*02 to produce HCDR3s of at least 20 amino acids in more than 10 antibodies. An antibody-producing cell (eg, a B-cell) that is a progeny of the cell of any one of clauses 3 to 14, wherein the antibody-producing cell comprises a heavy chain locus comprising a rearranged variable region produced by recombination of human JH6*02 with a D segment and a VH segment (eg, JH6*02 with human VH3-11 (eg, VH3-11*01) and D3-9; VH3-20 (eg, VH3-20*01) and D3-10; VH4-4 (eg, VH4-4*02) and D3-10; VH3-9 (eg, VH3-9*01) and D3-10; or VH1-8 (eg, VH1-8*01) and D310).
Such a variable region would be the product of in vivo somatic hypermutation in a non-hman vertebrate or cell of the invention. The cell of clause 15, which is a B-cell or hybridoma that expresses a target antigen-specific antibody comprising a heavy chain that comprises a rearranged variable region produced by recombination of human JH6*02 with a D segment and a VH segment (eg, JH6*02 with human VH3-11 (eg, VH3-11*01) and D3-9; VH3-20 (eg, VH3-20*01) and D3-10; VH4-4 (eg, VH4-4*02) and D3-10; VH3-9 (eg, VH3-9*01) and D3-10; or VH1-8 (eg, VH1-8*01) and D310).
Such a variable region would be the product of in vivo somatic hypermutation in a non-hman vertebrate or cell of the invention The vertebrate or cell of any preceding clause, wherein the antibody heavy chain specifically binds a target antigen. The vertebrate or cell of any preceding clause, wherein the antibody heavy chain has a HCDR3 length of at least 20 amino acids.
Optionally, the HCDR3 length is at least 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 amino acids. Additionally, in one example the length is no more than 35, 34, 33, 32 or 31 amino acids. For example, the HCDR3 length is 20, 21, 22, 23 or 24 amino acids.
The vertebrate or cell of any preceding clause, wherein the antibody heavy chain is a product of the recombination of JH6*02 with a human VH gene segment recited in clause 13 or 14 and/or a D gene segment recited in clause 10, 11 or 14. The vertebrate or cell of any preceding clause, wherein all endogenous non-human vertebrate heavy chain variable region gene segments have been inactivated in the genome (Eeg, by gene segment deletion or inversion). The vertebrate or cell of any preceding clause, wherein the genome is homozygous for said heavy chain locus. A heavy chain (eg, comprised by an antibody) isolated from a vertebrate of any one of clauses 1, 2, 5 to 14 and 17 to 21 wherein the heavy chain comprises a HCD 3 of at least 20 amino acids. The heavy chain of clause 22, wherein the HCDR3 is the product of recombination of human JH6*02 with a human VH gene segment recited in clause 13 or 14 and/or a D gene segment recited in clause 10, 11 or 14.
In an example, the heavy chain is chimaeric where the C region is non-human. In an example, the heavy chain is human where the C region is human. A heavy chain (eg, comprised by an antibody) whose VH variable domain is identical to the VH variable domain of the heavy chain of clause 22 or 23, and which comprises a human constant region or a human-mouse chimaeric constant region (eg, CHI is human and the other constant domains are mouse). The heavy chain of clause 22, 23 or 24, whose VH variable domain is specific for a target antigen. A method for producing a heavy chain, VH domain or an antibody specific to a target antigen, the method comprising immunizing a non-human vertebrate according to any one of clauses 1, 2, 5 to 14 and 17 to 21 with the antigen and isolating the heavy chain, VH domain or an antibody specific to a target antigen or a cell producing the heavy chain, VH domain or an antibody, wherein the heavy chain, VH domain or an antibody comprises a HCDR3 that is derived from the recombination of human JH6*02 with a VH gene segment and a D gene segment.
7. A method for producing a human heavy chain or antibody comprising carrying out the method of clause 26, wherein the constant region of the locus is a non-human vertebrate (eg, mouse or rat) constant region, and then replacing the non-human constant region of the isolated heavy chain or antibody with a human constant region (eg, by engineering of the nucleic acid encoding the antibody). 8. A heavy chain, VH domain or an antibody produced by the method of clause 26 or 27. Optionally the HCD 3 length is at least 20 amino acids as herein described. 9. A B-cell or hybridoma expressing a heavy chain VH domain that is identical to the VH domain of the heavy chain of clause 22, 23 or 28. 0. A nucleic acid encoding the VH domain of the heavy chain of clause 22, 23 or 28, or encoding the heavy chain of clause 22, 23, 24, 25 or 28. 1. A vector (eg, a CHO cell or HEK293 cell vector) comprising the nucleic acid of clause 30;
optionally wherein the vector is in a host cell (eg, a CHO cell or HEK293 cell). 2. A pharmaceutical composition comprising the antibody, heavy chain or VH domain (eg, comprised by an antibody) of any one of clauses 22 to 25 and 28, together with a
pharmaceutically-acceptable excipient, diluent or a medicament (eg, a further antigen-specific variable domain, heavy chain or antibody). 3. The antibody, heavy chain or VH domain (eg, comprised by an antibody) of any one of clauses 22 to 25 and 28 for use in medicine (eg, human medicine).
For example, the locus comprises the following human VH gene segments
IGHV6-1
IGHV3-7
IGHV1-8
IGHV3-9
IGHV3-11
IGHV3-13
IGHV1-18
IGHV3-30
IGHV4-31
IGHV4-39
IGHV4-59
Optionally also (i) and/or (ii) (i)
IGHV1-2
IGHV2-5 and
IGHV3-21
IGHV1 2
IGHV2 5
IGHV3 21
IGHV1 24
For example, the locus comprises the following human VH gene segment
IGHV6-1*01
IGHV3-7*01
IGHV1-8*01
IGHV3-9*01
IGHV3-11*01
IGHV3-13*01
IGHV1-18*01
IGHV3-30*18
IGHV4-31*03
IGHV4-39*01 and
IGHV4-59*01;
Optionally also (iii) or (iv) (ii)
IGHVl-2*04
IGHV2-5*10 and
IGHV3-21*03
(iv)
IGHVl-2*02
IGHV2-5*01
IGHV3-21*01 and
IGHV1-24*01
For example, the locus comprises the following human JH gene segment variants
IGHJ2*01
IGHJ3*02
IGHJ4*02
IGHJ5*02 and
IGHJ6*02
For example, the locus comprises the following human D gene segments
IGHDl-1
IGHD2-2
IGHD3-9
IGHD3-10
IGHD5-12
IGHD6-13
IGHD1-14
IGHD2-15
IGHD3-16
IGHD4-17
IGHD6-19
IGHD2-21
IGHD5-24
IGHDl-26 and
IGHD7-27 and optionally also (v) or (vi) (v)
IGHD3-3 (vi)
IGHD3-3
IGHD4-4
IGHD5-5
IGHD6-6
IGHD1-7
IGHD2-8 and
IGHD2-8
The present invention provides in a fifth confieuration:-
Constant Regions Tailored to Human Use & Antibody Humanisation
Additional rational design and bioinformatics has led the inventors to realise that specific human constant region variants are conserved across many diverse human populations. The inventors realised that this opens up the possibility of making a choice to humanise antibodies, chains and variable domains by using such specific constant regions in products, rather than arbitrarily choosing the human constant region (or a synthetic version of a human constant region). This aspect of the invention also enables one to tailor antibody-based drugs to specific human ethnic populations, thereby more closely matching drug to patient (and thus disease setting) than has hitherto been performed. It can be a problem in the state of the art that antibodies are humanised with an arbitrary choice of human constant region (presumably derived from one (often unknown) ethnic population or non-naturally occurring) that does not function as well in patients of a different human ethnic population. This is important, since the constant region has the major role in providing antibody effector functions, eg, for antibody recycling, cellular and complement recruitment and for cell killing.
As discussed further in WO2011066501, human IgG sub-types IgGl, lgG2, gG3 and lgG4 exhibit differential capacity to recruit immune functions, such as antibody-dependent cellular cytotoxicity (ADCC, e.g., IgGl and lgG3), antibody-dependent cellular phagocytosis (ADCP, e.g., IgGl, lgG2, lgG3 and lgG4), and complement dependent cytotoxicity (CDC, e.g., IgGl, lgG3). Sub-type-specific engagement of such immune functions is based on selectivity for Fc receptors on distinct immune cells and the ability to bind Clq and activate the assembly of a membrane attack complex (MAC).
Among the various types, relative affinity for FcY receptors (e.g., FcYRI, FcYRIIa/b/c, FcYRIIIa/b) is high for IgGl and lgG3, however, there is minimal affinity for lgG2 (restricted to the FcYRIIa 131H polymorphism), and lgG4 only has measurable affinity for FcYRI. Using comparative sequence analysis and co-crystal structures, the key contact residues for receptor binding have been mapped to the amino acid residues spanning the lower hinge and CH2 region. Using standard protein engineering techniques, some success in enhancing or reducing the affinity of an antibody preparation for Fc receptors and the Clq component of complement has been achieved.
Among the isotypes, lgG2 is least capable of binding the family of Fc receptors. Using lgG2 as the starting point, efforts have been made to find a mutant with diminished effector functions but which retains FcRn binding, prolonged stability, and low immunogenicity. Improved mutants of this nature may provide improved antibody therapeutics with retained safety. Human IgGl therapeutic
antibodies that bind to cell surface targets are able to engage effector cells that may mediate cell lysis of the target cell by antibody-dependent cellular cytotoxicity (ADCC) or complement dependent cytotoxicity (CDC). These mechanisms occur through interaction of the CH2 region of the antibody Fc domain to Fcy receptors on immune effector cells or with Clq, the first component of the complement cascade. Table 19 shows the activities of different human gamma sub-types. The skilled person may choose accordingly to promote or dampen-down activity depending upon the disease setting in humans of interest. For example, use of a human gamma-1 constant region is desirable when one wishes to isolated totally human heavy chains and antibodies that have relatively high complement activation activity by the classical pathway and FcYRl recognition in human patients. See also Mol Immunol. 2003 Dec;40(9):585-93; "Differential binding to human Fcgamma Rl la and Fcgamma Rllb receptors by human IgG wild type and mutant antibodies"; Armour KL et al, which is incorporated herein by reference.
lgG2 constant regions are well suited to producing antibodies and heavy chains according to the invention for binding to cytokines or soluble targets in humans, since lgG2 is essentially FcYRl, Ill- silent, FcYRl la-active and has little Complement activity.
IgGl constant regions have wide utility for human therapeutics, since IgGl antibodies and heavy chains are FcYRl, II, III- active and have complement activity. This can be enhanced by using a human gamma-1 constant region that has been activated by engineering as is known in the art.
The work of the inventors has therefore identified a collection of human constant region of different isotypes from which an informed choice can be made when humanising chimaeric antibody chains (or conjugating V domains, such as dAbs or Camelid VHH, to constant regions). The collection was identified on the basis of bioinformatics analysis of the 1000 Genomes database, the inventors selecting constant region variants that are frequently occurring across several human ethnic populations, as well as those that appear with relatively high frequency within individual populations (as assessed by the number of individuals whose genomes comprise the variant). By sorting through the myriad possible sequences on this basis, the inventors have provided a collection of human constant region variants that are naturally-occuring and which can be used when rationally designing
antibodies, heavy chains and other antibody-based formats that bear a human constant region. In particular, this is useful when humanising chimaeric heavy chains to produce totally human chains in which both the variable and constant regions are human. This is useful for compatibility with human patients receiving antibody-based drugs.
end, the invention provides the following aspects
1. A method of producing an antibody heavy chain, the method comprising
(a) providing an antigen-specific heavy chain variable domain (eg, VH (such as a human VH or dAb) or VHH or a humanised heavy chain variable domain); and
(b) combining the variable domain with a human heavy chain constant region to produce an antibody heavy chain comprising (in N- to C-terminal direction) the variable domain and the constant region;
wherein
the human heavy chain constant region is an IGHAref, IGHAla, IGHA2a, IGHA2b, IGHGlref, IGHG2ref, IGHG2a, IGHG3ref, IGHG3a, IGHG3b, IGHG4ref, IGHG4a, IGHDref, IGHEref, IGHMref, IGHMa or IGHMb constant region.
Step (b) can be carried out, eg, using recombinant DNA technology using the corresponding nucleotide sequences.
For the constant region according to any aspect of this configuration, either genomic DNA or equivalent (ie, having introns and exons and optionally also 5' UT sequences, eg, with native or a non-native leader sequence) can be used for the constant region. For example, any of the "GENOMIC" sequences disclosed as SEQ ID NO: 365 onwards herein. Alternatively, an intronless sequence can be used, for example any of the "CDS" sequences disclosed as SEQ ID NO: 365 onwards herein (eg, with native or a non-native leader sequence).
Optionally for any aspect of this configuration of the invention, the human heavy chain constant region is an IGHAref constant region.
Optionally for any aspect of this configuration of the invention, the human heavy chain constant region is an IGHAla constant region.
Optionally for any aspect of this configuration of the invention, the human heavy chain constant region is an IGHA2a constant region.
Optionally for any aspect of this configuration of the invention, the human heavy chain constant region is an IGHA2b constant region.
Optionally for any aspect of this configuration of the invention, the human heavy chain constant region is IGHGlref constant region.
Optionally for any aspect of this configuration of the invention, the human heavy chain constant region is an IGHG2ref constant region.
Optionally for any aspect of this configuration of the invention, the human heavy chain constant region is an IGHG2a constant region.
Optionally for any aspect of this configuration of the invention, the human heavy chain constant region is an IGHG3ref constant region.
Optionally for any aspect of this configuration of the invention, the human heavy chain constant region is an IGHG3a constant region.
Optionally for any aspect of this configuration of the invention, the human heavy chain constant region is an IGHG3b constant region.
Optionally for any aspect of this configuration of the invention, the human heavy chain constant region is an IGHG4ref constant region.
Optionally for any aspect of this configuration of the invention, the human heavy chain constant region is an IGHG4a constant region.
Optionally for any aspect of this configuration of the invention, the human heavy chain constant region is an IGHDref constant region.
Optionally for any aspect of this configuration of the invention, the human heavy chain constant region is an IGHEref constant region.
Optionally for any aspect of this configuration of the invention, the human heavy chain constant region is an IGHMref constant region.
Optionally for any aspect of this configuration of the invention, the human heavy chain constant region is an IGHMa constant region.
Optionally for any aspect of this configuration of the invention, the human heavy chain constant region is an IGHMb constant region.
Optionally, a derivative (eg, a mutant or conjugate) of the heavy chain or an antibody containing the heavy chain is produced. For example, a toxic payload can be conjugated (eg, for oncology applications). For example, one or more mutations can be introduced, as is known in the art, to inactivate or enhance Fc effector function.
The method of aspect 1, wherein the variable domain is a human variable domain.
A human variable domain is, for example, the product of recombination in a transgenic non- human vertebrate of human VH, D and JH gene segments. Alternatively, the variable domain is identified using in vitro display technology from a human VH library, eg, using phage display, ribosome display or yeast display, as is known in the art.
In another embodiment, the variable domain is a humanised variable domain, eg, comprising human frameworks with non-human (eg, mouse or rat) CD s). Humanisation technology is conventional in the art, and will be readily known to the skilled person.
The method of any preceding aspect, wherein the variable domain has previously been selected from a non-human vertebrate that has been immunised with the antigen.
For example, the vertebrate (such as a mouse or rat) genome comprises a chimaeric heavy chain locus comprising a human variable region (human V, D and JH gene segments) operably connected upstream of a non-human vertebrate constant region so that the locus is able to rearrange for the expression of heavy chains comprising human variable domains and non- human vertebrate constant regions.
In alternative embodiments, the variable domain is selected using an in vitro technology such as phage display, ribosome display or yeast display. In this case the variable domain may be displayed with or without an constant region, provided that it is later combined with a human constant region as per the invention.
The method of any preceding aspect, comprising providing an expression vector (Eg, a mammalian expression vector, such as a CHO or HEK293 vector) comprising a nucleotide sequence encoding the constant region; inserting a nucleotide sequence encoding the variable domain into the vector 5' of the constant region sequence; inserting the vector into a host cell and expressing the heavy chain by the host cell; the method further comprising isolating a heavy chain (eg, as part of an antibody) comprising the variable domain and the human constant region.
The vector comprises regulatory elements sufficient to effect expression of the heavy chain when the vector is harboured by a host cell, eg, a CHO or HEK293 cell.
The method of any preceding aspect, further comprising obtaining a nucleotide sequence encoding the heavy chain.
An antibody comprising a human heavy chain, the heavy chain comprising a variable domain that is specific for an antigen and a constant region that is an IGHAref, IGHAla, IGHA2a, IGHA2b, IGHGlref, IGHG2ref, IGHG2a, IGHG3ref, IGHG3a, IGHG3b, IGHG4ref, IGHG4a, IGHDref, IGHEref, IGHMref, IGHMa or IGHMb constant region.
A polypeptide comprising (in N- to C- terminal direction) a leader sequence, a human variable domain that is specific for an antigen and a human constant region that is an IGHAref, IGHAla, IGHA2a, IGHA2b, IGHGlref, IGHG2ref, IGHG2a, IGHG3ref, IGHG3a, IGHG3b, IGHG4ref, IGHG4a, IGHDref, IGHEref, IGHMref, IGHMa or IGHMb constant region; wherein (i) the leader sequence is not the native human variable domain leader sequence (eg, the leader sequence is another human leader sequence or a non-human leader sequence); and/or (ii) the variable domain comprises mouse AID-pattern somatic mutations or mouse terminal deoxynucleotidyl transferase (TdT)- pattern junctional mutations.
A nucleotide sequence encoding (in 5' to 3' direction) a leader sequence and a human antibody heavy chain, the heavy chain comprising a variable domain that is specific for an antigen and a constant region that is an IGHAref, IGHAla, IGHA2a, IGHA2b, IGHGlref, IGHG2ref, IGHG2a, IGHG3ref, IGHG3a, IGHG3b, IGHG4ref, IGHG4a, IGHDref, IGHEref, IGHMref, IGHMa or IGHMb constant region; and the leader sequence being operable for expression (eg, in a mammalian CHO or HEK293 cell) of the heavy chain and wherein the leader sequence is not the native human variable domain leader sequence (eg, the leader sequence is another human leader sequence or a non-human leader sequence).
In an example, the leader sequence is
ATGGGCTGGTCCTGCATCATCCTGTTTCTGGTGGCCACCGCCACCGGCGTGCACAGC
Which translates to
MGWSCIILFLVATATGVHS
A nucleotide sequence encoding (in 5' to 3' direction) a promoter and a human antibody heavy chain, the heavy chain comprising a variable domain that is specific for an antigen and a constant region that is an IGHAref, IGHAla, IGHA2a, IGHA2b, IGHGlref, IGHG2ref, IGHG2a, IGHG3ref,
IGHG3a, IGHG3b, IGHG4ref, IGHG4a, IGHDref, IGHEref, IGHMref, IGHMa or IGHMb constant region; and the promoter being operable for expression (eg, in a mammalian CHO or HEK293 cell) of the heavy chain and wherein the promoter is not the native human promoter.
In one embodiment, the promoter sequence is a human IGK 3-15 promoter.
The antibody, polypeptide or nucleotide sequence of any one of aspects 6 to 9, wherein the variable domain comprises mouse AID-pattern somatic mutations and/or mouse terminal deoxynucleotidyl transferase (TdT)- pattern junctional mutations.
For example, one way, in any aspect of this configuration of the invention, to provide mouse AID-pattern somatic mutations and/or mouse terminal deoxynucleotidyl transferase (TdT)- pattern junctional mutations is to select a variable domain from a non-human vertebrate or cell. For example, a vertebrate or cell as disclosed herein. A vector (eg, a CHO cell or HEK293 cell vector) comprising the nucleic acid of aspect 8, 9 or 10; optionally wherein the vector is in a host cell (eg, a CHO cell or HEK293 cell).
A pharmaceutical composition comprising the antibody or polypeptide of any one of aspects 6, 7 and 10, together with a pharmaceutically-acceptable excipient, diluent or a medicament (eg, a further antigen-specific variable domain, antibody chain or antibody).
The antibody or polypeptide of any one of aspects 6, 7 and 10 for use in treating and/or preventing a medical condition in a human patient.
Use of the antibody or polypeptide of any one of aspects 6, 7 and 10 for the manufacture of a medicament for treating and/or preventing a medical condition in a human patient.
The antibody, polypeptide or use of aspect 13 or 14, wherein the human is a member of a human population selected from population numbers 1-14, wherein the populations are numbered as follows (population labels being according to 1000 Genomes Project
nomenclature)
1= ASW;
2= CEU;
3=CHB;
4=CHS;
5=CLM;
6=FIN;
7=GB ;
8=IBS;
9=JPT;
10=LWK;
11=MXL;
12=PUR;
13=TSI;
14=Y I.
The antibody, polypeptide or use of aspect 15, wherein the constant region is a
(i) IGHAla constant region and the human population is selected from any population number 1-14;
(ii) IGHA2a constant region and the human population is selected from any population number 1-14;
(ill) IGHA2b constant region and the human population is selected from any population number 1-14;
(iV) IGHG2a constant region and the human population is selected from any population number 1-9 and 11-13;
(v) IGHG3a constant region and the human population is selected from any population number 1-14;
(vi) IGHG3b constant region and the human population is selected from any population number 1-8 and 11-13;
(vii) IGHG4a constant region and the human population is selected from any population number 1-9 and 11-13;
(viii) IGHMa constant region and the human population is selected from any population number 1-14; or
(ix) IGHMb constant region and the human population is selected from any population number 1-14;
Wherein the populations are numbered as follows (population labels being according to 1000
Genomes Project nomenclature)
1= ASW;
2= CEU;
3=CHB;
4=CHS;
5=CLM;
6=FIN;
7=GB ;
8=IBS;
9=JPT;
10=LWK;
11=MXL;
12=PUR;
13=TSI;
14=Y I.
17. A vector (eg, a CHO cell or HEK293 cell vector) comprising a IGHGlref, IGHG2ref, IGHG2a,
IGHG3ref, IGHG3a, IGHG3b, IGHG4ref or IGHG4a constant region nucleotide sequence that is 3' of a cloning site for the insertion of a human antibody heavy chain variable domain nucleotide sequence, such that upon insertion of such a variable domain sequence the vector comprises (in 5' to 3' direction) a promoter, a leader sequence, the variable domain sequence and the constant region sequence so that the vector is capable of expressing a human antibody heavy chain when present in a host cell.
The present invention provides in a Sixth confieuration:-
Multiple Variants in the Same Genome Cis or Trans
The inventors' analysis has revealed groupings of naturally-occurring human antibody gene segment variants as set out in Table 13 and Table 14. This revealed the possibility of producing transgenic genomes in non-human vertebrates and cells wherein the genomes contain more than the natural
human complement of specific human gene segments. In one example, this can be achieved by providing more than the natural human complement of a specific gene segment type on one or both of the respective Ig locus (eg, one or both chromosomes harbouring IgH in a mouse genome or mouse cell genome).
To this end, this configuration of the invention provides the following (as set out in numbered paragraphs):-
1. A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) having a genome comprising at least 3 human variable region gene segments of the same type (eg, at least 3 human VH6-1 gene segments, at least 3 human J H6 gene segments, at least 3 human VK1-39 gene segments, at least 3 human D2-2 gene segments or at least 3 human JKI gene segments), wherein at least two of the human gene segments are variants that are not identical to each other.
For example, the genome comprises a variable region that comprises V, D and J gene segments (for the variable region of a heavy chain locus) or V and J gene segments (for the variable region of a light chain locus) upstream of a constant region for expression of heavy or light chains respectively.
In an alternative, the skilled person can choose to provide more than the wild type human complement of a specific gene segment type by providing several copies of one variant type of the human gene segment. Thus, there is provided
A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) having a genome comprising at least 3 human variable region gene segments of the same type (eg, at least 3 human VH6-1 gene segments, at least 3 human J H6 gene segments, at least 3 human VK1-39 gene segments, at least 3 human D2-2 gene segments or at least 3 human JKI gene segments), wherein the human gene segments are identical variants.
For example, the genome comprises a variable region that comprises V, D and J gene segments (for the variable region of a heavy chain locus) or V and J gene segments (for the variable region of a light chain locus) upstream of a constant region for expression of heavy or light chains respectively.
A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) having a genome comprising at least 2 different non-endogenous variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 3 human JH6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments) cis at the same Ig locus.
In an alternative, the skilled person can choose to provide more than the wild type human complement of a specific gene segment type by providing several copies of one variant type of the human gene segment. Thus, there is provided
A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) having a genome comprising at least 2 non-endogenous variable region gene segments of the same variant type (eg, at least 2 human JH6*02 gene segments) cis at the same Ig locus.
A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) having a genome comprising at least 2 different human variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human J H6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments) trans at the same Ig locus; and optionally a third human gene segment of the same type, wherein the third gene segment is cis with one of said 2 different gene segments.
In an alternative, the skilled person can choose to provide more than the wild type human complement of a specific gene segment type by providing several copies of one variant type of the human gene segment. Thus, there is provided
A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) having a genome comprising at least 2 different human variable region gene segments of the same variant type (eg, at least 2 human JH6*02 gene segments) trans at the same Ig locus; and optionally a third human gene segment of the same variant type, wherein the third gene segment is cis with one of said 2 different gene segments.
A population of non-human vertebrates (eg, mice or rats) comprising a repertoire of human variable region gene segments, wherein the plurality comprises at least 2 human variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human J H6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments), a first of said different gene segments is provided in the genome of a first vertebrate of the population, and a second of said different gene segments being provided in the genome of a second vertebrate of the population, wherein the genome of the first vertebrate does not comprise the second gene segment.
A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) having a genome comprising at least 2 different non-endogenous variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human JH6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments), wherein the gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
A method of enhancing the human immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising at least 3 human variable region gene segments of the same type (eg, at least 3 human VH6-1 gene segments, at least 3 human J H6 gene segments, at least 3 human VK1-39 gene segments, at least 3 human D2-2 gene segments or at least 3 human JKI gene segments), wherein at least two of the human gene segments are variants that are not identical to each other.
A method of enhancing the immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising at least 2 different non-endogenous variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human JH6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments) cis at the same Ig locus.
A method of enhancing the immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising at least 2 different human variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human J H6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments) trans at the same Ig locus; and optionally a third human gene segment of the same type, wherein the third gene segment is cis with one of said 2 different gene segments.
A method of providing an enhanced human immunoglobulin variable region gene segment repertoire, the method comprising providing a population of non-human vertebrates (eg, a mouse or rat) comprising a repertoire of human variable region gene segments, wherein the method comprises providing at least 2 different human variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human JH6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments), wherein a first of said different gene segments is provided in the genome of a first vertebrate of the population, and a second of said different gene segments is provided in the genome of a second vertebrate of the population, wherein the genome of the first vertebrate does not comprise the second gene segment.
A method of enhancing the human immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising at least 2 different non-endogenous variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human J H6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments), wherein the gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
The vertebrate, cell or method of any preceding paragraph, wherein at least 2 or 3 of said different gene segments are provided cis at the same Ig locus in said genome.
The vertebrate, cell or method of any preceding paragraph, wherein the gene segments are derived from the genome sequence of different human individuals that are not genetically
related over at least 3 generations.
The vertebrate, cell or method of any preceding paragraph, wherein the gene segments are derived from the genome sequence of two or more different human individuals; optionally wherein the different human individuals are from different human populations.
The vertebrate, cell or method of paragraph 13, wherein the individuals are not genetically related.
A method of enhancing the human immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising at least 2 human variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human JH6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human J KI gene segments), wherein the gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations; optionally wherein at least 2 or 3 of said different gene segments are provided at the same Ig locus in said genome.
The method of paragraph 15, wherein the different human individuals are from different human populations.
The method of paragraph 15, wherein the individuals are not genetically related.
The vertebrate, cell or method of preceding paragraph, wherein at least one of the different segments is a synthetic mutant of a human germline gene segment.
The vertebrate, cell or method of any preceding paragraph, wherein each of said gene segments occurs in 10 or more different human populations.
The vertebrate, cell or method of preceding paragraph, wherein each of said gene segments has a human frequency of 5% or greater (eg, 10, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, or 95% or greater).
In this respect, the skilled person can be guided by the information provided in Table 14. Frequency can, for example, be cumulative frequency in the 1000 Genomes database.
The vertebrate, cell or method of paragraph 20, wherein each of said gene segments occurs in 10 or more different human populations.
The vertebrate, cell or method of any preceding paragraph, wherein each of said gene segments occurs in the 1000 Genomes database in more than 50 individuals.
The vertebrate, cell or method of preceding paragraph, wherein each of said gene segments (i) has a human frequency of 5% or greater (eg, 10, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, or 95% or greater); and (ii) occurs in 10 or more different human populations.
In this respect, the skilled person can be guided by the information provided in Table 14.
Frequency can, for example, be cumulative frequency in the 1000 Genomes database.
A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) having a genome comprising first and second human Ig locus gene segments of the same type (eg, first and second human JH6 gene segments; or first and second lgG2 gene segments; or first and second human J\7 gene segments), wherein the first gene segment is a gene segment selected from Table 14 (eg, IGHJ6-a) and the second gene segment is the corresponding reference sequence (eg, IGHJ6 ref; SEQ ID NO: 244).
Table 14 lists commonly-occurring natural human variants. It can be seen that these occur across many human populations and thus usefully have wide applicability for human antibody- based drugs.
For example, the gene segments are provided as targeted insertions into an endogenous non- human vertebrate Ig locus. Alternatively, random integration (eg, using YACs) as is know in the art can be performed.
For example, the genome comprises a variable region that comprises V, D and J gene segments (for the variable region of a heavy chain locus) or V and J gene segments (for the variable region of a light chain locus) upstream of a constant region for expression of heavy or light chains respectively.
In another embodiment, the invention enables the skilled person to select two or more different naturally-occurring human gene segment variants for combination into the genome of a non- human vertebrate or cell. A reference sequence need not be included. It may be desirable to use one or more rare gene segments to increase diversity of the repertoire. Additionally or alternatively, it may be desirable to include a mixture of frequent and rare variants of the same type to provide repertoire diversity. The variants may be chosen additionally or alternatively to tailor the gene segment inclusion to one or more specific human populations as indicated by the information provided in Table 13 or Table 14.
Thus, the invention provides
A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) having a genome comprising first and second human Ig locus gene segments of the same type (eg, first and second human JH6 gene segments; or first and second lgG2 gene segments; or first and second human J\7 gene segments), wherein the gene segments are gene segments selected from Table 13 or Table 14; and optionally wherein one or more of the gene segments appears in Table 14 (eg, IGHJ6-a) or is a reference sequence (eg, IGHJ6 ref; SEQ. ID NO: 244).
The vertebrate or cell of paragraph 24, wherein the genome comprises a third human gene segment of said type, the third gene segment being different from the first and second gene segments.
The vertebrate or cell of paragraph 24 or 25, wherein the first and second gene segments are cis on the same chromosome; and optionally the third gene segment is also cis on said
chromosome.
The vertebrate or cell of paragraph 26, wherein the gene segments are targeted insertions into an endogenous non-human Ig locus.
For example, the gene segments are heavy chain gene segments and the non-human locus is an IgH locus. For example, the gene segments are light chain (kappa or lambda) gene segments and the non-human locus is an IgL locus.
The vertebrate or cell of paragraph 24 or 25, wherein the first and second gene segments are trans on different chromosomes.
Thus, the chromosomes are the same type (eg, both mouse chromosome 6 or rat chromosome 4).
The vertebrate or cell of any one of paragraphs 24 to 28, wherein the first gene segment is a gene segment selected from any one of Tables 1 to 7 and 9 to 14 (eg, selected from Table 13 or 14) and the second gene segment is the corresponding reference sequence.
A population of non-human vertebrates (eg, mice or rats) comprising first and second human Ig locus gene segments of the same type (eg, first and second human JH6 gene segments; or first and second lgG2 gene segments; or first and second human J\7 gene segments), wherein the first gene segment is a gene segment selected from any one of Tables 1 to 7 and 9 to 14 (eg, Table 13 or 14) (eg, IGHJ6-a) and the second gene segment is the corresponding reference sequence (eg, SEQ. ID NO: 7), wherein the first gene segment is provided in the genome of a first vertebrate of the population, and the second gene segment is provided in the genome of a second vertebrate of the population.
31. The population of paragraph 30, wherein the genome of the first vertebrate does not comprise the second gene segment.
32. The population of paragraph 30 or 31, wherein the population comprises a third human gene segment of said type, the third gene segment being different from the first and second gene segments and optionally wherein the first and third gene segments are present in the genome of the first vertebrate.
33. The population of paragraph 30, 31 or 32, wherein the gene segments are targeted insertions into an endogenous non-human Ig locus in the respective genome.
For example, the gene segments are heavy chain gene segments and the non-human locus is an IgH locus. For example, the gene segments are light chain (kappa or lambda) gene segments and the non-human locus is an IgL locus.
34. The population of of any one of paragraphs 30 to 33, wherein the first gene segment is a gene segment selected from any one of Tables 1 to 7 and 9 to 14 (eg, Table 13 or 14) and the second gene segment is the corresponding reference sequence.
35. A method of enhancing the human immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising first and second human Ig locus gene segments of the same type (eg, first and second human JH6 gene segments; or first and second lgG2 gene segments; or first and second human J\7 gene segments), wherein the first gene segment is a gene segment selected from any one of Tables 1 to 7 and 9 to 14 (eg, Table 13 or 14) (eg, IGHJ6-a) and the second gene segment is the corresponding reference sequence (eg, SEQ. ID NO: 7).
36. A method of providing an enhanced human immunogolobulin gene segment repertoire, the method comprising providing a population according to any one of paragraphs 30 to 33.
Variants Prevalent in Few Populations
In another aspect, it is of note that certain human gene segment variants may appear relatively frequently in one or a small number of populations, but is not found prevalently across many different human populations. There is thinking that specific germl ine gene segment repertoires have evolved in individual human ethnic populations due to iterative exposure to antigens (eg, disease pathogen antigens) to which the population is often exposed. Repeated exposure and mutation may have lead to the evolution of gene segment variants that can provide an effective response to the antigen (pathogen) in the population, and this may explain the conservation of the gene segments in those populations (as opposed to other human ethnic populations that may not have frequently encountered the antigen). With this in mind, the inventors identified gene segment variants from their analysis that are relatively prevalent in a small number of human populations, and not across many populations. The inventors realized that inclusion of one or more of such gene segments in the configurations of the invention (eg, in transgenic Ig loci, vertebrates and cells) would be useful for producing antibodies, Ig chains and variable domains that can address antigens (eg, disease- causing antigens or pathogens) to which the small number of human populations may become exposed. Such products would be useful for treating and/or preventing disease or medical conditions in members of such a population. This aspect could also be useful for addressing infectious disease pathogens that may have been common in the small number of populations, but which in the future or relatively recently in evolution has become a more prevalent disease-causing pathogen in other human populations (ie, those not listed in Table 13 against the gene segment variant(s) in question). To this end, from the 1000 Genomes database the inventors have identified the gene segment variants listed in Table 20.
Thus, according to any configuration or aspect described herein, one, more or all of the gene segments used in the present invention can be a gene segment listed in Table 20A, 20B, 20C or 20D.
Multiple JH Gene Segment Variants
A specific application of this configuration is the provision of multiple human JH gene segments as follows.
A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B- cell) having a genome comprising at least 3 human JH gene segments of the same type (JH1, JH2, JH3, JH4, JH5 or JH6), wherein at least two of the human JH gene segments are variants that are not
identical to each other.
In an example, any cell of the invention is an isolated cell. An "isolated" cell is one that has been identified, separated and/or recovered from a component of its production environment (eg, naturally or recombinantly). Preferably, the isolated cell is free of association with all other components from its production environment, eg, so that the cell can produce an antibody to an FDA-approvable or approved standard. Contaminant components of its production environment, such as that resulting from recombinant transfected cells, are materials that would typically interfere with research, diagnostic or therapeutic uses for the resultant antibody, and may include enzymes, hormones, and other proteinaceous or non-proteinaceous solutes. In preferred embodiments, the polypeptide will be purified: (1) to greater than 95% by weight of antibody as determined by, for example, the Lowry method, and in some embodiments, to greater than 99% by weight; (2) to a degree sufficient to obtain at least 15 residues of N-terminal or internal amino acid sequence by use of a spinning cup sequenator, or (3) to homogeneity by SDS-PAGE under non- reducing or reducing conditions using Coomassie blue or, preferably, silver stain. Ordinarily, however, an isolated cell will be prepared by at least one purification step.
A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B- cell) having a genome comprising at least 2 different non-endogenous JH gene segments (eg, human gene segments) of the same type (JH1, JH2, JH3, JH4, JH5 or JH6) cis at the same Ig (eg, IgH, eg, endogenous IgH, eg, mouse or rat IgH) locus. In an example, the genome comprises a human VH, D and JH repertoire comprising said different JH gene segments. Optionally the non-endogenous JH gene segments are non-mouse or non-rat, eg, human JH gene segments. In an example one or more or all of the non-endogenous gene segments are synthetic.
A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B- cell) having a genome comprising at least 2 different human JH gene segments of the same type (JH1, JH2, JH3, JH4, JH5 or JH6) trans at the same Ig (eg, IgH, eg, endogenous IgH, eg, mouse or rat IgH) locus; and optionally a third human JH gene segments of the same type, wherein the third JH is cis with one of said 2 different JH gene segments.
A population of non-human vertebrates (eg, mice or rats) comprising a repertoire of human JH gene segments, wherein the plurality comprises at least 2 different human JH gene segments of the same type (JH1, JH2, JH3, JH4, JH5 or JH6), a first of said different JH gene segments is provided in the genome of a first vertebrate of the population, and a second of said different JH gene segments being provided in the genome of a second vertebrate of the population, wherein the genome of the first vertebrate does not comprise the second JH gene segment.
A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B- cell) having a genome comprising at least 2 different non-endogenous (eg, human) JH gene segments of the same type (JH1, JH2, JH3, JH4, JH5 or JH6), wherein the JH gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations (eg, 3, 4, 5 or 6 generations). Optionally the non-endogenous JH gene segments are human JH gene segments. In an example one or more or all of the non-endogenous gene segments are synthetic.
A method of enhancing the human immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising at least 3 human JH gene segments of the same type (JH1, JH2, JH3, JH4, JH5 or JH6), wherein at least two of the human JH gene segments are variants that are not identical to each other.
A method of enhancing the immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising at least 2 different non-endogenous (eg, human) JH gene segments of the same type (JH1, JH2, JH3, JH4, JH5 or JH6) cis at the same Ig (eg, IgH, eg, endogenous IgH, eg, mouse or rat IgH) locus). Optionally the non-endogenous JH gene segments are non-mouse or non-rat, eg, human JH gene segments. In an example one or more or all of the non-endogenous gene segments are synthetic.
A method of enhancing the immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising at least 2 different human JH gene segments of the same type (JH1, JH2, JH3, JH4, JH5 or JH6) trans at the same Ig (eg, IgH, eg, endogenous IgH, eg, mouse or rat IgH) locus; and optionally a third human JH
gene segments of the same type, wherein the third JH is cis with one of said 2 different JH gene segments.
A method of providing an enhanced human immunoglobulin JH gene segment repertoire, the method comprising providing a population of non-human vertebrates (eg, a mouse or rat) comprising a repertoire of human JH gene segments, wherein the method comprises providing at least 2 different human JH gene segments of the same type (JH1, JH2, JH3, JH4, JH5 or JH6), wherein a first of said different J H gene segments is provided in the genome of a first vertebrate of the population, and a second of said different JH gene segments is provided in the genome of a second vertebrate of the population, wherein the genome of the first vertebrate does not comprise the second JH gene segment.
A method of enhancing the human immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising at least 2 different non-endogenous (eg, human) JH gene segments of the same type (JH1, JH2, JH3, JH4, JH5 or JH6), wherein the JH gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations (eg, 3, 4, 5, or 6 generations). Optionally the non-endogenous JH gene segments are human JH gene segments. In an example one or more or all of the non-endogenous gene segments are synthetic.
In an example of the vertebrate or cell or the method of the invention at least 2 or 3 of said different gene segments are provided cis at the same Ig locus in said genome.
In an example of the vertebrate or cell or the method of the invention the JH gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations (eg, 3, 4, 5, or 6 generations).
In an example of the vertebrate or cell or the method of the invention the JH gene segments are derived from the genome sequence of two or more different human individuals; optionally wherein the different human individuals are from different human populations.
In an example of the vertebrate or cell or the method of the invention the individuals are not genetically related (eg, going back 3, 4, 5, or 6 generations).
In an example of the vertebrate or cell or the method of the invention at least one of the different JH segments is a synthetic mutant of a human germline JH gene segment.
The invention also provides a method of enhancing the human immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising at least 2 human JH gene segments of the same type (JH1, JH2, J H3, JH4, JH5 or JH6), wherein the JH gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations (eg, 3, 4, 5, or 6 generations); optionally wherein at least 2 or 3 of said different gene segments are provided at the same IgH locus in said genome.
In an example of the vertebrate or cell or the method of this embodiment of the invention the genome comprises a substantially complete functional repertoire of human JH gene segment types supplemented with one, two or more human JH gene segments, wherein said substantially complete functional repertoire and the supplementary JH gene segments are not found together in the germline genome of a human individual.
In an example of the population of the invention, the population comprises a substantially complete functional repertoire of human JH gene segment types supplemented with one, two or more human JH gene segments, wherein said substantially complete functional repertoire and the supplementary JH gene segments are not found together in the germline genome of a human individual.
A non-human vertebrate (eg, a mouse or rat) or a non-human cell (eg, an ES cell or a B-cell) having a genome comprising a substantially complete functional repertoire of human JH gene segment types supplemented with one, two or more human JH gene segments, wherein said substantially complete functional repertoire and the supplementary JH gene segments are not found together in the germline genome of a human individual.
A population of non-human vertebrates (eg, mice or rats) comprising a substantially complete functional repertoire of human JH gene segment types supplemented with one, two or more human JH gene segments, wherein said substantially complete functional repertoire and the supplementary JH gene segments are not found together in the germline genome of a human individual.
In an example of the vertebrate or the population, at least one of said JH gene segments is SEQ ID NO: 1, 2, 3 or 4. For example, at least one of said JH gene segments is SEQ ID NO: 1 and at least one, two or more of said supplementary JH gene segments is a variant according to any example above. For example, at least one of said JH gene segments is SEQ ID NO: 2 and at least one, two or more of said supplementary JH gene segments is a variant according to any one of the examples above. For example, at least one of said JH gene segments is SEQ ID NO: 2 and at least one, two or more of said supplementary JH gene segments is a variant according to any one of the examples above.
In an embodiment, the non-human vertebrate or vertebrate cell of the invention comprises a genome that comprises VH, D and JH gene repertoires comprising human gene segments, the JH gene repertoire (eg, a human JH gene segment repertoire) comprising a plurality of JH1 gene segments provided by at least 2 different JH1 gene segments in cis at the same Ig locus in said genome;
a plurality of JH2 gene segments provided by at least 2 different JH2 gene segments in cis at the same Ig locus in said genome;
a plurality of JH3 gene segments provided by at least 2 different JH3 gene segments in cis at the same Ig locus in said genome;
a plurality of JH4 gene segments provided by at least 2 different JH4 gene segments in cis at the same Ig locus in said genome;
a plurality of JH5 gene segments provided by at least 2 different JH5 gene segments in cis at the same Ig locus in said genome; and/or
a plurality of JH6 gene segments provided by at least 2 different JH6 gene segments in cis at the same Ig locus in said genome;
optionally wherein the JH gene segments are derived from the genome sequence of two or more different human individuals.
Optionally said at least 2 different JH gene segments are human gene segments or synthetic gene segments derived from human gene segments.
Optionally, the Ig locus is a IgH locus, eg, an endogenous locus, eg, a mouse or rat IgH locus.
In an embodiment, the non-human vertebrate or vertebrate cell of the invention comprises a genome that comprises VH, D and JH gene repertoires comprising human gene segments, the JH gene repertoire (eg, a human JH gene segment repertoire) comprising
a plurality of JH1 gene segments provided by at least 3 different JH1 gene segments;
a plurality of JH2 gene segments provided by at least 3 different JH2 gene segments;
a plurality of JH3 gene segments provided by at least 3 different JH3 gene segments;
a plurality of JH4 gene segments provided by at least 3 different JH4 gene segments;
a plurality of JH5 gene segments provided by at least 3 different JH5 gene segments; and/or a plurality of JH6 gene segments provided by at least 3 different JH6 gene segments;
optionally wherein the JH gene segments are derived from the genome sequence of two or three different human individuals;
optionally wherein at least 2 or 3 of said different gene segments are provided in cis at the same Ig locus in said genome.
Optionally said at least 3 different JH gene segments are human gene segments or synthetic gene segments derived from human gene segments.
Optionally, the Ig locus is a IgH locus, eg, an endogenous locus, eg, a mouse or rat IgH locus.
Optionally in the vertebrate or cell the different human individuals are from different human populations.
Optionally in the vertebrate or cell the individuals are not genetically related (eg, Going back 3, 4, 5 or 6generations).
Optionally in the vertebrate or cell at least one of the different JH segments is a synthetic mutant of a human germline JH gene segment.
In an embodiment of a non-human vertebrate or vertebrate cell (optionally an ES cell or B-cell) according to the invention, the vertebrate or cell genome comprises human VH, D and JH gene repertoires, the JH gene repertoire (eg, a human JH gene repertoire) comprising
a plurality of JH1 gene segments provided by at least 2 different human JH1 gene segments, optionally in cis at the same Ig locus in said genome;
a plurality of JH2 gene segments provided by at least 2 different human JH2 gene segments, optionally in cis at the same Ig locus in said genome;
a plurality of JH3 gene segments provided by at least 2 different human JH3 gene segments, optionally in cis at the same Ig locus in said genome;
a plurality of JH4 gene segments provided by at least 2 different human JH4 gene segments, optionally in cis at the same Ig locus in said genome;
a plurality of JH5 gene segments provided by at least 2 different human JH5 gene segments, optionally in cis at the same Ig locus in said genome; and/or
a plurality of JH6 gene segments provided by at least 2 different human JH6 gene segments, optionally in cis at the same Ig locus in said genome;
wherein the JH gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations (eg, 3, 4, 5 or 6 generations).
Optionally said at least 2 different JH gene segments are human gene segments or synthetic gene segments derived from human gene segments.
Optionally, the Ig locus is a IgH locus, eg, an endogenous locus, eg, a mouse or rat IgH locus. Optionally in the vertebrate or cell the human individuals are from different human populations.
JH5
An embodiment provides a vertebrate, cell or population of the invention whose genome comprises a plurality of JH5 gene segments, wherein the plurality comprises a human JH5 gene variant of SEQ ID NO: 1, wherein the variant comprises a nucleotide mutation at one or more positions
corresponding to positions
106,330,024
106,330,027
106,330,032
106,330,041
106,330,044
106,330,045
106,330,062
106,330,063
106,330,065
106,330,066
106,330,067
106,330,068 and
106,330,071
on human chromosome 14.
In the vertebrate, cell or population optionally the plurality comprises a human JH5 gene variant of SEQ ID NO: 1, wherein the variant comprises a guanine at a position corresponding to position 106,330,067 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
Optionally the variant comprises additionally a mutation at a position corresponding to (i) position 106,330,071 on human chromosome 14 (optionally the additional mutation being a guanine); (ii) position 106,330,066 on human chromosome 14 (optionally the additional mutation being a guanine); and/or (iii) position 106,330,068 on human chromosome 14 (optionally the additional mutation being a thymine).
Optionally the plurality comprises a human JH5 gene variant of SEQ ID NO: 1, wherein the variant comprises a guanine at a position corresponding to position 106,330,071 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
Optionally the variant comprises additionally a mutation at a position corresponding to (i) position 106,330,063 on human chromosome 14 (optionally the additional mutation being an adenine); and/or (ii) position 106,330,067 on human chromosome 14 (optionally the additional mutation being a guanine).
Optionally the plurality comprises a human JH5 gene variant of SEQ ID NO: 1, wherein the variant comprises a cytosine at a position corresponding to position 106,330,045 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
Optionally the plurality comprises a human JH5 gene variant of SEQ ID NO: 1, wherein the variant comprises an adenine at a position corresponding to position 106,330,044 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
Optionally the variant comprises additionally a mutation at a position corresponding to (i) position
106.330.066 on human chromosome 14 (optionally the additional mutation being a guanine); and/or (ii) position 106,330,068 on human chromosome 14 (optionally the additional mutation being a thymine).
Optionaly the plurality comprises a human JH5 gene variant of SEQ I D NO: 1, wherein the variant comprises a guanine at a position corresponding to position 106,330,066 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
Optionally the variant comprises additionally a mutation at a position corresponding to (i) position
106.330.067 on human chromosome 14 (optionally the additional mutation being a guanine); and/or (ii) position 106,330,068 on human chromosome 14 (optionally the additional mutation being a thymine).
Optionally the plurality comprises a human JH5 gene variant of SEQ ID NO: 1, wherein the variant comprises a thymine at a position corresponding to position 106,330,068 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
Optionally the variant comprises additionally a mutation at a position corresponding to (i) position 106,330,067 on human chromosome 14 (optionally the additional mutation being a guanine); and/or (ii) position 106,330,066 on human chromosome 14 (optionally the additional mutation being a guanine).
Optionally the plurality comprises a human JH5 gene variant of SEQ ID NO: 1, wherein the variant comprises a cytosine at a position corresponding to position 106,330,027 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
Optionally the plurality comprises a human JH5 gene variant of SEQ ID NO: 1, wherein the variant comprises an adenine at a position corresponding to position 106,330,024 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
Optionally the plurality comprises a human JH5 gene variant of SEQ ID NO: 1, wherein the variant comprises a thymine at a position corresponding to position 106,330,032 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
Optionally the plurality comprises a human JH5 gene variant of SEQ ID NO: 1, wherein the variant comprises a thymine at a position corresponding to position 106,330,041 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
Optionally the plurality comprises a human JH5 gene variant of SEQ ID NO: 1, wherein the variant comprises an adenine or thymine at a position corresponding to position 106,330,063 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
Optionally the variant comprises additionally a mutation at a position corresponding to position 106,330,071 on human chromosome 14 (optionally the additional mutation being a guanine).
Optionally the plurality comprises a human JH5 gene variant of SEQ ID NO: l,wherein the variant comprises a cytosine at a position corresponding to position 106,330,062 on human chromosome
14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
Optionally the genome comprises SEQ ID NO:l; optionally in cis at the same Ig locus as one, two or more of the variants.
JH6
An embodiment provides a vertebrate, cell or population of the invention whose genome comprises a plurality of JH6 gene segments, wherein the plurality comprises a human JH6 gene variant of SEQ ID NO: 2, wherein the variant comprises a nucleotide mutation at one or more positions corresponding to positions
106,329,411
106,329,413
106,329,414
106,329,417
106,329,419
106,329,426
106,329,434
106,329,435, and
106,329,468
on human chromosome 14.
Optionally the genome of the vertebrate, cell or population comprises a plurality of JH6 gene segments, wherein the plurality comprises a human JH6 gene variant of SEQ ID NO: 2, wherein the variant comprises a guanine at a position corresponding to position 106,329,435 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 2.
Optionally the variant comprises additionally a mutation at a position corresponding to (i) position 106,329,468 on human chromosome 14 (optionally the additional mutation being a guanine); (ii) position 106,329,419 on human chromosome 14 (optionally the additional mutation being an adenine); (iii) position 106,329,434 on human chromosome 14 (optionally the additional mutation
being a cytosine) and/or position 106,329,414 on human chromosome 14 (optionally the additional mutation being a guanine); (iv) position 106,329,426 on human chromosome 14 (optionally the additional mutation being an adenine); (v) position 106,329,413 on human chromosome 14 (optionally the additional mutation being an adenine); (vi) position 106,329,417 on human chromosome 14 (optionally the additional mutation being a thymine); (vii) position 106,329,411 on human chromosome 14 (optionally the additional mutation being a thymine); (viii) position 106,329,451 on human chromosome 14 (optionally the additional mutation being an adenine); (ix) position 106,329,452 on human chromosome 14 (optionally the additional mutation being a cytosine); and/or (x) position 106,329,453 on human chromosome 14 (optionally the additional mutation being a cytosine).
Optionally the variant comprises additionally mutations at positions corresponding to position
106.329.451 on human chromosome 14, the additional mutation being an adenine; position
106.329.452 on human chromosome 14, the additional mutation being a cytosine; and position
106.329.453 on human chromosome 14, the additional mutation being a cytosine.
The vertebrate, cell or population optionally comprises a plurality of JH6 gene segments,, wherein the plurality comprises a human JH6 gene variant of SEQ ID NO: 2, wherein the variant comprises a guanine at a position corresponding to position 106,329,468 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 2.
Optionally the variant comprises additionally a mutation at a position corresponding to position 106,329,435 on human chromosome 14 (optionally the additional mutation being a guanine).
Optionally the vertebrate, cell or population comprises a plurality of JH6 gene segments,, wherein the plurality comprises a human JH6 gene variant of SEQ ID NO: 2, wherein the variant comprises a thymine at a position corresponding to position 106,329,417 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 2.
Optionally the variant comprises additionally a mutation at a position corresponding to position 106,329,435 on human chromosome 14 (optionally the additional mutation being a guanine).
Optionally the vertebrate, cell or population comprises a plurality of JH6 gene segments,, wherein the plurality comprises a human JH6 gene variant of SEQ ID NO: 2, wherein the variant comprises a
cytosine at a position corresponding to position 106,329,434 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 2.
Optionally the variant comprises additionally a mutation at a position corresponding to (i) position 106,329,414 on human chromosome 14 (optionally the additional mutation being a guanine); and/or (ii) position 106,329,435 on human chromosome 14 (optionally the additional mutation being a guanine).
Optionally the vertebrate, cell or population comprises a plurality of JH6 gene segments, wherein the plurality comprises a human JH6 gene variant of SEQ ID NO: 2, wherein the variant comprises a thymine at a position corresponding to position 106,329,411 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 2.
Optionally the variant comprises additionally a mutation at a position corresponding to position 106,329,435 on human chromosome 14 (optionally the additional mutation being a guanine).
Optionally the vertebrate, cell or population comprises a plurality of JH6 gene segments, wherein the plurality comprises a human JH6 gene variant that is an antisense sequence of a variant described above.
Optionally the genome comprises SEQ ID NO:2; optionally cis at the same Ig locus as one, two or more of the JH6 variants.
JH2
An embodiment provides a vertebrate, cell or population of the invention whose genome comprises a plurality of JH2 gene segments, wherein the plurality comprises a human JH2 gene variant of SEQ ID NO: 3, wherein the variant comprises a nucleotide mutation at one or more positions
corresponding to positions
106,331,455
106,331,453, and
106,331,409
on human chromosome 14.
Optionally the vertebrate, cell or population comprises said plurality of JH2 gene segments, wherein the plurality comprises a human JH2 gene variant of SEQ ID NO: 3, wherein the variant comprises a guanine at a position corresponding to position 106,331,455 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 3.
Optionally the variant comprises additionally a mutation at a position corresponding to (i) position 106,331,453 on human chromosome 14 (optionally the additional mutation being an adenine); and/or (ii) position 106,331,409 on human chromosome 14 (optionally the additional mutation being an adenine); (iii) position 106,329,434 on human chromosome 14 (optionally the additional mutation being an adenine).
Optionally the vertebrate, cell or population comprises a plurality of JH2 gene segments, wherein the plurality comprises a human JH2 gene variant of SEQ ID NO: 3, wherein the variant comprises an adenine at a position corresponding to position 106,331,453 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 3.
Optionally the variant comprises additionally a mutation at a position corresponding to position 106,331,409 on human chromosome 14 (optionally the additional mutation being an adenine).
Optionally the vertebrate, cell or population comprises a plurality of JH2 gene segments, wherein the plurality comprises a human JH2 gene variant of SEQ ID NO: 3, wherein the variant comprises an adenine at a position corresponding to position 106,331,409 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 3.
Optionally the vertebrate, cell or population comprises a plurality of JH2 gene segments, wherein the plurality comprises a human JH2 gene variant that is an antisense sequence of a variant described above.
Optionally the genome comprises SEQ ID NO:3; optionally cis at the same Ig locus as one, two or more of the JH2 variants.
Optionally the vertebrate, cell or population genome comprises two or more different JH gene segments selected from SEQ ID NOs: 1 to 3 and variants described above; optionally wherein said JH gene segments are cis at the same immunoglobulin Ig locus.
Multiple Human D Gene Segment Variants
A specific application of this configuration is the provision of multiple human D gene segments as follows (as set out in numbered clauses, starting at clause number 154).
154. A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) having a genome comprising at least 3 human D gene segments of the same type (eg, D2-2 gene segments), wherein at least two of the human D gene segments are variants that are not identical to each other (eg, D2-2ref and D2-2a).
In an example of any aspect of the sixth configuration of the invention (V, D, J or C), one or more or all of the variants are naturally-occurring human gene segments.
In an example of any aspect of the sixth configuration of the invention (V, D, J or C), one or more of the variants may be a synthetic variant of a human gene segment.
155. A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) having a genome comprising at least 2 different non-endogenous D gene segments of the same type type (eg, D2-2ref and D2-2a) cis at the same Ig locus.
156. A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) having a genome comprising at least 2 different human D gene segments of the same type (eg, D2-2ref and D2-2a) trans at the same Ig locus; and optionally a third human D gene segment (eg, (eg, D2-2ref, D2-2a or D2-2b) of the same type, wherein the third D is cis with one of said 2 different D gene segments.
157. A population of non-human vertebrates (eg, mice or rats) comprising a repertoire of human D gene segments, wherein the plurality comprises at least 2 different human D gene segments of the same type (eg, D2-2 gene segments), a first of said different D gene segments (eg, D2-2ref) is provided in the genome of a first vertebrate of the population, and a second of said different D gene segment (eg, D2-2a) being provided in the genome of a second vertebrate of the
population, wherein the genome of the first vertebrate does not comprise the second D gene segment.
158. A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) having a genome comprising at least 2 different non-endogenous D gene segments of the same type (eg, human D2-2 gene segments), wherein the D gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
159. A method of enhancing the human immunoglobulin gene diversity of a non-human
vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising at least 3 human D gene segments of the same type (eg, D2-2 gene segments), wherein at least two of the human D gene segments are variants that are not identical to each other (eg, D2-2ref and D2-2a).
160. A method of enhancing the immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising at least 2 different non-endogenous D gene segments of the same type (eg, human D2-2 gene segments) cis at the same Ig locus.
161. A method of enhancing the immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising at least 2 different human D gene segments of the same type (eg, D2-2ref and D2-2a) trans at the same Ig locus; and optionally a third human D gene segment (eg, D2-2ref, D2-2a or D2-2b) of the same type, wherein the third D is cis with one of said 2 different D gene segments.
162. A method of providing an enhanced human immunoglobulin D gene segment repertoire, the method comprising providing a population of non-human vertebrates (eg, a mouse or rat) comprising a repertoire of human D gene segments, wherein the method comprises providing at least 2 different human D gene segments of the same type (eg, D2-2ref and D2-2a), wherein a first of said different D gene segments is provided in the genome of a first vertebrate of the population, and a second of said different D gene segments is provided in the genome of a second vertebrate of the population, wherein the genome of the first vertebrate does not
comprise the second D gene segment.
163. A method of enhancing the human immunoglobulin gene diversity of a non-human
vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising at least 2 different non-endogenous D gene segments of the same type (eg, D2-2ref and D2-2a), wherein the D gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
164. The vertebrate or cell of clause 154, 156 or 158, or the method of clause 159, 161 or 163, wherein at least 2 or 3 of said different gene segments are provided cis at the same Ig locus in said genome.
165. The vertebrate or cell of clause 154, 155 or 156, or the method of any one of clauses 159 to 162 and 164, wherein the D gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
166. The vertebrate or cell of any one of clauses 154 to 157, or the method of any one of clauses 159 to 162 and 165, wherein the D gene segments are derived from the genome sequence of two or more different human individuals; optionally wherein the different human individuals are from different human populations.
167. The vertebrate, cell or method of clause 166, wherein the individuals are not genetically related.
168. The vertebrate, cell or method of any one of clauses 154 to 167, wherein at least one of the different D segments is a synthetic mutant of a human germline D gene segment.
169. A method of enhancing the human immunoglobulin gene diversity of a non-human
vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising at least 2 human D gene segments of the same type (eg, D2-2ref and D2-2a), wherein the D gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations; optionally wherein at least 2 or 3 of said different gene segments are provided at the same IgH locus in said genome.
170. The vertebrate or cell of any one of clauses 154 to 158 and 164 to 168, wherein the genome comprises a substantially complete functional repertoire of human D gene segment types supplemented with one, two or more variant human D gene segments, wherein said substantially complete functional repertoire and the supplementary D gene segments are not found together in the germline genome of a human individual.
171. The population of clause 157, wherein the population comprises a substantially complete functional repertoire of human D gene segment types supplemented with one, two or more variant human D gene segments, wherein said substantially complete functional repertoire and the supplementary D gene segments are not found together in the germline genome of a human individual.
172. A non-human vertebrate (eg, a mouse or rat) or a non-human cell (eg, an ES cell or a B-cell) having a genome comprising a substantially complete functional repertoire of human D gene segment types supplemented with one, two or more variant human D gene segments, wherein said substantially complete functional repertoire and the supplementary D gene segments are not found together in the germline genome of a human individual.
173. A population of non-human vertebrates (eg, mice or rats) comprising a substantially
complete functional repertoire of human JH gene segment types supplemented with one, two or more variant human D gene segments, wherein said substantially complete functional repertoire and the supplementary D gene segments are not found together in the germline genome of a human individual.
174. The vertebrate or cell of clause 172 or the population of clause 173, comprising first and second D gene segments selected from
D2-2ref and D2-2a; or
D2-21ref and D2-21a; or
D3-10ref and D3-10a; or
D3-16ref and D3-16a; or
D2-8ref and D2-8a; or
D3-3ref and D3-3a; or
D4-23ref and D4-23a; or
D6-13ref and D6-13a; or
D3-9ref and D3-9a; or
D4-4ref and D4-4a; or
D7-27ref and D7-27a;
Optionally wherein the first and/or second D gene segment is present in two or more copies.
For example, there are provided two or three copies of the first gene segment, optionally with one, two or three copies of the second gene segment. Copies can be arranged in cis or trans.
175. The vertebrate, cell or population of clause 174, comprising human gene segments D2-2ref and D2-2a; and D3-3ref and D3-3a; and optionally also D2-15.
In an example, the vertebrate, cell or population comprises one or more D segments selected from human D3-3, D2-15, D3-9; D4-17; D3-10; D2-2; D5-24; D6-19; D3-22; D6-13; D5-12; Dl-26; Dl-20; D5-18; D3-16; D2-21; Dl-14; D7-27; Dl-1; D6-25; D2-14 and D4-23 (eg, selected from D3- 9*01; D4-17*01; D3-10*01; D2-2*02; D5-24*01; D6-19*01; D3-22*01; D6-13*01; D5-12*01; Dl- 26*01; Dl-20*01; D5-18*01; D3-16*02; D2-21*02; Dl-14*01; D7-27*02; Dl-l*01; D6-25*01; D2-15*01; and D4-23*01), together with the reference sequence(s) of said selected segment(s). These were found in variable domains having a HCD 3 length of at least 20 amino acids (see examples herein).
176. A non-human vertebrate or vertebrate cell according to clause 155, comprising a genome that comprises VH, D and JH gene repertoires comprising human gene segments, the D gene repertoire comprising one or more of a plurality of D2-2 gene segments provided by at least 2 different D2-2 gene segments in cis at the same Ig locus in said genome;
a plurality of D2-21 gene segments provided by at least 2 different D2-21 gene segments in cis at the same Ig locus in said genome;
a plurality of D3-10 gene segments provided by at least 2 different D3-10 gene segments in cis at the same Ig locus in said genome;
a plurality of D3-16 gene segments provided by at least 2 different D3-16 gene segments in cis at the same Ig locus in said genome;
a plurality of D2-8 gene segments provided by at least 2 different D2-8 gene segments in cis at the same Ig locus in said genome;
a plurality of D3-3 gene segments provided by at least 2 different D3-3 gene segments in cis at the same Ig locus in said genome;
a plurality of D4-23 gene segments provided by at least 2 different D4-23 gene segments in cis at the same Ig locus in said genome;
a plurality of D6-13 gene segments provided by at least 2 different D6-13 gene segments in cis at the same Ig locus in said genome;
a plurality of D3-9 gene segments provided by at least 2 different D3-9 gene segments in cis at the same Ig locus in said genome;
a plurality of D4-4 gene segments provided by at least 2 different D4-4 gene segments in cis at the same Ig locus in said genome; and
a plurality of D7-27 gene segments provided by at least 2 different D7-27 gene segments in cis at the same Ig locus in said genome; optionally wherein the D gene segments are derived from the genome sequence of two or more different human individuals. . A non-human vertebrate or vertebrate cell according to clause 155, comprising a genome that comprises VH, D and JH gene repertoires comprising human gene segments, the D gene repertoire comprising one or more of a plurality of D2-2 gene segments provided by at least 2 different D2-2 gene segments in trans in said genome;
a plurality of D2-21 gene segments provided by at least 2 different D2-21 gene segments in trans in said genome;
a plurality of D3-10 gene segments provided by at least 2 different D3-10 gene segments in trans in said genome;
a plurality of D3-16 gene segments provided by at least 2 different D3-16 gene segments in trans in said genome;
a plurality of D2-8 gene segments provided by at least 2 different D2-8 gene segments in trans in said genome;
a plurality of D3-3 gene segments provided by at least 2 different D3-3 gene segments in trans in said genome;
a plurality of D4-23 gene segments provided by at least 2 different D4-23 gene segments in trans in said genome;
a plurality of D6-13 gene segments provided by at least 2 different D6-13 gene segments in trans in said genome;
a plurality of D3-9 gene segments provided by at least 2 different D3-9 gene segments in trans in said genome;
a plurality of D4-4 gene segments provided by at least 2 different D4-4 gene segments in trans in said genome; and
a plurality of D7-27 gene segments provided by at least 2 different D7-27 gene segments in trans in said genome; optionally wherein the D gene segments are derived from the genome sequence of two or more different human individuals.
A non-human vertebrate or vertebrate cell (optionally an ES cell or B-cell), according to clause 154, comprising a genome that comprises VH, D and JH gene repertoires comprising human gene segments, the D gene repertoire comprising one or more of a plurality of D2-2 gene segments provided by at least 3 different D2-2 gene segments;
a plurality of D2-21 gene segments provided by at least 3 different D2-21 gene segments;
a plurality of D3-10 gene segments provided by at least 3 different D3-10 gene segments;
a plurality of D3-16 gene segments provided by at least 3 different D3-16 gene segments;
a plurality of D2-8 gene segments provided by at least 3 different D2-8 gene segments;
a plurality of D3-3 gene segments provided by at least 3 different D3-3 gene segments;
a plurality of D4-23 gene segments provided by at least 3 different D4-23 gene segments;
a plurality of D6-13 gene segments provided by at least 3 different D6-13 gene segments;
a plurality of D3-9 gene segments provided by at least 3 different D3-9 gene segments;
a plurality of D4-4 gene segments provided by at least 3 different D4-4 gene segments; and a plurality of D7-27 gene segments provided by at least 3 different D7-27 gene segments; optionally wherein the D gene segments are derived from the genome sequence of two or three different human individuals; optionally wherein at least 2 or 3 of said different gene segments are provided in cis at the same
Ig locus in said genome.
179. The vertebrate or cell of clause 176, 177 or 178, wherein the different human individuals are from different human populations.
180. The vertebrate or cell of any one of clauses 176 to 179, wherein the individuals are not genetically related.
181. The vertebrate or cell of any one of clauses 176 to 180, wherein at least one of the different D segments is a synthetic mutant of a human germline D gene segment.
182. A non-human vertebrate or vertebrate cell (optionally an ES cell or B-cell) according to clause 158, comprising a genome comprising human VH, D and JH gene repertoires, the D gene repertoire comprising of one or more of a plurality of D2-2 gene segments provided by at least 2 different D2-2 gene ; optionally in cis in said genome;
a plurality of D2-21 gene segments provided by at least 2 different D2-21 gene ; optionally in cis in said genome;
a plurality of D3-10 gene segments provided by at least 2 different D3-10 gene ; optionally in cis in said genome;
a plurality of D3-16 gene segments provided by at least 2 different D3-16 gene ; optionally in cis in said genome;
a plurality of D2-8 gene segments provided by at least 2 different D2-8 gene ; optionally in cis in said genome;
a plurality of D3-3 gene segments provided by at least 2 different D3-3 gene ; optionally in cis in said genome;
a plurality of D4-23 gene segments provided by at least 2 different D4-23 gene ; optionally in cis in said genome;
a plurality of D6-13 gene segments provided by at least 2 different D6-13 gene ; optionally in cis in said genome;
a plurality of D3-9 gene segments provided by at least 2 different D3-9 gene ; optionally in cis in said genome;
a plurality of D4-4 gene segments provided by at least 2 different D4-4 gene ; optionally in cis in
said genome; and
a plurality of D7-27 gene segments provided by at least 2 different D7-27 gene ; optionally in cis in said genome; wherein the D gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
183. The vertebrate or cell of clause 182, wherein the human individuals are from different
human populations.
184. The vertebrate, cell or population of any one of clauses 154 to 183, wherein one or more of the D gene segments is a variant of a human germline D gene segment, wherein the variant gene segment encodes an amino acid sequence that differs by 1, 2 or 3 amino acids from the corresponding amino acid sequence encoded by the human germline D gene segment, provided in that said amino acid sequence encoded by the variant does not include a stop codon when said corresponding amino acid sequence does not include a stop codon.
Optionally, the variant and germline D gene segments encode the respective amino acid sequences in reading frame 2 (IMGT numbering). See Briney et al 2012.
185. The vertebrate, cell or population of clause 184, wherein said corresponding amino acid sequence encoded by the human germline D gene segment is a hydrophilic or hydrophobic sequence (according to J Mol Biol. 1997 Jul 25;270(4):587-97; Corbett SJ et al; Table 2).
186. The vertebrate, cell or population of clause 184 or 185, comprising said variant and said germline human D gene segments; optionally wherein the variant and germline human D gene segments are cis on the same chromosome.
187. The vertebrate, cell or population of any one of clauses 184 to 186, wherein germline human D gene segment is a D2, D3, D5 or D6 family gene segment; optionally a D2-2, D2-15, D3-3, D3-9, D3-10, D3-22, D5-5, D5-18, D6-6, D6-13, D6-19 gene segment.
These D segments are usable in all three reading frames.
Optionally a variant of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or all of these human germline D gene segments is used.
188. The vertebrate, cell or population of any one of clauses 154 to 187, comprising a plurality of D2-2 gene segments, wherein the plurality comprises D2-2 gene segments that vary from each other at one or more nucleotide positions corresponding to positions
106,382,687 and
106,382,711
on human chromosome 14.
189. The vertebrate, cell or population of clause 188, wherein the plurality comprises a human D2-2 gene segment ((optionally two copies and/or in homozygous state) comprising a thymine at a position corresponding to position 106,382,687 on human chromosome 14; and optionally no further mutation from the sequence of D2-2ref.
190. The vertebrate, cell or population of clause 188 or 189, wherein the plurality comprises a human D2-2 gene segment comprising a cytosine at a position corresponding to position 106,382,687 on human chromosome 14; and optionally no further mutation from the sequence of D2-2a.
191. The vertebrate, cell or population of any one of clauses 188 to 190, wherein the plurality comprises a human D2-2 gene segment comprising an adenine at a position corresponding to position 106,382,711 on human chromosome 14; and optionally no further mutation from the sequence of D2-2b.
192. The vertebrate, cell or population of any one of clauses 188 to 191, wherein the plurality comprises a human D2-2 gene segment comprising an thymine at a position corresponding to position 106,382,711 on human chromosome 14; and optionally no further mutation from the sequence of D2-2ref.
193. The vertebrate, cell or population of any one of clauses 154 to 192, comprising a plurality of D7-27 gene segments, wherein the plurality comprises D7-27 gene segments that vary from each other at a nucleotide position corresponding to position 106,331,767 on human chromosome 14.
194. The vertebrate, cell or population of clause 193, wherein the plurality comprises a human D7-27 gene segment (optionally two copies and/or in homozygous state) comprising a cytosine at a position corresponding to position 106,331,767 on human chromosome 14; and optionally no further mutation from the sequence of D7-27ref.
195. The vertebrate, cell or population of clause 193 or 194, wherein the plurality comprises a human D7-27 gene segment comprising a guanine at a position corresponding to position 106,331,767 on human chromosome 14; and optionally no further mutation from the sequence of D7-27a.
196. The vertebrate, cell or population of any one of clauses 154 to 195, comprising a plurality of D4-23 gene segments, wherein the plurality comprises D4-23 gene segments that vary from each other at a nucleotide position corresponding to position 106,350,740 on human chromosome 14.
197. The vertebrate, cell or population of clause 196, wherein the plurality comprises a human D4-23 gene segment (optionally two copies and/or in homozygous state) comprising an adenine at a position corresponding to position 106,350,740 on human chromosome 14; and optionally no further mutation from the sequence of D4-23ref.
198. The vertebrate, cell or population of clause 196 or 197, wherein the plurality comprises a human D4-23 gene segment (optionally two copies and/or in homozygous state) comprising an guanine at a position corresponding to position 106,350,740 on human chromosome 14; and optionally no further mutation from the sequence of D4-23a.
199. The vertebrate, cell or population of any one of clauses 154 to 197, comprising a plurality of D2-21 gene segments, wherein the plurality comprises D2-21 gene segments that vary from each other at a nucleotide position corresponding to position 106,354,418 on human chromosome 14.
200. The vertebrate, cell or population of clause 199, wherein the plurality comprises a human D2-21 gene segment (optionally two copies and/or in homozygous state) comprising an adenine
at a position corresponding to position 106,354,418 on human chromosome 14; and optionally no further mutation from the sequence of D2-21ref.
201. The vertebrate, cell or population of clause 199 or 200, wherein the plurality comprises a human D2-21 gene segment (optionally two copies and/or in homozygous state) comprising a guanine at a position corresponding to position 106,354,418 on human chromosome 14; and optionally no further mutation from the sequence of D2-21a.
202. The vertebrate, cell or population of any one of clauses 154 to 201, comprising a plurality of D3-16 gene segments, wherein the plurality comprises D3-16 gene segments that vary from each other at a nucleotide position corresponding to position 106,354,418 on human chromosome 14.
203. The vertebrate, cell or population of clause 202, wherein the plurality comprises a human D3-16 gene segment (optionally two copies and/or in homozygous state) comprising a thymine at a position corresponding to position 106,361,515 on human chromosome 14; and optionally no further mutation from the sequence of D3-16ref.
204. The vertebrate, cell or population of clause 202 or 203, wherein the plurality comprises a human D3-16 gene segment (optionally two copies and/or in homozygous state) comprising a cytosine at a position corresponding to position 106,361,515 on human chromosome 14; and optionally no further mutation from the sequence of D3-16a.
205. The vertebrate, cell or population of any one of clauses 154 to 204, comprising a plurality of D6-13 gene segments, wherein the plurality comprises D6-13 gene segments that vary from each other at a nucleotide position corresponding to position 106,367,013 on human chromosome 14.
206. The vertebrate, cell or population of clause 205, wherein the plurality comprises a human D6-13 gene segment (optionally two copies and/or in homozygous state) comprising a thymine at a position corresponding to position 106,367,013 on human chromosome 14; and optionally no further mutation from the sequence of D6-13ref.
207. The vertebrate, cell or population of clause 205 or 206, wherein the plurality comprises a human D6-13 gene segment (optionally two copies and/or in homozygous state) comprising a cytosine at a position corresponding to position 106,367,013 on human chromosome 14; and optionally no further mutation from the sequence of D6-13a.
208. The vertebrate, cell or population of any one of clauses 154 to 207, comprising a plurality of D3-10 gene segments, wherein the plurality comprises D3-10 gene segments that vary from each other at one or more nucleotide positions corresponding to positions
106,370,370 and
106,370,371
on human chromosome 14.
209. The vertebrate, cell or population of clause 208, wherein the plurality comprises a human D3-10 gene segment (optionally two copies and/or in homozygous state) comprising a thymine at a position corresponding to position 106,370,370 on human chromosome 14; and optionally no further mutation from the sequence of D3-10ref.
210. The vertebrate, cell or population of clause 208 or 209, wherein the plurality comprises a human D3-10 gene segment (optionally two copies and/or in homozygous state) comprising a cytosine at a position corresponding to position 106,370,370 on human chromosome 14; and optionally no further mutation from the sequence of D3-10a.
211. The vertebrate, cell or population of clause 208, 209 or 210 wherein the plurality comprises a human D3-10 gene segment (optionally two copies and/or in homozygous state) comprising an adenine at a position corresponding to position 106,370,371 on human chromosome 14; and optionally no further mutation from the sequence of D3-10ref.
212. The vertebrate, cell or population of any one of clauses 208 to 211, wherein the plurality comprises a human D3-10 gene segment (optionally two copies and/or in homozygous state) comprising a guanine at a position corresponding to position 106,370,371 on human chromosome 14; and optionally no further mutation from the sequence of D3-10b.
213. The vertebrate, cell or population of any one of clauses 154 to 212, comprising a plurality of D3-9 gene segments, wherein the plurality comprises D3-9 gene segments that vary from each
other at a nucleotide position corresponding to position 106,370,567 on human chromosome 14.
214. The vertebrate, cell or population of clause 213, wherein the plurality comprises a human D3-9 gene segment (optionally two copies and/or in homozygous state) comprising an adenine at a position corresponding to position 106,370,567 on human chromosome 14; and optionally no further mutation from the sequence of D3-9ref.
215. The vertebrate, cell or population of clause 213 or 214, wherein the plurality comprises a human D3-9 gene segment (optionally two copies and/or in homozygous state) comprising a thymine at a position corresponding to position 106,370,567 on human chromosome 14; and optionally no further mutation from the sequence of D3-9a.
216. The vertebrate, cell or population of any one of clauses 154 to 215, comprising a plurality of D2-8 gene segments, wherein the plurality comprises D2-8 gene segments that vary from each other at one or more nucleotide positions corresponding to positions
106,373,085;
106,373,086 and
106,373,089
on human chromosome 14.
217. The vertebrate, cell or population of clause 216, wherein the plurality comprises a human D2-8 gene segment (optionally two copies and/or in homozygous state) comprising a cytosine at a position corresponding to position 106,373,085 on human chromosome 14.
218. The vertebrate, cell or population of clause 216 or 217, wherein the plurality comprises a human D2-8 gene segment (optionally two copies and/or in homozygous state) comprising a thymine at a position corresponding to position 106,373,085 on human chromosome 14; and optionally no further mutation from the sequence of D2-8b.
219. The vertebrate, cell or population of clause 216, 217 or 218 wherein the plurality comprises a human D2-8 gene segment (optionally two copies and/or in homozygous state) comprising a cytosine at a position corresponding to position 106,373,086 on human chromosome 14; and
optionally no further mutation from the sequence of D2-8ref.
220. The vertebrate, cell or population of any one of clauses 216 to 219, wherein the plurality comprises a human D2-8 gene segment comprising a thymine at a position corresponding to position 106,373,086 on human chromosome 14; and optionally no further mutation from the sequence of D2-8ref.
221. The vertebrate, cell or population of any one of clauses 154 to 220, comprising a plurality of D4-4 gene segments, wherein the plurality comprises D4-4 gene segments that vary from each other at one or more nucleotide positions corresponding to positions
106,379,086; and
106,379,089
on human chromosome 14.
222. The vertebrate, cell or population of clause 221, wherein the plurality comprises a D4-4 gene segment (optionally two copies and/or in homozygous state) comprising a cytosine at a position corresponding to position 106,379,086 on human chromosome 14; and optionally no further mutation from the sequence of D4-4ref.
223. The vertebrate, cell or population of clause 221 or 222, wherein the plurality comprises a human D4-4 gene segment (optionally two copies and/or in homozygous state) comprising a thymine at a position corresponding to position 106,379,086 on human chromosome 14; and optionally no further mutation from the sequence of D4-4a.
224. The vertebrate, cell or population of clause 221, 222 or 223 wherein the plurality comprises a human D4-4 gene segment (optionally two copies and/or in homozygous state) comprising a cytosine at a position corresponding to position 106,379,089 on human chromosome 14; and optionally no further mutation from the sequence of D4-4ref or a cytosine at a position corresponding to position 106,379,086 on human chromosome 14.
225. The vertebrate, cell or population of any one of clauses 221 to 224, wherein the plurality comprises a human D4-4 gene segment (optionally two copies and/or in homozygous state) comprising a thymine at a position corresponding to position 106,373,089 on human
chromosome 14; and optionally no further mutation from the sequence of D4-4a.
226. The vertebrate, cell or population of any one of clauses 154 to 225, comprising a plurality of D3-3 gene segments, wherein the plurality comprises D3-3 gene segments that vary from each other at one or more nucleotide positions corresponding to positions
106,380,241; and
106,380,246
on human chromosome 14.
227. The vertebrate, cell or population of clause 226, wherein the plurality comprises a D3-3 gene segment (optionally two copies and/or in homozygous state) comprising a thymine at a position corresponding to position 106,380,241 on human chromosome 14; and optionally no further mutation from the sequence of D3-3ref.
228. The vertebrate, cell or population of clause 226 or 227, wherein the plurality comprises a human D3-3 gene segment (optionally two copies and/or in homozygous state) comprising a cytosine at a position corresponding to position 106,380,241 on human chromosome 14; and optionally no further mutation from the sequence of D3-3a.
229. The vertebrate, cell or population of clause 226, 227 or 228 wherein the plurality comprises a human D3-3 gene segment (optionally two copies and/or in homozygous state) comprising an adenine at a position corresponding to position 106,380,246 on human chromosome 14; and optionally no further mutation from the sequence of D3-3ref.
230. The vertebrate, cell or population of any one of clauses 226 to 229, wherein the plurality comprises a human D3-3 gene segment (optionally two copies and/or in homozygous state) comprising a thymine at a position corresponding to position 106,380,246 on human chromosome 14; and optionally no further mutation from the sequence of D3-3a.
Multiple Human JL Gene Segment Variants
A specific application of this configuration is the provision of multiple human JL gene segments ( and/or i\) as follows (as set out in numbered paragraphs, starting at paragraph number 80).
80. A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) having a genome comprising at least 3 human JL gene segments of the same type (eg, JKI), wherein at least two of the human J L gene segments are variants that are not identical to each other.
81. A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) having a genome comprising at least 2 different non-endogenous JL gene segments of the same type (eg, JKI) cis at the same Ig locus.
82. A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) having a genome comprising at least 2 different human JL gene segments of the same type (eg, JKI) trans at the same Ig locus; and optionally a third human JL gene segment of the same type, wherein the third JL is cis with one of said 2 different JL gene segments.
83. A population of non-human vertebrates (eg, mice or rats) comprising a repertoire of human JL gene segments, wherein the plurality comprises at least 2 different human JL gene segments of the same type (eg, JKI), a first of said different J L gene segments is provided in the genome of a first vertebrate of the population, and a second of said different JL gene segments being provided in the genome of a second vertebrate of the population, wherein the genome of the first vertebrate does not comprise the second JL gene segment.
84. A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) having a genome comprising at least 2 different non-endogenous JL gene segments of the same type (eg, JKI), wherein the JL gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
85. A method of enhancing the human immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising at least 3 human JL gene segments of the same type (eg, JKI), wherein at least two of the human JL gene segments are variants that are not identical to each other.
86. A method of enhancing the immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising at least 2 different non-endogenous JL gene segments of the same type (eg, JKI) cis at the same Ig
locus.
87. A method of enhancing the immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising at least 2 different human JL gene segments of the same type(eg, JKI) trans at the same Ig locus; and optionally a third human JL gene segment of the same type, wherein the third JL is cis with one of said 2 different J L gene segments.
88. A method of providing an enhanced human immunoglobulin JL gene segment repertoire, the method comprising providing a population of non-human vertebrates (eg, a mouse or rat) comprising a repertoire of human JL gene segments, wherein the method comprises providing at least 2 different human JL gene segments of the same type (eg, JKI), wherein a first of said different JL gene segments is provided in the genome of a first vertebrate of the population, and a second of said different J L gene segments is provided in the genome of a second vertebrate of the population, wherein the genome of the first vertebrate does not comprise the second JL gene segment.
89. A method of enhancing the human immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising at least 2 different non-endogenous JL gene segments of the same type (eg, JKI), wherein the JL gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
90. The vertebrate or cell of paragraph 80, 82 or 84, or the method of paragraph 85, 82 or 89,
wherein at least 2 or 3 of said different gene segments are provided cis at the same Ig locus in said genome.
91. The vertebrate or cell of paragraph 80, 81 or 82, or the method of paragraph 85, 86 or 87,
wherein the JL gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
92. The vertebrate or cell of paragraph 80, 81 or 82, or the method of paragraph 85, 86 or 87,
wherein the JL gene segments are derived from the genome sequence of two or more different human individuals; optionally wherein the different human individuals are from different human
populations.
93. The vertebrate, cell or method of paragraph 92, wherein the individuals are not genetically related.
94. The vertebrate, cell or method of any one of paragraphs 80 to 93, wherein at least one of the different J L segments is a synthetic mutant of a human germline J L gene segment.
95. A method of enhancing the human immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising at least 2 human J L gene segments of the same type (eg, JKI), wherein the J L gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations; optionally wherein at least 2 or 3 of said different gene segments are provided at the same IgL locus in said genome.
96. The vertebrate or cell of any one of paragraphs paragraph 80 to 82 and 84, wherein the genome comprises a substantially complete functional repertoire of human JK and/or iX gene segment types supplemented with one, two or more human JK and/or iX gene segments respectively, wherein said substantially complete functional repertoire and the supplementary gene segments are not found together in the germline genome of a human individual.
97. The population of paragraph 83, wherein the population comprises a substantially complete functional repertoire of human J L gene segment types supplemented with one, two or more human JK and/or iX gene segments respectively, wherein said substantially complete functional repertoire and the supplementary gene segments are not found together in the germline genome of a human individual.
98. A non-human vertebrate (eg, a mouse or rat) or a non-human cell (eg, an ES cell or a B-cell) having a genome comprising a substantially complete functional repertoire of human JK and/or iX gene segment types supplemented with one, two or more human JK and/or iX gene segments respectively, wherein said substantially complete functional repertoire and the supplementary gene segments are not found together in the germline genome of a human individual.
A population of non-human vertebrates (eg, mice or rats) comprising a substantially complete functional repertoire of human JK and/or iX gene segment types supplemented with one, two or more human JK and/or iX gene segments respectively, wherein said substantially complete functional repertoire and the supplementary gene segments are not found together in the germline genome of a human individual.
A non-human vertebrate or vertebrate cell according to paragraph 81, comprising a genome that comprises VL and J L gene repertoires comprising human gene segments, the J L gene repertoire comprising a plurality of human JKI gene segments provided by at least 2 different human JKI gene segments in cis at the same Ig locus in said genome;
a plurality of human JK2 gene segments provided by at least 2 different human JKI gene segments in cis at the same Ig locus in said genome;
a plurality of human JK3 gene segments provided by at least 2 different human JKI gene segments in cis at the same Ig locus in said genome;
a plurality of human JK4 gene segments provided by at least 2 different human JKI gene segments in cis at the same Ig locus in said genome;
a plurality of human JK5 gene segments provided by at least 2 different human JKI gene segments in cis at the same Ig locus in said genome;
a plurality of human J\l gene segments provided by at least 2 different human J\l gene segments in cis at the same Ig locus in said genome;
a plurality of human J\2 gene segments provided by at least 2 different human J\2 gene segments in cis at the same Ig locus in said genome;
a plurality of human J\3 gene segments provided by at least 2 different human J\3 gene segments in cis at the same Ig locus in said genome;
a plurality of human J\4 gene segments provided by at least 2 different human J\4 gene segments in cis at the same Ig locus in said genome;
a plurality of human J\5 gene segments provided by at least 2 different human J\5 gene segments in cis at the same Ig locus in said genome;
a plurality of human J\6 gene segments provided by at least 2 different human J\6 gene segments in cis at the same Ig locus in said genome; or
a plurality of human J\7 gene segments provided by at least 2 different human J\7 gene segments in cis at the same Ig locus in said genome;
optionally wherein the J L gene segments are derived from the genome sequence of two or more different human individuals. . A non-human vertebrate or vertebrate cell (optionally an ES cell or B-cell), according to paragraph 80, comprising a genome that comprises VL and J L gene repertoires comprising human gene segments, the J L gene repertoire comprising a plurality of human JKI gene segments provided by at least 3 (eg, 3, 4, 5, 6, or 7) different human JKI gene segments;
a plurality of human JK2 gene segments provided by at least 3 (eg, 3, 4, 5, 6, or 7) different human JKI gene segments;
a plurality of human JK3 gene segments provided by at least 3 (eg, 3, 4, 5, 6, or 7) different human JKI gene segments;
a plurality of human JK4 gene segments provided by at least 3 (eg, 3, 4, 5, 6, or 7) different human JKI gene segments;
a plurality of human JK5 gene segments provided by at least 3 (eg, 3, 4, 5, 6, or 7) different human JKI gene segments;
a plurality of human J\l gene segments provided by at least 3 (eg, 3, 4, 5, 6, or 7) different human J\l gene segments;
a plurality of human J\2 gene segments provided by at least 3 (eg, 3, 4, 5, 6, or 7) different human J\2 gene segments;
a plurality of human J\3 gene segments provided by at least 3 (eg, 3, 4, 5, 6, or 7) different human J\3 gene segments;
a plurality of human J\4 gene segments provided by at least 3 (eg, 3, 4, 5, 6, or 7) different human J\4 gene segments;
a plurality of human J\5 gene segments provided by at least 3 (eg, 3, 4, 5, 6, or 7) different human J\5 gene segments;
a plurality of human J\6 gene segments provided by at least 3 (eg, 3, 4, 5, 6, or 7) different human J\6 gene segments; or
a plurality of human J\7 gene segments provided by at least 3 (eg, 3, 4, 5, 6, or 7) different human J\7 gene segments; optionally wherein the J L gene segments are derived from the genome sequence of two or three
different human individuals; optionally wherein at least 2 or 3 of said different gene segments are provided in cis at the same Ig locus in said genome.
102. The vertebrate or cell of paragraph 104 or 105, wherein the different human individuals are from different human populations.
103. The vertebrate or cell of any one of paragraphs 104 to 106, wherein the individuals are not genetically related.
104. The vertebrate or cell of any one of paragraphs 104 to 107, wherein at least one of the different J L segments is a synthetic mutant of a human germline J L gene segment.
105. A non-human vertebrate or vertebrate cell (optionally an ES cell or B-cell) according to paragraph 84, comprising a genome comprising human VL and J L gene repertoires, the J L gene repertoire comprising a plurality of human JKI gene segments provided by at least 2 different human JKI gene segments, optionally in cis at the same Ig locus in said genome;
a plurality of human JK2 gene segments provided by at least 2 different human JKI gene segments, optionally in cis at the same Ig locus in said genome;
a plurality of human JK3 gene segments provided by at least 2 different human JKI gene segments, optionally in cis at the same Ig locus in said genome;
a plurality of human JK4 gene segments provided by at least 2 different human JKI gene segments, optionally in cis at the same Ig locus in said genome;
a plurality of human JK5 gene segments provided by at least 2 different human JKI gene segments, optionally in cis at the same Ig locus in said genome;
a plurality of human J\l gene segments provided by at least 2 different human J\l gene segments, optionally in cis at the same Ig locus in said genome;
a plurality of human J\2 gene segments provided by at least 2 different human J\2 gene segments, optionally in cis at the same Ig locus in said genome;
a plurality of human J\3 gene segments provided by at least 2 different human J\3 gene segments, optionally in cis at the same Ig locus in said genome;
a plurality of human J\4 gene segments provided by at least 2 different human J\4 gene segments, optionally in cis at the same Ig locus in said genome;
a plurality of human J\5 gene segments provided by at least 2 different human J\5 gene segments, optionally in cis at the same Ig locus in said genome;
a plurality of human J\6 gene segments provided by at least 2 different human J\6 gene segments, optionally in cis at the same Ig locus in said genome; or
a plurality of human J\7 gene segments provided by at least 2 different human J\7 gene segments, optionally in cis at the same Ig locus in said genome;
wherein the JL gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
106. The vertebrate or cell of paragraph 109, wherein the human individuals are from different human populations.
The skilled person will realise that standard molecular biology techniques can be used to provide vectors comprising synthetic combinations of immunoglobulin gene segments (eg, V, D and/or J) for use in the invention, such that the vectors can be used to build a transgenic immunoglobulin locus (eg, using homologous recombination and/or recombinase mediated cassette exchange as known in the art, eg, see US7501552 (Medarex), US5939598 (Abgenix), US6130364 (Abgenix), WO02/066630 ( egeneron), WO2011004192 (Genome Research Limited), WO2009076464, WO2009143472 and WO2010039900 (Ablexis), the disclosures of which are explicitly incorporated herein. For example, such synthetic combinations of gene segments can be made using standard recombineering techniques in E coli to construct BAC vectors harbouring the synthetic combination prior to insertion in embryonic stem cells using homologous recombination or RMCE (eg, using cre/lox site-specific recombination). Details of recombineering can be found at www.genebridges.com and in
EP1034260 and EP1204740 the disclosures of which are explicitly incorporated herein.
In one embodiment, it is useful to bias the immune response of the vertebrate (and thus resultant lead antibodies) to a predetermined gene segment, eg, one known to be commonly used in natural human immune responses to antigens, such as antigens of infectious disease pathogens. For example, VH1-69 is commonly used to produce antibodies in humans against Infulenza virus; it is possible, therefore, to include two or more polymorphic DNA versions of the VH segment VH1-69 in
the locus of the invention. The examples below illustrate how such a transgenic locus can be constructed in which diversity is extended by extending the VH1-69 gene segment repertoire based on naturally-occurring VH1-69 polymorphic variants.
In one embodiment in any configuration of the invention, the genome has been modified to prevent or reduce the expression of fully-endogenous antibody. Examples of suitable techniques for doing this can be found in PCT/GB2010/051122, US7501552, US6673986, US6130364, WO2009/076464, EP1399559 and US6586251, the disclosures of which are incorporated herein by reference. In one embodiment, the non-human vertebrate VDJ region of the endogenous heavy chain immunoglobulin locus, and optionally VJ region of the endogenous light chain immunoglobulin loci (lambda and/or kappa loci), have been inactivated. For example, all or part of the non-human vertebrate VDJ region is inactivated by inversion in the endogenous heavy chain immunoglobulin locus of the mammal, optionally with the inverted region being moved upstream or downstream of the endogenous Ig locus (see, eg, WO2011004192, the disclosure of which is incorporated herein by reference). For example, all or part of the non-human vertebrate VJ region is inactivated by inversion in the endogenous kappa chain immunoglobulin locus of the mammal, optionally with the inverted region being moved upstream or downstream of the endogenous Ig locus. For example, all or part of the non-human vertebrate VJ region is inactivated by inversion in the endogenous lambda chain immunoglobulin locus of the mammal, optionally with the inverted region being moved upstream or downstream of the endogenous Ig locus. In one embodiment the endogenous heavy chain locus is inactivated in this way as is one or both of the endogenous kappa and lambda loci.
Additionally or alternatively, the vertebrate has been generated in a genetic background which prevents the production of mature host B and T lymphocytes, optionally a AG-l-deficient and/or RAG-2 deficient background. See US5859301 for techniques of generating RAG-1 deficient animals.
Thus, in one embodiment of any configuration or aspect of the invention herein, endogenous heavy and light chain expression has been inactivated.
In one embodiment each said locus constant region is a heavy chain endogenous non-human vertebrate (optionally host mouse or rat) constant region.
In one embodiment each said locus constant region is a light chain endogenous non-human vertebrate (optionally host mouse or rat) constant region.
The invention provides a monoclonal or polyclonal antibody composition prepared by immunisation of at least one vertebrate (eg, mouse or rat) according to the invention, optionally wherein the antigen is an antigen of an infectious disease pathogen (eg, a bacterial or viral pathogen antigen), optionally wherein the same antigen is used to immunise all the vertebrates; optionally wherein the antibody or antibodies are IgG-type (eg, IgGl).
The invention also provides a monoclonal or polyclonal antibody mixture produced by the method of the invention or a derivative antibody or mixture thereof, eg, where one or more constant region has been changed (eg, replaced with a different constant region such as a human constant region; or mutated to enhance or ablate Fc effector function). In an aspect of the invention, the monoclonal or polyclonal antibody mixture is provided for therapy and/or prophylaxis of a disease or condition in a human, eg, for the treatment and/or prevention of an infectious disease, wherein optionally wherein each antibody binds an antigen of an infectious disease pathogen, preferably the same antigen.
In an aspect of the invention, there is provided the use of an isolated, monoclonal or polyclonal antibody according to the invention, or a mutant or derivative antibody thereof in the manufacture of a medicament for the treatment and/or prevention of a disease or condition in a human, eg, an infectious disease, optionally wherein the infectious disease is a disease caused by a bacterial or viral pathogen.
An example of a mutant antibody is one that bears up to 15 or 10 amino acid mutations in its variable regions relative to an isolated antibody (eg, IgG-type, such as IgGl-type, antibody) obtainable or obtained by the method of the invention. An example of a derivative is one that has been modified to replace a constant region with a different constant region such as a human constant region; or mutated to enhance or ablate Fc effector function.
Examples of infectious diseases are diseases caused or mediated by a bacterial or viral pathogen. For example, the infectious disease is selected from the group consisting of a disease caused by a pathogen selected from the group consisting of Haemophilus influenza, E coli, Neisseria meningitidis, a herpes family virus, cytomegalovirus (CMV), HIV and influenza virus.
Tailoring V(D J Incorporation Into Immunoelobin Loci For The Generation of Antibodies Against
Infectious Disease
The inventors realised that it would be desirable to provide for vertebrates, cells, methods etc for the production of therapeutic and/or prophylactic antibodies based on natural human immune responses to antigens, such as antigens of infectious disease pathogens. In this respect, the literature observes frequently used immunoglobulin gene segments to raise anti-infective responses in humans (Table 9).
In the various configurations, aspects, embodiments and examples above, the invention provides the skilled addressee with the possibility of choosing immunoglobulin gene segments in a way that tailors or biases the repertoire for application to generating antibodies to treat and/or prevent infectious diseases. The inventors have categorised the following groups of gene segments for use in the invention according to the desired application of resultant antibodies.
List A:
Immunoglobulin gene segments for antibodies that bind an antigen expressed by a Pathogen
(a) a VL gene segment selected from the group consisting of a νλΙ Ι gene family member, V¾VI I 4A, νλΙ Ι 2.1, VxVI I 4A, a Vxl gene family member, a Vx3gene family member, IGLV1S2, Vx3-cM L70, Ialh2, lalvl, Ia3h3, Kv325, a VKI gene family member, κΙ-15Α (KL012), VKI I family member, a VKI I I family member, a VKI gene family member, κΙ-15Α (KL012), VKI I A2 (optionally the A2a variant), VK A27 (Humkv325) and a gene segment at least 80% identical thereto.
(b) a Vx gene segment selected from a νλΙ Ι gene family member, VAVI I 4A, νλΙ Ι 2.1, VAVI I 4A, a νλ1 gene family member, a Vx3gene family member, IGLV1S2, Vx3-cM L70, Ialh2, lalvl, Ia3h3 and a gene segment at least 80% identical thereto.
(c) a VK gene segment selected from Kv325, a VKI gene family member, κΙ-15Α (KL012), VKI I family member, a VKI I I family member, a VKI gene family member, κΙ-15Α (KL012), VKI I A2 (optionally the A2a variant), VK A27 (Humkv325) and a gene segment at least 80% identical thereto.
(d) a VH gene segment a VHI II gene family member (optionally, a VHI IIa or VHI II b family member), a VHIV gene family member, VHI I I 9.1 (VH3-15), VHI II VH26 (VH3-23), VH3-21, LSG6.1, LSG12.1, DP77 (V3-21), VH H ll, VH1G , ha3h2, VHl-halcl, VHI I I-VH2-1, VH4.18, ha4h3, Hvl051, 71-2, HvlflO, VH4.11, 71-4, VH251, VH 1-69 and a gene segment at least 80% identical thereto.
(e) a ix gene segment selected from Jx2, Jx3 and a gene segment at least 80% identical thereto.
(f) a D gene segment selected from Dkl, Dxp'l, Dn4r, D2r and a gene segment at least 80% identical thereto.
List Al:
Immunoglobulin gene segments for antibodies that bind an antigen expressed by a Bacterial Pathogen
(a) a νλ gene segment selected from a νλΙΙ gene family member, V¾VII 4A, νλΙΙ 2.1, V¾VII 4A and a gene segment at least 80% identical thereto.
(b) a VK gene segment selected from a VKI gene family member, κΙ-15Α (KL012), VKI I family member, a VKIII family member, a VKI gene family member, κΙ-15Α (KL012), VKI I A2 (optionally the A2a variant), VK A27 (Humkv325) and a gene segment at least 80% identical thereto.
(c) a VH gene segment a VH3 gene family member (optionally, a VHIIIa or VHIIIb family member), VHIII 9.1 (VH3-15), VHIII VH26 (VH3-23), VH3-21, LSG6.1, LSG12.1, DP77 (V3-21), VH Hll and a gene segment at least 80% identical thereto.
(d) a ix gene segment selected from ϋλ2, ϋλ3 and a gene segment at least 80% identical thereto.
(e) a JH gene segment selected from JH2, JH3, JH4 and a gene segment at least 80% identical thereto.
List Al.l:
Immunoglobulin gene segments for antibodies that bind an antigen expressed by H influenza
(a) a νλ gene segment selected from a νλΙΙ gene family member, V¾VII 4A, νλΙΙ 2.1, V¾VII 4A and a gene segment at least 80% identical thereto.
(b) a VK gene segment selected from a VKI I family member, a VKIII family member, a VKI gene family member, κΙ-15Α (KL012), VKI I A2 (optionally the A2a variant), VK A27 (Humkv325) and a gene segment at least 80% identical thereto.
(c) a VH gene segment a VH3 gene family member (optionally, a VHIIIb family member), VHMI 9.1 (VH3-15), VHIII VH26 (VH3-23), VH3-21, LSG6.1, LSG12.1, DP77 (V3-21) and a gene segment at least 80% identical thereto.
(d) a ix gene segment selected from ϋλ2, ϋλ3 and a gene segment at least 80% identical thereto.
List A1.2:
Immunoglobulin gene segments for antibodies that bind an antigen expressed by E Coli or Neisseria meningitidis
(a) a VH gene segment a VH3 gene family member (optionally a VH II la or VH II Ib member), VHI II 9.1 (VH3-15), VH Hll, VHI II VH26 (VH3-23) a gene segment at least 80% identical thereto, eg, VHI II 9.1 + JH3; or VH H ll + JH4; or VHI II VH26 + JH2.
(b) a VK gene segment selected from a VKI gene family member, κΙ-15Α (KL012) and a gene segment at least 80% identical thereto.
(c) a νλ gene segment selected from a νλΙ Ι gene family member, νλΙ Ι 2.1 and a gene segment at least 80% identical thereto.
(d) a JH gene segment selected from JH2, JH3, JH4 and a gene segment at least 80% identical thereto.
A2:
Immunoglobulin gene segments for antibodies that bind an antigen expressed by a viral Pathogen
(a) a VH gene segment selected from a VHI II gene family member, a VHIV gene family member, VHII I- VH26 (VH3-23), VH1G , ha3h2, VHl-halcl, VHI I I-VH2-1, VH4.18, ha4h3, Hvl051, 71-2, HvlflO, VH4.11, 71-4, VH251, VH 1-69 and a gene segment at least 80% identical thereto.
(b) a νλ gene segment selected from a νλ1 gene family member, a V 3gene family member, IGLV1S2, Vx3-cM L70, Ialh2, lalvl, Ia3h3 and a gene segment at least 80% identical thereto.
(c) a Vk gene segment selected from Kv325 and a gene segment at least 80% identical thereto.
(d) a JH gene segment selected from JH3, JH5, JH6 and a gene segment at least 80% identical thereto.
(e) a D gene segment selected from Dkl, Dxp'l, Dn4r, D2r and a gene segment at least 80%
identical thereto.
(f) a ix gene segment selected from ϋλ2, ϋλ3 and a gene segment at least 80% identical thereto.
A2.1:
Immunoglobulin gene segments for antibodies that bind an antigen expressed by Herpes Virus Family (eg. VZV or HSV
(a) a VH gene segment selected from a VHI II gene family member, a VHIV gene family member, VHII I- VH26 (VH3-23), VH1GRR, ha3h2, VHl-halcl, VHI I I-VH2-1, VH4.18, ha4h3, and a gene segment at least 80% identical thereto.
(b) a νλ gene segment selected from a νλ1 gene family member, a Vx3gene family member, IGLV1S2, Vx3-cM L70, Ialh2, lalvl, Ia3h3 and a gene segment at least 80% identical thereto.
(c) a JH gene segment selected from JH3, JH5, JH6 and a gene segment at least 80% identical thereto.
(d) a D gene segment selected from Dkl, Dxp'l, Dn4r, D2r and a gene segment at least 80%
identical thereto.
(e) a ix gene segment selected from ϋλ2, ϋλ3 and a gene segment at least 80% identical thereto.
A2.2:
Immunoglobulin gene segments for antibodies that bind an antigen expressed by CMV
(a) a VH gene segment selected from Hvl051 and a gene segment at least 80% identical thereto.
(b) a Vk gene segment selected from Kv325 and a gene segment at least 80% identical thereto.
A2.3:
Immunoglobulin gene segments for antibodies that bind an antigen expressed by HIV
(a) a VH gene segment selected from 71-2, HvlflO, VH4.11, 71-4, VH251, VH 1-69 and a gene
segment at least 80% identical thereto.
A2.4:
Immunoglobulin gene segments for antibodies that bind an antigen expressed by Influenza Virus (a) a VH gene segment selected from VH 1-69 and a gene segment at least 80% identical thereto.
Thus,
Where one wishes to generate an antibody or antibody mixture to treat and/or prevent an infectious disease, one or more V, D and/or or all J gene segments used in any configuration, aspect, method, example or embodiment of the invention can be selected from List Al. Thus, for example in (a) of the first configuration of the invention, the recited heavy chain V gene segment is selected from the VH gene segments in List A, optionally with a D in that list.
Where one wishes to generate an antibody or antibody mixture to treat and/or prevent an infectious disease caused or mediated by a bacterial pathogen, one or more or all V, D a nd/or J gene
segments used in any configuration, aspect, method, example or embodiment of the invention can be selected from List Al.
Where one wishes to generate an antibody or antibody mixture to treat and/or prevent an infectious disease caused or mediated by a viral pathogen, one or more or all V, D and/or J gene segments used in any configuration, aspect, method, example or embodiment of the invention can be selected from List A2.
Where one wishes to generate an antibody or antibody mixture to treat and/or prevent an infectious disease caused or mediated by H influenza, one or more or all V, D and/or J gene segments used in any configuration, aspect, method, example or embodiment of the invention can be selected from List Al.l.
Where one wishes to generate an antibody or antibody mixture to treat and/or prevent an infectious disease caused or mediated by E Coli or Neisseria meningitidis, one or more or all V, D and/or J gene segments used in any configuration, aspect, method, example or embodiment of the invention can be selected from List A1.2.
Where one wishes to generate an antibody or antibody mixture to treat and/or prevent an infectious disease caused or mediated by Herpes Virus Family (eg, VZV or HSV), one or more or all V, D and/or J gene segments used in any configuration, aspect, method, example or embodiment of the invention can be selected from List A2.1.
Where one wishes to generate an antibody or antibody mixture to treat and/or prevent an infectious disease caused or mediated by CMV, one or more or all V, D and/or J gene segments used in any configuration, aspect, method, example or embodiment of the invention can be selected from List A2.2.
Where one wishes to generate an antibody or antibody mixture to treat and/or prevent an infectious disease caused or mediated by HIV, one or more or all V, D and/or J gene segments used in any configuration, aspect, method, example or embodiment of the invention can be selected from List A2.3.
Where one wishes to generate an antibody or antibody mixture to treat and/or prevent an infectious disease caused or mediated by Influenza Virus, one or more or all V, D and/or J gene
segments used in any configuration, aspect, method, example or embodiment of the invention can be selected from List A2.4.
Optionally each VH segment in the locus of the invention is selected from List Al, A2, Al.l, A1.2, A2.1, A2.2, A2.3 or A2.4.
Optionally each VL segment in the locus of the invention is selected from List Al, A2, Al.l, A1.2, A2.1, A2.2, A2.3 or A2.4
Optionally each D segment in the locus of the invention is selected from List Al, A2, Al.l, A1.2, A2.1, A2.2, A2.3 or A2.4.
Optionally each JL segment in the locus of the invention is selected from List Al, A2, Al.l, A1.2, A2.1, A2.2, A2.3 or A2.4.
Antibodies For Therapy & Prophylaxis of Patients of Specific Ancestry
The inventors, having undertaken the extensive Bioinformatics analysis exercise described herein, realised that the output of that analysis has made it possible to identify specific gene segments that are useful to produce antibody- and VH domain-based drugs that are tailored specifically to a patient's ancestry (ie, genotype). That is, antibodies can be selected on the basis that they are made in vivo in a transgenic non-human vertebrate (eg, mouse or rat with transgenic IgH loci) and particularly derived from gene segments that are relatively prevalent in members of the patient's population, ie, from individuals of the same human ancestry. Since variant distributions differ across different populations (see Table 13), this presumably reflects the effects of evolution, adaptation and conservation of useful variant gene types in those populations. Thus, by tailoring the antibody- based drugs according to the invention, it is possible to match the drug to the population gene biases, thus with the aim of making better drugs for that specific population of humans. Better can, for example, mean more efficacious, better neutralising, higher target antigen affinity, less immunogenic, less patient reactions to the drug etc. This can be determined empirically, as is standard in drug research and development processes.
Thus, the invention provides the following embodiments (numbered from clause 345 onwards):-
345. An isolated antibody for administration to a Chinese patient, the antibody comprising a human heavy chain, the heavy chain comprising a variable domain that is specific for an antigen
and a constant region, wherein the constant region is a human constant region selected from a constant region (eg, an IGHG constant region) inTable 13 found in a Chinese population and with a cumulative frequency of at least 1 or 5%;, and wherein
(i) the variable domain is derived from the recombination of said human gene segments in a non-human vertebrate (eg, in a mouse or a rat); and/or ( ii) the variable domain comprises non- human vertebrate (eg, mouse or rat) AID-pattern mutations and non-human vertebrate (eg, mouse or rat) terminal deoxynucleotidyl transferase (TdT)-pattern mutations.
In another embodiment, the invention provides
An isolated antibody for administration to a Chinese patient, the antibody comprising a human heavy chain, the heavy chain comprising a variable domain that is specific for an antigen and a constant region, wherein the constant region is a human constant region selected from a constant region (eg, an IGHG constant region) present in a Chinese population with a cumulative frequency of at least 5%;, and wherein
(i) the variable domain is derived from the recombination of said human gene segments in a non-human vertebrate (eg, in a mouse or a rat);and/ or ( ii) the variable domain comprises non- human vertebrate (eg, mouse or rat) AID-pattern mutations and non-human vertebrate (eg, mouse or rat) terminal deoxynucleotidyl transferase (TdT)-pattern mutations.
In an example, the constant region is found in the 1000 Genomes database. In an example, the constant region is found in Table 13.
346. The antibody of clause 345 wherein the constant region is a IGHGla, IGHG2a, IGHG3a, IGHG3b or IGHG4a constant region.
347. The antibody of clause 345 or 346, wherein the variable domain is derived from the
recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the VH gene segment being selected from a VH in Table 13 found in a Chinese population and with a cumulative frequency of at least 5%.
In another embodiment, the invention provides
The antibody of clause 345 or 346, wherein the variable domain is derived from the
recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the VH gene segment being selected from a VH present in a Chinese population with a cumulative frequency of at least 5%.
In an example, the gene segment is found in the 1000 Genomes database. In an example, the gene segment is found in Table 13.
348. The antibody of clause 345, 346 or 347, wherein the variable domain is derived from the recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the D gene segment being selected from a D in Table 13 found in a Chinese population and with a cumulative frequency of at least 5%.
In another embodiment, the invention provides
The antibody of clause 345, 346 or 347, wherein the variable domain is derived from the recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the D gene segment being selected from a D present in a Chinese population with a cumulative frequency of at least 5%.
In an example, the gene segment is found in the 1000 Genomes database. In an example, the gene segment is found in Table 13.
349. The antibody of clause 345, 346, 347 or 348 wherein the variable domain is derived from the recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the JH gene segment being selected from a JH in Table 13 found in a Chinese population and with a cumulative frequency of at least 5%.
In another embodiment, the invention provides
The antibody of clause 345, 346, 347 or 348 wherein the variable domain is derived from the recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the JH gene segment being selected from a JH present in a Chinese population with a cumulative frequency of at least 5%.
In an example, the gene segment is found in the 1000 Genomes database. In an example, the gene segment is found in Table 13.
350. An isolated VH domain identical to a variable domain as recited in any one of clauses 347 to 349, optionally fused at its C-terminus to a polypeptide (eg, an antibody Fc).
In an embodiment, there is provided an isolated VH domain identical to a variable domain as recited in any one of clauses 347 to 349 which is part of a conjugate, conjugated with a label (eg, for imaging in the patient) or a toxin (eg, a radioactive toxic payload, such as for cancer treatment in the patient) or a half-life-extending moiety (eg, PEG of human serum albumin).
351. A pharmaceutical composition comprising the antibody or variable domain of any one of clauses 345 to 350 together with a pharmaceutically-acceptable excipient, diluent or a medicament (eg, a further antigen-specific variable domain, antibody chain or antibody).
352. An isolated antibody for administration to a Chinese patient, the antibody comprising a human heavy chain, the heavy chain comprising a variable domain that is specific for an antigen
and a constant region, wherein the variable domain is derived from the recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the VH gene segment being selected from a VH in Table 13 found in a Chinese population and with a cumulative frequency of at least 5%; and wherein
(i) the variable domain is derived from the recombination of said human gene segments in a non-human vertebrate (eg, in a mouse or a rat); and/or ( ii) the variable domain comprises non- human vertebrate (eg, mouse or rat) AID-pattern mutations and non-human vertebrate (eg, mouse or rat) terminal deoxynucleotidyl transferase (TdT)-pattern mutations.
In another embodiment, the invention provides
An isolated antibody for administration to a Chinese patient, the antibody comprising a human heavy chain, the heavy chain comprising a variable domain that is specific for an antigen and a constant region, wherein the variable domain is derived from the recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the VH gene segment being selected from a VH present in a Chinese population with a cumulative frequency of at least 5%; and wherein
(i) the variable domain is derived from the recombination of said human gene segments in a non-human vertebrate (eg, in a mouse or a rat); and/or ( ii) the variable domain comprises non- human vertebrate (eg, mouse or rat) AID-pattern mutations and non-human vertebrate (eg, mouse or rat) terminal deoxynucleotidyl transferase (TdT)-pattern mutations.
353. The antibody of clause 352, wherein the variable domain is derived from the recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the D gene segment being selected from a D in Table 13 found in a Chinese population and with a cumulative frequency of at least 5%.
In another embodiment, the invention provides
The antibody of clause 352, wherein the variable domain is derived from the recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the D gene segment being selected from a D present in a Chinese population with a cumulative frequency of at least 5%.
In an example, the gene segment is found in the 1000 Genomes database. In an example, the gene segment is found in Table 13.
354. The antibody of clause 352 or 353, wherein the variable domain is derived from the
recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the JH gene segment being selected from a JH in Table 13 found in a Chinese population and with a cumulative frequency of at least 5%.
In another embodiment, the invention provides
The antibody of clause 352 or 353, wherein the variable domain is derived from the
recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the JH gene segment being selected from a JH present in a Chinese population with a cumulative frequency of at least 5%.
In an example, the gene segment is found in the 1000 Genomes database. In an example, the gene segment is found in Table 13.
355. An isolated VH domain identical to a variable domain as recited in any one of clauses 352 to 354, optionally fused at its C-terminus to a polypeptide (eg, an antibody Fc).
In an embodiment, there is provided a VH domain identical to a variable domain as recited in any one of clauses 352 to 354 which is part of a conjugate, conjugated with a label (eg, for imaging in the patient) or a toxin (eg, a radioactive toxic payload, such as for cancer treatment in the patient) or a half-life-extending moiety (eg, PEG of human serum albumin).
356. A pharmaceutical composition comprising the antibody or variable domain of any one of clauses 352 to 355 together with a pharmaceutically-acceptable excipient, diluent or a medicament (eg, a further antigen-specific variable domain, antibody chain or antibody).
357. An antibody heavy chain or VH domain (eg, provided as part of an antibody) for therapy and/or prophylaxis of a disease or medical condition in a Chinese patient, wherein the heavy chain is a heavy chain produced by the following steps (or is a copy of such a heavy chain):-
(a) Selection of an antigen-specific antibody heavy chain or VH domain from a non-human vertebrate (eg, a mouse or a rat), wherein the heavy chain or VH domain is derived from the recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the VH gene segment being selected from a VH in Table 13 found in a Chinese population and with a cumulative frequency of at least 5%;
(b) Optional humanisation of the heavy chain by combining the variable domain of the heavy chain with a human constant region; or optional humanisation of the selected VH domain by combining with a human constant region.
In another embodiment, the invention provides
An antibody heavy chain or VH domain (eg, provided as part of an antibody) for therapy and/or prophylaxis of a disease or medical condition in a Chinese patient, wherein the heavy chain is a heavy chain produced by the following steps (or is a copy of such a heavy chain):-
(a) Selection of an antigen-specific antibody heavy chain or VH domain from a non-human vertebrate (eg, a mouse or a rat), wherein the heavy chain or VH domain is derived from the
recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the VH gene segment being selected from a VH present in a Chinese population with a cumulative frequency of at least 5%;
(b) Optional humanisation of the heavy chain by combining the variable domain of the heavy chain with a human constant region; or optional humanisation of the selected VH domain by combining with a human constant region.
In an example, the VH gene segment is found in the 1000 Genomes database. In an example, the gene segment is found in Table 13.
358. The antibody heavy chain or VH domain of clause 357, wherein the human constant region is as recited in clause 345 or 346.
359. An antibody heavy chain or VH domain as recited in clause 357 or 358 for use in a
medicament for therapy and/or prophylaxis of a disease or medical condition in a Chinese patient.
360. A method of treating and/or preventing a disease or medical condition in a Chinese patient, the method comprising administering to the patient a therapeutically or prophylactically- effective amount of the antibody heavy chain or VH domain as recited in clause 357 or 358.
361. An isolated antibody for administration to a patient of European, East Asian, West African, South Asian or Americas ancestry, the antibody comprising a human heavy chain, the heavy chain comprising a variable domain that is specific for an antigen and a constant region, wherein the constant region is a human constant region selected from a constant region (eg, an IGHG constant region) in Table 13 found in a population of European, East Asian, West African, South Asian or Americas ancestry respectively and with a cumulative frequency of at least 1 or 5%;, and wherein
(i) the variable domain is derived from the recombination of said human gene segments in a non-human vertebrate (eg, in a mouse or a rat); or ( ii) the variable domain comprises non- human vertebrate (eg, mouse or rat) AID-pattern mutations and non-human vertebrate (eg, mouse or rat) terminal deoxynucleotidyl transferase (TdT)-pattern mutations.
In another embodiment, the invention provides
An isolated antibody for administration to a patient of European, East Asian, West African, South Asian or Americas ancestry, the antibody comprising a human heavy chain, the heavy chain comprising a variable domain that is specific for an antigen and a constant region, wherein the constant region is a human constant region selected from a constant region (eg, an IGHG constant region) present in a population of European, East Asian, West African, South Asian or Americas ancestry respectively with a cumulative frequency of at least 1 or 5%;, and wherein
(i) the variable domain is derived from the recombination of said human gene segments in a
non-human vertebrate (eg, in a mouse or a rat); or ( ii) the variable domain comprises non- human vertebrate (eg, mouse or rat) AID-pattern mutations and non-human vertebrate (eg, mouse or rat) terminal deoxynucleotidyl transferase (TdT)-pattern mutations.
In an example, the constant region is found in the 1000 Genomes database. In an example, the constant region is found in Table 13.
362. The antibody of clause 361 wherein the constant region is a IGHGla, IGHG2a, IGHG3a, IGHG3b or IGHG4a constant region and the patient is of European ancestry.
363. The antibody of clause 361 or 362, wherein the variable domain is derived from the
recombination of a human VH gene segment with a human D gene segment and a human JH gene segment, the VH gene segment being selected from a VH in Table 13 found in said population and with a cumulative frequency of at least 1 or 5%.
In another embodiment, the invention provides
The antibody of clause 361 or 362, wherein the variable domain is derived from the
recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the VH gene segment being selected from a VH present in a Chinese population with a cumulative frequency of at least 5%.
In an example, the gene segment is found in the 1000 Genomes database. In an example, the gene segment is found in Table 13.
364. The antibody of clause 361, 362 or 363, wherein the variable domain is derived from the recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the D gene segment being selected from a D in Table 13 found in said population and with a cumulative frequency of at least 1 or 5%.
In another embodiment, the invention provides
The antibody of clause 361, 362 or 363, wherein the variable domain is derived from the recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the D gene segment being selected from a D present in a Chinese population with a cumulative frequency of at least 5%.
In an example, the gene segment is found in the 1000 Genomes database. In an example, the gene segment is found in Table 13.
365. The antibody of clause 361, 362, 363 or 364 wherein the variable domain is derived from the recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the JH gene segment being selected from a JH in Table 13 found in said population and with a cumulative frequency of at least 1 or 5%.
In another embodiment, the invention provides
The antibody of clause 361, 362, 363 or 364 wherein the variable domain is derived from the recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the JH gene segment being selected from a JH present in a Chinese population with a cumulative frequency of at least 5%.
In an example, the gene segment is found in the 1000 Genomes database. In an example, the gene segment is found in Table 13.
366. An isolated VH domain identical to a variable domain as recited in any one of clauses 363 to 365, optionally fused at its C-terminus to a polypeptide (eg, an antibody Fc).
367. A pharmaceutical composition comprising the antibody or variable domain of any one of clauses 361 to 366 together with a pharmaceutically-acceptable excipient, diluent or a medicament (eg, a further antigen-specific variable domain, antibody chain or antibody).
368. An isolated antibody for administration to a patient of European, East Asian, West African or Americas ancestry, the antibody comprising a human heavy chain, the heavy chain comprising a variable domain that is specific for an antigen and a constant region, wherein the variable domain is derived from the recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the VH gene segment being selected from a VH in Table 13 found in a population of European, East Asian, West African, South Asian or Americas ancestry respectively and with a cumulative frequency of at least 1 or 5%; and wherein
(i) the variable domain is derived from the recombination of said human gene segments in a non-human vertebrate (eg, in a mouse or a rat); or ( ii) the variable domain comprises non- human vertebrate (eg, mouse or rat) AID-pattern mutations and non-human vertebrate (eg, mouse or rat) terminal deoxynucleotidyl transferase (TdT)-pattern mutations.
In another embodiment the invnention provides:-
An isolated antibody for administration to a patient of European, East Asian, West African or Americas ancestry, the antibody comprising a human heavy chain, the heavy chain comprising a variable domain that is specific for an antigen and a constant region, wherein the variable domain is derived from the recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the VH gene segment being selected from a VH present in a population of European, East Asian, West African, South Asian or Americas ancestry respectively with a cumulative frequency of at least 1 or 5%; and wherein
(i) the variable domain is derived from the recombination of said human gene segments in a non-human vertebrate (eg, in a mouse or a rat); or ( ii) the variable domain comprises non- human vertebrate (eg, mouse or rat) AID-pattern mutations and non-human vertebrate (eg,
mouse or rat) terminal deoxynucleotidyl transferase (TdT)-pattern mutations.
In an example, the VH gene segment is found in the 1000 Genomes database. In an example, the gene segment is found in Table 13.
369. The antibody of clause 368, wherein the variable domain is derived from the recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the D gene segment being selected from a D in Table 13 found in said population and with a cumulative frequency of at least 1 or 5%.
In another example there is provided
The antibody of clause 368, wherein the variable domain is derived from the recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the D gene segment being selected from a D present in said population with a cumulative frequency of at least 1 or 5%.
In an example, the D gene segment is found in the 1000 Genomes database. In an example, the gene segment is found in Table 13.
370. The antibody of clause 368 or 369, wherein the variable domain is derived from the
recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the JH gene segment being selected from a JH in Table 13 found in said population and with a cumulative frequency of at least 1 or 5%.
In another example there is provided
The antibody of clause 368 or 369, wherein the variable domain is derived from the
recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the JH gene segment being selected from a JH present in said population and with a cumulative frequency of at least 1 or 5%.
In an example, the JH gene segment is found in the 1000 Genomes database. In an example, the gene segment is found in Table 13.
371. An isolated VH domain identical to a variable domain as recited in any one of clauses 368 to 370, optionally fused at its C-terminus to a polypeptide (eg, an antibody Fc).
372. A pharmaceutical composition comprising the antibody or variable domain of any one of clauses 368 to 371 together with a pharmaceutically-acceptable excipient, diluent or a medicament (eg, a further antigen-specific variable domain, antibody chain or antibody).
373. An antibody heavy chain or VH domain (eg, provided as part of an antibody) for therapy and/or prophylaxis of a disease or medical condition in a patient of European, East Asian, West African, South Asian or Americas ancestry, wherein the heavy chain is a heavy chain produced by
the following steps (or is a copy of such a heavy chain):-
(a) Selection of an antigen-specific antibody heavy chain or VH domain from a non-human vertebrate (eg, a mouse or a rat), wherein the heavy chain or VH domain is derived from the recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the VH gene segment being selected from a VH in Table 13 found in said population and with a cumulative frequency of at least 1 or 5%;
(b) Optional humanisation of the heavy chain by combining the variable domain of the heavy chain with a human constant region; or optional humanisation of the selected VH domain by combining with a human constant region.
In another embodiment, there is provided:-
An antibody heavy chain or VH domain (eg, provided as part of an antibody) for therapy and/or prophylaxis of a disease or medical condition in a patient of European, East Asian, West African South Asian or Americas ancestry, wherein the heavy chain is a heavy chain produced by the following steps (or is a copy of such a heavy chain):-
(a) Selection of an antigen-specific antibody heavy chain or VH domain from a non-human vertebrate (eg, a mouse or a rat), wherein the heavy chain or VH domain is derived from the recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the VH gene segment being selected from a VH present in said population with cumulative frequency of at least 1 or 5%;
(b) Optional humanisation of the heavy chain by combining the variable domain of the heavy chain with a human constant region; or optional humanisation of the selected VH domain by combining with a human constant region.
In an example, the VH gene segment is found in the 1000 Genomes database. In an example, the gene segment is found in Table 13.
374. The antibody heavy chain or VH domain of clause 373, wherein the human constant region as recited in clause 361 or 362.
375. An antibody heavy chain or VH domain as recited in clause 373 or 374 for use in a
medicament for therapy and/or prophylaxis of a disease or medical condition in a patient of sai ancestry.
376. A method of treating and/or preventing a disease or medical condition in a patient of European, East Asian, West African, South Asian or Americas ancestry, the method comprising administering to the patient a therapeutically or prophylactically-effective amount of the antibody heavy chain or VH domain as recited in clause 373 or 374.
In embodiments herein, a Chinese patient can be a Han Chinese patient.
In embodiments herein, a patient of European ancestry can be a patient of Northern or Western European ancestry, Italian ancestry, British or Scottish ancestry, Finnish ancestry or Iberian ancestry.
In embodiments herein, a patient of East Asian ancestry can be a patient of Han Chinese ancestry, Japanese ancestry Chinese Dai ancestry, Vietnamese ancestry or Kinh ancestry.
In embodiments herein, a patient of West African ancestry can be a patient of Yoruba ancestry, Luhya ancestry, Gambian ancestry or Malawian ancestry.
In embodiments herein, a patient of Americas ancestry can be a patient of African American ancestry, African Caribbean ancestry, Mexican ancestry, Puerto ican ancestry, Colombian ancestry or Peruvian ancestry.
In embodiments herein, a patient of South Asian ancestry can be a patient of Ahom ancestry, Kayadtha ancestry, Reddy ancestry, Maratha ancestry, or Punjabi ancestry.
In an example of any aspect, the cumulative frequency is at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90 or 95%.
It will be understood that particular embodiments described herein are shown by way of illustration and not as limitations of the invention. The principal features of this invention can be employed in various embodiments without departing from the scope of the invention. Those skilled in the art will recognize, or be able to ascertain using no more than routine study, numerous equivalents to the specific procedures described herein. Such equivalents are considered to be within the scope of this invention and are covered by the claims. All publications and patent applications mentioned in the specification are indicative of the level of skill of those skilled in the art to which this invention pertains. All publications and patent applications are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference. The use of the word "a" or "an" when used in conjunction with the term "comprising" in the claims and/or the specification may mean "one," but it is also consistent with the meaning of "one or more," "at least one," and "one or more than one." The use
of the term "or" in the claims is used to mean "and/or" unless explicitly indicated to refer to alternatives only or the alternatives are mutually exclusive, although the disclosure supports a definition that refers to only alternatives and "and/or." Throughout this application, the term "about" is used to indicate that a value includes the inherent variation of error for the device, the method being employed to determine the value, or the variation that exists among the study subjects.
As used in this specification and claim(s), the words "comprising" (and any form of comprising, such as "comprise" and "comprises"), "having" (and any form of having, such as "have" and "has"), "including" (and any form of including, such as "includes" and "include") or "containing" (and any form of containing, such as "contains" and "contain") are inclusive or open-ended and do not exclude additional, unrecited elements or method steps
The term "or combinations thereof" as used herein refers to all permutations and combinations of the listed items preceding the term. For example, "A, B, C, or combinations thereof is intended to include at least one of: A, B, C, AB, AC, BC, or ABC, and if order is important in a particular context, also BA, CA, CB, CBA, BCA, ACB, BAC, or CAB. Continuing with this example, expressly included are combinations that contain repeats of one or more item or term, such as BB, AAA, MB, BBC, AAABCCCC, CBBAAA, CABABB, and so forth. The skilled artisan will understand that typically there is no limit on the number of items or terms in any combination, unless otherwise apparent from the context.
Any part of this disclosure may be read in combination with any other part of the disclosure, unless otherwise apparent from the context.
All of the compositions and/or methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this invention have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the compositions and/or
methods and in the steps or in the sequence of steps of the method described herein without departing from the concept, spirit and scope of the invention. All such similar su bstitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims.
The present invention is described in more detail in the following non limiting prophetic Examples.
EXAMPLES
EXAMPLE 1
" ecombineered BAC Vectors to add Polymorphic V-regions to the Mouse Genome"
Figure 1 through 3 depict recombineering methods (see references above) that can be used to introduce polymorphic V-gene regions into genomic DNA. In one embodiment, a genomic fragment from the human heavy chain region is inserted into a bacterial artificial chromosome (BAC) vector by standard techniques. Preferably, such a BAC, which can range in size from 20-kb to 200-kb or more, can be isolated from libraries of BACs by standard techniques including sequence searches of commercially available libraries or by hybridization to bacterial colonies containing BACs to identify those with a BAC of interest.
A BAC is chosen that has several VH gene segments; in Figure 1, these are generically identified as VH [a] through VH [z] for example. One skilled in the art will readily identify appropriate genomic fragments, for example, an approximately 120-kb fragment from human VH5-78 through VH 1-68 which includes 5 endogenous active VH gene segments and 7 VH psuedogenes. Using
recombineering techniques, the endogenous VH gene segments can be replaced by polymorphic VH or VL gene segments. In this example, two steps are required. The first step replaces the V-region coding exon of an endogenous VH gene segment with a positive-negative selection operon, in this example, an operon encoding an ampicillin resistance gene (Amp) and a streptomycin-sensitizing ribosomal protein (rpsL). Certain strains of bacteria can be selected for the absence of the rpsL gene by resistance to streptomycin. Short stretches of DNA homologous to sequences flanking the
endogenous VH gene exon are placed 5' and 3' of the rpsL-Amp operon. In the presence of appropriate recombination factors per standard recombineering techniques (see references above) recombination between the operon fragment and the BAC will result in replacement of the endogenous VH gene exon with the operon (Figure la) which are selected by resistance to ampicillin. The second step uses the same homologous sequences in order to replace the inserted operon with a desired polymorphic VH gene segment. In this example, a human VH 1-69 gene is inserted (Figure lb and lc). In particular the *02 variant of VH 1-69 is used [ref I MGT and Figure 5]. Successful integrations of the polymorphic VH gene segment are selected in bacteria that become resistant to streptomycin due to the loss of the operon, specifically the rpsL portion.
In this example, the two step process as described can be repeated for each of the endogenous VH gene segments or for as many endogenous gene segments that one wishes to replace with polymorphic V gene segments (Figure Id).
As is apparent, any polymorphic V gene segment can be inserted in this manner and any endogenous V gene segment can act as a target, including pseudogenes. V gene segments in each of the heavy chain and two light chain loci can be replaced using this technique with appropriate genomic fragments available as BAC inserts.
Figure 2 depicts another method for creating a genomic fragment encoding polymorphic V gene segments. In this example, polymorphic V gene segments are inserted into a region of genomic DNA devoid of other genes, control elements or other functions. Such 'desert' regions can be selected based on sequence analysis and corresponding DNA fragments cloned into BACs or identified in existing BAC libraries. Starting with such a genomic fragment, recombineering techniques can be used to insert polymorphic V gene segments at intervals of, for example, 10-kb. In this example, a 150-kb genomic fragment might accommodate insertion of up to 15 polymorphic V gene segments. Insertion of the segments is a two-step process. The first recombineering step inserts the rpsL-Amp operon at a specific site. Sequences homologous to a specific site are used to flank the operon. These are used by the recombineering system to insert the element specifically into the BAC genomic fragment and positive events are selected by resistance to ampicillin (Figure 2a). The second step replaces the operon in the genomic fragment with a polymorphic V gene segment by a similar recombineering step using the same sequence homology (Figure 2b). In this example, both
exons and promoter element of a polymorphic VH gene segment are inserted, resulting in replacement of the rpsL-Amp operon and therefore resistance to streptomycin (Figure 2c).
The two step technique for inserting polymorphic V gene segments into a specific site on the genomic fragment can be repeated multiple times resulting in a BAC genomic fragment with several polymorphic gene segments, including their promoter elements. It is apparent that the examples shown in Figures 1 and 2 can be combined wherein the technique for insertion can be used to add extra polymorphic V gene segments to a BAC genomic fragment as depicted in Figure 1. One might choose to add these extra segments to an IG genomic fragment since such a fragment would be more amenable to proper IG gene expression once inserted into a non-human mammal's genome. It is known that a genomic fragment can have elements such as enhancers or elements that contribute to certain chromatin conformations, both important in wild-type gene expression.
Figure 3 depicts an additional method to create genomic fragments with polymorphic V gene segments. This method depends upon the efficiency with which short (around 50 to 150 bases, preferably 100 bases) single stranded DNA fragments recombine with a homologous sequence using recombineering (Nat Rev Genet. 2001 Oct;2(10):769-79; Recombineering: a powerful new tool for mouse functional genomics; Copeland NG, Jenkins NA, Court DL). The recombinases used in recombineering preferentially bind and use such short single-stranded fragments of DNA as a substrate for initiating homologous recombination. The efficiency can be as high as 10-2, that is, a positive event can be found in approximately 100 randomly picked (not selected) clones resulting from recombineering. A positive event in this example occurring when one or more single nucleotide changes introduced into the single-stranded fragment get transferred to the BAC insert containing V gene segments and surrounding genomic DNA, said nucleotide change or changes occurring at a homologous sequence on the BAC.
Polymorphic V gene segments can differ from endogenous V gene segments by only 1 or 2, or up to 10 or 15 nucleotide changes, for example. An example of such nucleotide polymorphisms are depicted in Figure 5. Short single stranded regions that encompass the polymorphic nucleotide changes can be chemically synthesized using standard techniques. The resulting single stranded DNA fragments are introduced into bacteria and via recombineering techniques approximately 1 in 100 BAC fragments will have incorporated the polymorphic nucleotides via homologous incorporation of
the single stranded fragment (Figure 3a). BACs with the desired nucleotide change can be identified by screening for example several hundred individual clones by polymerase chain reaction (PCR) amplification and sequencing, both by standard techniques. In the example, two nucleotide changes will convert a VH1-69*01 gene segment into a VHl-69*02 gene segment (Figure 3b).
It is clear that this process can be repeated for multiple endogenous V gene segments contained on a single BAC genomic fragment. In addition, the techniques depicted in Figure 2 can be used to add additional polymorphic V gene segments by insertion into regions between existing V gene segments. As would be evident to one skilled in the art, a combination of these techniques can be used to create numerous variations of both polymorphic and endogenous human V gene segments. And it would be evident that several different genomic fragments with engineered polymorphic V gene segments and endogenous human V gene segments can be combined to create even more variations.
EXAMPLE 2
"Adding Polymorphic V-regions to the Genome using SRMCE of Modified BACs"
Modified BACs with polymorphic V gene segments created using the methods described in
Example 1 can be used to alter the genome of non-human mammals. These alterations can result in an intact IG locus in which normal immunoglobin region recombination results in VDJ or VJ combinations which includes the human V gene segments. An example of how such an animal can be created is by altering the genome of, for example, mouse embryonic stem (ES) cells using the strategy outlined in Figure 4.
One technique to integrate modified BACs with polymorphic V gene segments into a genome is sequential recombinase mediated cassette exchange (SRMCE). The technique is described in WO2011004192 (Genome Research Limited), which is incorporated here in its entirety by reference.
S MCE provides for a locus modified with a 'landing pad' inserted at a specific location. This insertion can either be de novo via homologous recombination or as a consequence of a previous BAC insertion. In this example, the landing pad is inserted in the mouse IGH locus between the most 3' J gene segment and the Cμ gene segment and a previous BAC insertion via SRMCE techniques have resulted in the addition of 5 human V gene segments and 2 V region pseudogenes. The landing pad has elements as shown in Figure 4 that will allow the selection of correct insertion of a second targeting BAC fragment. The specificity of this insertion is provided by ere recombinase-mediated exchange between permissive lox sites. A lox site is permissive for recombination only with a compatible lox site. In this example, the loxP site will only recombine with loxP and \ox2272 will only recombine with \ox2272. This provides directionality to the insertion of the BAC fragment as depicted in Figure 4b and 4c.
ES cell clones with correct insertions are selected from a pool of clones without insertions or with non-productive insertions by resistance to puromycin. Resistance to puromycin results from the juxtaposition of an active promoter element, PGK, with the puroTK coding region. Correct insertions are verified by standard techniques including PCR of junctions, PCR of internal elements, Southern blotting, comparative genomic hybridization (CGH), sequencing and etc. In the example, correct I ox2272-1 ox2272 and loxP-loxP recombination also results in two intact sets of piggyBac elements that did not exist prior to insertion. An intact piggyBac element is comprised of a set of inverted repeats which are depicted in the figure by "PB5"' and "PB3"'. An appropriated oriented set of piggyBac elements are the substrate of piggyBac transposase which can catalyse recombination between the elements, resulting in deletion of intervening sequences as well as both elements. The DNA remaining after a piggyBac transposition is left intact and is lacking any remnant of the piggyBac element. In the example, ES cell clones with successful piggyBac transposition are selected by loss of the active puroTK element which renders the cells resistant to the drug FIAU (Figure 4c and 4d).
The final product of the SRMCE method in this example is a IGH locus with several polymorphic V gene segments inserted along with a set of endogenous unmodified VH gene segments between sequences of the mouse genome on the 5' side and the mouse IGH constant region gene segments on the 3' side. The polymorphic V gene segments are positioned such that they can participate in the recombination events associated with B cell maturation yielding VDJ gene segments. These gene
segments can then be transcribed and spliced to the mouse constant region. Translation of these transcripts will result in the production of an antibody heavy chain encoded by the polymorphic V gene segment, a human DH gene segment, a human JH gene segment and a mouse constant heavy chain gene segment.
As is well known to those skilled in the art, an ES cell clone can be used to create a line of genetically modified mice via injection of said cells into a mouse blastocyst embryo, transferring the injected embryo to a suitable recipient and breeding the chimeric offspring that result. The modified gene locus can be propagated through breeding and made either heterozygous or homozygous depending on the genetic cross.
It is evident from the structure of the IGH locus provided in this example and by knowledge of the mechanisms involved in B cell receptor (BC ) and antibody gene rearrangements that a large set of different combinations of polymorphic V gene segments with various DH and JH gene segments will result and these can contribute to a large repertoire of functional antibody genes in a population of B cells in genetically modified animals. In this example, several different human VH1-69 polymorphs are incorporated to provide superhuman VH diversity. This particular VH gene segment is known to be prevalent in antibodies that bind infectious disease pathogens (such as influenza virus) and therefore the antibody repertoire of a mouse with the genetic modification of this example would be expected to produce antibodies with a bias in favour of those that bind infectious disease pathogens. The repertoire, in other words, would have a larger subset of antibodies with superior affinities for pathogen antigens. Examples of such pathogens include influenza virus, hepatitis C virus (HCV) and human immunodeficiency virus-1 (HIV-1) (see also table above).
EXAMPLE 3
"Alignment of 13 VH1-69 Alleles"
Building a more diverse antibody repertoire by incorporating additional V gene segment polymorphs requires availability of polymorphic variants of V gene segments. One source of such variants include sequence databases. In this example, 13 distinct variants of the VH1-69 gene segment are provided.
These variant sequences and comparisons are drawn from the "IMmunoGeneTics" IMGT
Information System (www.imgt.com) database. Figure 5 is a diagram of the alignment of variants *02 through *13 with the *01 variant. The VH1-69*01 nucleotide and amino acid sequence is provided at the top of the figure. Where the remaining variants are identical to the *01 variant sequence a dash is inserted below the sequence. Nucleotide differences are noted alongside the appropriate variant and if the sequence change results in a protein coding change, the amino acid change is indicated above the triplet.
Figure 5 depicts between 1 and 4 amino acid changes for each variant in comparison to the *01 variant. All of the amino acid changes occur in the part of the heavy chain protein encoding the complementarity determining regions (CD s). These regions are responsible for antigen specificity and the affinity of the antibody for the antigen. It is evident that providing additional polymorphic CDRs in a repertoire of antibodies will increase the likelihood of there being an antibody with superior binding characteristics for various antigens. In several reports, it has been observed that the VHl-69-encoded variable region of the heavy chain is often found in antibodies that bind influenza virus, HCV and HIV-1 antigens (see table above). Therefore incorporating the polymorphic V gene segments of this example into a transgenic animal model using the methods of Examples 1 and 2 would likely result in an antibody repertoire in said transgenic animal with more antibodies that bind to antigens associated with these and other pathogens. And as is known in the art, a larger repertoire increases the probability of finding monoclonal antibodies using, for example, hybridoma technology, that bind with high affinity and specificity to a desired antigen.
This disclosure therefore describes in these examples a transgenic mouse model which can be immunized with pathogen or other antigens. Plasma B cells from such an immunized mouse can be used to make a hybridoma library that can be screened for production of antibodies that bind the pathogen antigens. This library will be superior to libraries from traditional transgenic mice for finding such antibodies given the addition of polymorphic VHl-69 gene segments to the IGH locus in said transgenic mouse.
These examples are not limiting to the human polymorphic V gene segments that can be chosen or to the methods used to introduce them into an animal model. The method can be used to construct a transgenic locus with immunoglobulin D and/or J segments. The V, D, J segments can be from a plurality of human sources (optionally more than one human ethnic population).
EXAMPLE 4
Human leH JH Gene Variants Selected from the 1000 Genomes Database
Data is presented for human JH2, 5 and 6 variants. In Tables 10A, 11A and 12A samples from humans from various populations are listed where the sequence analysis of the inventors has revealed the presence of polymorphisms in one or both IgH JH alleles. The population codes are explained in Table 8 above. The polymorphisms are nucleotide variants from J H2, 5 and 6 reference sequences (SEQ ID NOs: 1, 2 and 3 respectively; see below). All references are sequences taken from the EnsembI database (www.ensembl.org). The J H5 reference is human IgH J5-001 disclosed in that database. The J H6 reference is human IgH J6-001 disclosed in that database. The J H2 reference is human IgH J2-001 disclosed in that database.
The reference nucleotide and encoded amino acid sequences are shown on the next page.
Alignments with encoded amino acid sequences are also provided, including the corresponding position numbers on human chromosome 14.
Variant Frequencies are shown in Tables 10A, 11A and 12A and these relate to the frequency of the variants in the 1000 Genomes Database (release current at October 2011).
Tables 10B, 11B and 12B show the non-synonymous nucleotide polymorphisms in the human J H variants, as sorted by the present inventors from the 1000 Genomes database. Position numbers corresponding to nucleotide positions on human chromosome 14 are shown for variant positions (chromosome 14 being the chromosome bearing the IgH locus in humans). Thus, for example, the first entry in Table 11B is "14:106330027:A/C" which refers to a position in a variant J H5 sequence wherein the position corresponds to position 106,330,027 on human chromosome 14, such position being A (adenine) in the reference sequence. The "C" indicates that the present inventors observed a mutation to cytosine at this position in the variants found in the 1000 Genomes database. This change leads to a change at the amino acid level of the encoded sequence (ie, a "non-synonymous" change), in this case a change from a serine (found in the reference) to an alanine in the variant.
Example 5:
Human Antibody Gene Segment Variant Identification & Population Analysis
The genomic coding region coordinates for each target gene for variant analysis were identified from the Ensembl WWW site (www.ensembl.org) using coordinates from the GRCh.p8 Human Genome assembly (www.ncbi.nlm.nih.gov/proiects/genome/assemblv/grc). Using the collected gene location coordinates, variant data was extracted from the public ftp site of the 1000 Genomes Project using the Perl 'Variant Pattern Finder' (VPF - www.1000genomes.org/variation-pattern- finder-api-documentation).
Data extracted by VPF was post processed using software to extract all non-synonymous (NSS) variants with their associated genotype calls. Genotypes calls were assembled to form unique haplotypes, representing groups of NSS variants associated with 1000 Genome population groups and frequency of occurrence within those populations.
The output of the analysis results in tables such as in Table 13. The main body of the table describes each haplotype in turn giving a unique ID for that gene (in the range a-z,aa-zz), the population frequencies and occurrence in individuals and unique population groups; one or more subsequent columns describe the DNA base calls at each location that form the haplotype giving both the base from the reference sequence or the variant base call.
Table 13 was constructed in this manner. The table can be read as follows:
The first four columns (left to right) consist of (1) the haplotype ID letter ('re indicates reference - the DNA base call at each genomic location from the GRCh37 Human Reference Assembly) (2) the observed cumulative frequency of the haplotype among the different populations (3) the number of individuals in which a specific haplotype was observed (4) the number of unique population groups that the identified individuals belong to (the actual population group identifiers are displayed as a string of ID's in the most right hand column for each haplotype. For example haplotype 'a' has a population ID string of '3,4,9,13').
The populations are numbered as follows (population labels being according to 1000 Genomes
Project nomenclature)
1= ASW;
2= CEU;
3=CHB;
4=CHS;
5=CLM;
6=FIN;
7=GBR;
8=IBS;
9=1 PT;
10=LWK;
11=MXL;
12=PU ;
13=TSI;
14=Y I.
Subsequent columns detail a single point variant and have the following format (top to bottom) (1) the human genomic location of the variant (format [chromosome number]: [location] e.g.
'14:106204113'); (2) The identifier for the point variant as defined in DbSNP
(www.ncbi.nlm.nih.gov/proiects/SNP/): (3) One or additional rows show the amino acid change as result of the variant for a specific transcript (denoted by the EnsembI transcript ID in the most right- hand column for each row), the format is the amino acid in the reference sequence followed by '->' and the amino acid caused by the substitution of the variant in the reference sequence (e.g. 'Gly- >Arg' means a that the translated reference sequence would result in a glycine at that location, whereas the substitution of the identified variant would result in translated protein containing arginine) using the lUPAC three letter amino acid codes
(https://pac.iupac.org/publications/pac/pdf/1972/pdf/3104x0639.pdf). Subsequent rows (one per haplotype) show the DNA base at each location, bases matching the reference sequence are shown in black on white back ground, bases varying from the reference are shown as white text on a black background.
The most right-hand column contains the EnsembI transcript ID's (e.g. 'ENST00000390542') for each of the gene transcript and relates to the amino acid changes to the left of this column. Because the transcripts are differing lengths each variant position may or may not have an associated amino acid change at the that position.
Example 6:
Transgenic Mice. B-cells. Hvbridomas. Antibodies & Heaw Chains Based on Human JH6*02
A functional human gene segment repertoire (from VH2-26 to JH6, see the IMGT database for the structure of the human IgH locus;
https://www.imgt.org/IMGTrepertoire/index. php?section=LocusGenes&repertoire=locus&species=h uman&group=IGK ) was sectored by the inventors to produce two different transgenic heavy chain alleles (denoted S2F and S3F) and corresponding mice. The transgenic alleles were expressed in the mice and the heavy chain repertoires were assessed at the RNA transcript level. Deep sequence
analysis was carried out using Bioinformatics methods to assess V, D and JH gene usage, including in variable domain sequences having a HCD 3 length of at least 20 amino acids. Endogenous, mouse variable region gene segments were inactivated by inversion (as per the method described in WO2011004192, this disclosure being incorporated herein by reference).
Sequencing of Human Donor DNA Samples: Identification of Conserved JH6*02 Variant
DNA samples from 9 anonymised consenting human donors were obtained by taking cheek swabs.
The samples were processed and the DNA Samples were extracted follow the protocol of QJAamp DNA Mini Kit (Cat.No.51304, Qiagen).
PCR reactions were set up to amplify the JH6 region and PCR products were sequenced (PCR Oligos sequence: Fwd. 5'-AGGCCAGCAGAGGGTTCCATG-3' (SEQ ID NO: 444), Rev. 5'- GGCTCCCAGATCCTCAAGGCAC-3' (SEQ ID NO: 445)).
Sequence analysis was carried out by comparing to the JH6 reference sequence from IMGT annotated database (https://www.imgt.org/), and this identified that all 9 donor genomes contained the human JH6*02 variant, with this variant being in the homozygous state in 7 out of the 9 donors. The inventors also consulted the genomic sequences publicly available for Jim Watson and Craig Venter at Ensembl human genome database [https://www.ensembl.org/]. These too contained the human JH6*02 variant. This confirmed to the inventors that human JH6*02 is a common, conserved variant in humans, and thus a good candidate for construction of a transgenic IgH locus as per the invention
Identification of Suitable Human DNA Sequence BACs
A series of human bacterial artificial chromosome (BAC) clones were identified from Ensemble (https://www.ensembl.org/index.html) or UCSC (https://genome.ucsc.edu/) human database searches based on gene name (IGH) or location (chromosome 14: 106026574-107346185). Seven human RP11 BAC clones (see an extract of the UCSC databse in Figure 10, identified BACs being circled) were selected, RP11-1065N8 BAC carrying human JH6*02. In total, the following BACs were
identified as sources of human IgH locus DNA: RP11-1065N8, RP11-659B19, RP11-141I7, RP-112H5, RP11-101G24, RP11-12F16 and RP11-47P23.
With a similar approach, different BAC clones (eg, different RPll clone I Ds or different sources from RPll) or genetically engineered BACs can be selected for insertion into the mouse IGH locus to provide different sets of human repertoires in the transgenic mouse.
Construction of Transgenic IgH Loci
Insertion of human heavy gene segments from a 1st IGH BAC (RP11-1065N8) into the IGH locus of mouse AB2.1 ES cells (Baylor College of Medicine) was performed to create a heavy chain allele denoted the SI allele. The inserted human sequence corresponds to the sequence of human chromosome 14 from position 106494908 to position 106328951 and comprises functional heavy gene segments VH2-5, VH7-4-l, VH4-4, VHl-3, VHl-2, VH6-1, Dl-1, D2-2, D3-9, D3-10, D4-11, D5-12, D6-13, Dl-14, D2-15, D3-16, D4-17, D5-18, D6-19, Dl-20, D2-21, D3-22, D4-23, D5-24, D6-25, Dl-26, D7-27, JH1, JH2, Jh3, Jh4, Jh5 and JH6 (in 5' to 3' order), wherein the JH6 was chosen to be the human J H6*02 variant. The insertion was made between positions 114666435 and 114666436 on mouse chromosome 12, which is upstream of the mouse Cμ region. The mouse VH, D and JH gene segments were retained in the locus, immediately upstream of (5' of) the inserted human heavy chain DNA.
A second allele, S2 was constructed in which more human functional VH gene segments were inserted upstream (5') of the 5'-most VH inserted in the SI allele by the sequential insertion of human DNA from a second BAC (BAC2). The inserted human sequence from BAC2 corresponds to the sequence of human chromosome 14 from position 106601551 to position 106494909 and comprises functional heavy chain gene segments VH3-13, VH3-11, VH3-9, VHl-8, VH3-7. The mouse VH, D and JH gene segments were retained in the locus, immediately upstream of (5' of) the inserted human heavy chain DNA. In a subsequent step, these were inverted to inactivate them, thereby producing S2F mice in which only the human heavy chain variable region gene segments are active.
A third allele, S3 was constructed in which more human functional VH gene segments were inserted upstream (5') of the 5'-most VH inserted in the S2 allele by the sequential insertion of human DNA
from a third BAC (BAC3). The inserted sequence corresponds to the sequence of human chromosome 14 from position 106759988 to position 106609301, and comprises functional heavy chain gene segments, VH2-26, VHl-24, VH3-23, VH3-21, VH3-20, VH1-18, and VH3-15. The mouse VH, D and JH gene segments were retained in the locus, immediately upstream of (5' of) the inserted human heavy chain DNA. In a subsequent step, these were inverted to inactivate them, thereby producing S3F mice in which only the human heavy chain variable region gene segments are active.
Mice bearing either the S2F or S3F insertion into an endogenous heavy chain locus were generated from the ES cells using standard procedures. The other endogenous heavy chain locus was inactivated in the mice by insertion of an inactivating sequence comprising neoR into the mouse JH- Cμ intron (to produce the "HA" allele).
Immunisation procedure
Transgenic mice of the S2F or S3F genotype were primed with 20-40ug recombinant proteins obtained commercially or produced in house with Antigen 1 (OVA (Sigma A7641); Antigen 2 (a human infectious disease pathogen antigen) and Antigen 3 (a human antigen) via the ip route in complete Freunds adjuvant (Sigma F 5881) and lOug/animal CpG (CpG oligo; Invivogen, San Diego, California, USA) and then boosted twice in about two weekly intervals with about half the amount of antigen in incomplete Freunds adjuvant (Sigma F 5506) and lOug/animal CpG. Final boosts were administered two weeks later iv without any adjuvant and contained 5-10 ug protein in PBS.
Hvbridoma fusion procedure
Spleens were taken 3 days after the final boost and spleenocytes were treated with CpG (25 μιτι final concentration) for and left until the following day. Cells were then fused with SP0/2 Agl4 myeloma cells (HPA Cultures Cat No 85072401) using a BTX ECM2001 electrofusion instrument. Fused cells were left to recover for 20 minutes then seeded in a T75 flask until next morning. Then the cells were spun down and plated out by dilution series on 96-well culture plates and left for about 10 days before screening. Media was changed 1-3 times during this period.
Screening
Screening
Culture supernatants of the hybridoma wells above were screened using homogenious time resolved fluorescence assay (htrf) using Europium cryptate labelled anti-mouse IgG (Cisbio anti-mouse Ig Europium Cryptate) and a biotin tagged target antigen with a commercially available streptavidin conjucated donor (Cisbio; streptaviding conjugated D2) or by IgG-specific 384 well ELISA. Positive wells identified by htrf were scaled to 24-well plates or immediately counterscreened using an IgG- specific detection ELISA method. Positives identified by primary ELISA screen were immediately expanded to 24-well plates. Once cultures were expanded to 24-well stage and reached conflueny, supernatants were re-tested using htrf or IgG-specific ELISA to confirm binding to target antigen. Supernatant of such confirmed cultures were then also analysed by surface plasmon resonance using a Bio ad ProteOn XPR36 instrument. For this, antibody expressed in the hybridoma cultures was captured on a biosensor GLM chip (BioRad 176-512) which had an anti-mouse IgG (GE
Healthcare BR-1008-38) )covalently coupled the biosensor chip surface. The antigen was then used as the analyte and passed over the captured hybridoma antibody surface. For Antigen 2 and Antigen 3, concentrations of 256nM, 64nM, 16nM, 4nM and InM were typically used, for Antigen 1, concentrations of 1028nM, 256nM, 64nM, 16nM and 4nM were typically used, binding curves were double referenced using a OnM injection (i.e. buffer alone). Kinetics and overall affinities were determined using the 1:1 model inherent to the BioRad ProteOn XPR36 analysis software.
Any clones with confirmed binding activity were used for preparing total RNA and followed by PCR to recover the heavy chain variable region sequences. Standard 5'-RACE was carried out to analyse RNA transcripts from the transgenic heavy chain loci in the S2F and S3F mice. Additionally, deep sequence analysis of almost 2000 sequences produced by the mice was carried out.
Bionformatics Analysis
Sequences for analysis were obtained from two different methods:
• The first is from RNA extracted from the spleen: first cDNA strand was synthesized using an oligo based on the Cmu region of the mouse IGH locus as a PCR template. PCR was performed using this oligo with an oligo dT-anchor primer. Then PCR product was cloned into pDrive vector (Qiagen) and then sequenced.
• The second is from hybridomas generated through electro-fusion: total NA was extracted from hybridoma lines of interest using standard Trizol methods and frozen at -80 °C for long term storage. cDNA was generated from lOOng total RNA using standard Superscript III reverse transcriptase and a gene-specific reverse primer binding to all mouse IgG isotypes for heavy chain and a mouse kappa constant region primer for the light chain amplification. 2-3 ul of cDNA were then used as template in a PCR reaction using Pfu DNA polymerase and a panel of degenerate forward primers annealing to the leader sequence of the human immunoglobulin variable domain as well as one mouse pan-lgG reverse primer. PCR products were run out of a 1% agarose gel and bands of approximately 350-450 basepairs extracted and purified. DNA was then sequenced.
The sequences from the first method can either be from IgM from Naive mice or IgG from immunised mice. The samples from the second method are all from IgG from immunised mice, and specific to the immunising antigen. Almost 2000 sequences were analysed.
The sequences were obtained as a pair of forward and reverse reads. These were first trimmed to remove low-quality base calls from the ends of the reads (trimmed from both ends until a 19 nucleotide window had an average quality score of 25 or more). The reads were combined together by taking the reverse complement of the reverse read, and aligning it against the forward read. The alignment scoring was 5 for a match, -4 for a mismatch, a gap open penalty of 10 and a gap extension penalty of 1. A consensus sequence was then produced by stepping through the alignment and comparing bases. When there was a disagreement the base with the highest quality value from sequencing was used.
The BLAST+ (Basic Local Alignment Search Tool) (Camacho C, Coulouris G., Avagyan V., Ma N., Papadopoulos J., Bealer K., & Madden T.L (2008) "BLAST+: architecture and applications." BMC Bioinformatics 10:421 https://www.ncbi.nlm.nih.gov/pubmed/20003500) program 'blastn' was then used to find the germline J and V segments used in each sequence. A wordsize of 30 was used for V matching, and 15 for J matching. The database searched against was constructed from the NGS sequencing of the BACs which were used to generate the Kymouse.
If a sequence matched both a V and a J segment, the sequence between the two was then compared to a database of germline D segments in the mouse using 'blastn' with a wordsize of 4 and the options 'blastn-short' and 'ungapped'. This was used to assign a D segment, if possible. The CDR3 was identified by searching for the conserved "TATTACTGT" sequence in the V segment, and the "CTGGGG" in the J segment. If these motifs were not found, then up to 4 mismatches were allowed. The IMGT definition of CDR3 was used, so the CDR3 length is calculated from after the "TGT" in the V to before the "TGG" in the J. Sequences with an out of frame junction (those which do not have a CDR3 nucleotide length divisible by 3) or which contained a stop codon ("TAA", "TAG" or "TGA") were excluded.
The identity of the matching V, J and D segments as well as the CDR3 length from this assignment were then saved as a table for downstream analysis. The ratio of IGHJ6*02 used increased from the naive to immunised mice, as well as being enriched in the sub-population of sequences with a long HCDR3 (defined as consisting of 20 or more amino acids):
All HCDR3>20
JH6*02% Total Count JH6*02% i Total Count % HCDR3>20
Naive 22.31% 1340 91.11% 1 45 3.36%
Immunised 37.50% 256 66.67% ! 9 3.52%
Hybridoma 36.13% 119 63.64% ! 11 9.24%
This shows that the JH6*02 gene segment is selected for by immunisation, as the proportion of JH6*02 usage increases after immunisation. JH6*02 is also used in the majority of antibodies with a long HCDR3 length, which is desirable for targets which are specifically bound by long HCDR3 length antibodies.
SEQ ID NO: 1 (JH5 Reference)
T T G A C C A A G C G G T C C C T T G G
A G A G G A G T C JH5 Alignment:
(top line=SEQ ID NO: 1, Middle line=-SEQ ID NO:5, Bottom line=SEQ ID NO:6)
ώ s s G G G G G A C C C C G G T C C C T ,! G G G g C C A G T G G C § G A G G § G T ca φ φ
iu U) C C C C C T G G G G C C A G G G A ¾ ¾ C C 3 G G T C A C C G I C T C C hC C A
W W Q
SEQ ID NO: 2 (JH6 Reference)
A T G A T G A T G A T G A T G A T G T A
C c T G c A G A C C c C G T T T c C c T
G G T G c C A G T G G C A G A G G A G T c
JH6 Alignment:
(top line=SEQ ID NO: 2, Middle line=-SEQ ID N0:7, Bottom line=SEQ ID N0:8)
o O O O o o
<_>
ώ
T G A T G A T G A T G A T G /^. "i <!f. T A C C T G C A G A C C C C G f T
A C T A C T A C T A C T A C lo & dS A T G G A C G T C T G G G G C A? A
Y Y Y Y Y Y M D V W G
G G G A C C A C G G T C A C C G T C T C C T C A G G T T V T V S S
SEQ ID NO: 3 (JH2 Reference)
JH2 Alignment:
(top line=SEQ ID NO: 3, Middle line=-SEQ ID N0:9, Bottom line=SEQ ID NO:10)
C C C C G C A C C G G A C C A G T G A C A G A G G A
W W
TABLES
tables, the notation is illustrated by the following example
Polymorphic variant IGV lambda Vl-40*02 has Genbank Accession No. X53936 and when compared to the *01 variant, the Vl-40*02 variant has mutati at positions 9, 10 and 4. For example, at position 9, a "C" appears instead of a "G" that is present in the *01 variant. The " | " is simply a notation separa and does not indicate any mutation. For example the "g282 I" notation indicates no change (ie, position 282 is a g). "del#" means that the residue at th position is absent.
10
Table 1: Human IgH V Polymorphic Variants
All variant sequences appearing in Genbank under the listed Accession Numbers are incorporated herein in their entirety by reference as though
15 explicitly recited herein and for possible inclusion in any of the claims herein.
IGHV3- L06615 al50>g
30*04
IGHV3- M77323 cl01>g,tl02>c,A34>G
30*05 a293>g,D98>G
IGHV3- L06617 c75>g cl01>c,tl02>c,A34>G
30*06
IGHV3- L06614
30*07 It288>c|
IGHV3- M62737 gl8>c,E6>D g80>c,G27>A
30*08
IGHV3- M77300 al50>g
30*09 a229>g,T77>A
IGHV3- M77326
30*10 g202>a,A68>T
IGHV3- M77331 c75>g
30*11
IGHV3- M77338 a27>g| |c75>g| | cl01>g,tl02>c,A34>G | 30*12 It288>c|
IGHV3- M77339 |cl01>g,tl02>c,A34>G|
30*13 |c257>g,T86>R|
Table 2: Human IgH D Polymorphic Variants
All variant sequences appearing in Genbank under the listed Accession Numbers are incorporated herein in their entirety by reference as though explicitly recited herein and for possible inclusion in any of the claims herein.
Underlined nucleotides in the *01 variant are positions that are different in other variants, eg, GOCG for IGHD3-16*02 indicates that GC in the *01 variant is instead CG in the *02 variant. All other positions are identical to between the *01 and other variant. Similar notation is used in other tabl below to denote changes between variants of gene segments.
Table 3: Human IgH J Polymorphic Variants
All variant sequences appearing in Genbank under the listed Accession Numbers are incorporated herein in their entirety by reference as though explicitly recited herein and for possible inclusion in any of the claims herein.
GG>GC
Table 4: Human Ig Vk Polymorphic Variants
All variant sequences appearing in Genbank under the listed Accession Numbers are incorporated herein in their entirety by reference as though explicitly recited herein and for possible inclusion in any of the claims herein.
CTC CTG ATC TAT GAT GCC TCC AGT TTG GAA AGT GGG
GTC CCA ... TCA AGG TTC AGC GGC AGT GGA TCT GGG ACA GAA TTC
ACT CTC ACC ATC AGC AGC CTG CAG CCT GAT GAT TTT GCA ACT TAT TAC TGC CAA CAG TAT AAT AGT TAT TCT CC
IGKV1- M23851 AOAT
5*02
IGKV1- X72813 GAT>AAG
5*03
GCC>GCG TCC>TCT TTG>TTA
IGKV1-6 IGKV1- M64858 SEQ ID NO: 101
6*01
IGKV1-8 IGKV1- Z00014 SEQ ID NO: 102
8*01
IGKV1D-8 Z00008 SEQ ID NO: 103
8*01
IGKV1-9 IGKV1- Z00013 SEQ ID NO: 104
9*01
IGKV1-12 IGKV1- V01577 SEQ ID NO: 105
Table 5: Human Ig VA Polymorphic Variants
All variant sequences appearing in Genbank under the listed Accession Numbers are incorporated herein in their entirety by reference as though explicitly recited herein and for possible inclusion in any of the claims herein.
Table 6: Human IgH Jk Polymorphic Variants
All variant sequences appearing in Genbank under the listed Accession Numbers are incorporated herein in their entirety by reference as though explicitly recited herein and for possible inclusion in any of the claims herein.
Table 7: Human IgH JA Polymorphic Variants
All variant sequences appearing in Genbank under the listed Accession Numbers are incorporated herein in their entirety by reference as though explicitly recited herein and for possible inclusion in any of the claims herein.
TABLE 8: 1000 GENOMES PROJECT HUMAN POPULATIONS
Below is a summary of the ethnic population origin of samples that the 1000 Genomes Project sequences.
Population European ancestry
Utah residents (CEPH) with Northern and Western European ancestry (CEU) Toscani in Italia (TSI)
British from England and Scotland (GBR) Finnish from Finland (FIN)
Iberian populations in Spain (IBS)
East Asian ancestry
Han Chinese in Beijing, China (CHB) Japanese in Toyko, Japan (JPT)
Han Chinese South (CHS) Chinese Dai in Xishuangbanna (CDX)
Kinh in Ho Chi Minh City, Vietnam (KHV) Chinese in Denver, Colorado (CHD) (pilot 3 only)
West African ancestry
Yoruba in Ibadan, Nigeria (YRI)
Luhya in Webuye, Kenya (LWK) Gambian in Western Division, The Gambia (GWD)
Malawian in Blantyre, Malawi (MAB)
K00004-1 WO
Population
West African Population (TBD)
Americas
African Ancestry in Southwest US (ASW) African American in Jackson, MS (AJM)
African Caribbean in Barbados (ACB) Mexican Ancestry in Los Angeles, CA (MXL)
Puerto ican in Puerto Rico (PUR)
Colombian in Medellin, Colombia (CLM)
Peruvian in Lima, Peru (PEL)
South Asian ancestry
Ahom in the State of Assam, India
Kayadtha in Calcutta, India
Reddy in Hyderabad, India
Maratha in Bombay, India
Punjabi in Lahore, Pakistan
Table 9: Immunoglobulin Gene Usage in Human Antibody Responses to Infectious Disease Pathogens
KAPPA V GEN ES Haemophilus influenzae type b Haemophilus influenzae 1. Lonberg, Nat Biotech 2005; Vk I I germline gene A2 + J K3 polysaccharide (Hib PS) [human PBMCs]
Vk I I family gene + J K4 2. Adderson et al, J Clin Invest 1992; 94% identical to the A27 [Human PBLs]
(Humkv325) germ line gene 3. Chung et al, J Immunol 1993 a VKI gene family member; κΙ- 4. Nadel et al, J Immunol 1998 15A (KL012) 5. Feeney et al, J Clin Invest 1996
6. Lucas et al, Infect Immun 1994;
LAMBDA V GENES [Human PBLs]
Four νλ VI I family members that 7. Adderson et al, J Clin Invest 1993; are 96-98% identical to each [Human PBLs]
other 8. Granoff et al, J Clin Invest 1993; νλ I I family members (82, 89 and [human PBLs]
91% homologous to VA2.1 gene) 9. Azmi et al, Infect Immun 1994; + VH II I segments closely [human tonsil cells]
homologous to germline gene
9.1
VxVI I 4A
All with JX homologous to
germline JA2 and JA3
VH GEN ES
VH 96% identical to the VH germ
line gene segment DP77 (V3-21)
Table lOAiHuman IgH JH5 Variant Occurrences
HUMAN POPULATION
NA12814; NA18617;
NA12763 NA18636
and 1 and 2 HG00683; HG00261; NA19448;
NA19835 other(s) other(s) HG00590 HG01359 HG00189 HG00136 NA18987 NA19331 HG00740 NA20799 0.017
NA18934;
NA19147
HG00595; HG00267; NA19456; and 1
NA11994 HG00584 HG00276 HG00137 NA19332 NA20542 other(s) 0.011
HG01494 HG00351 HG00234 NA19005 NA19719 0.005
NA19921 NA12815 HG00650 HG00177 NA18517 0.005
NA12829;
NA12890
and 1
other(s) HG00358 NA20503 NA19093 0.005
ZZ£0/ZlOZaO/13d
240
Table llA:Human IgH JH6 Variant Occurrences
HUMAN POPULATION
NA20289; NA12546; NA18532; HG00628; HG01456; HG00278; HG00259; HG01619; NA19083; NA19395; NA19777; HG 00640; NA20798; NA19172;
NA20294 NA12046 NA18562 HG00690 HG01275 HG00313 HG00129 HG01626 NA18986 NA19321 NA19795 HG01167 NA20513 NA18909 and 19 and 41 and 58 and 57 and 33 and 57 and 53 and 7 and 48 and 20 and 48 and 22 and 58 and 8
other(s) other(s) other(s) other(s) other(s) other(s) other(s) other(s) other(s) other(s) other(s) other(s) other(s) other(s) 0.509
NA20127; NA12348; NA18558; HG00464; HG01495; HG00358; HG00135; HG01620; NA18942; NA19038; NA19725; HG01108; NA20787; NA19116;
NA20414 NA10851 NA18579 HG00683 HG01550 HG00362 HG00245 HG01625 NA19004 NA19451 NA19773 HG01072 NA20754 NA18517 and 11 and 17 and 9 and 16 and 7 and 12 and 6 and 1 and 11 and 17 and 6 and 12 and 14 and 22 other(s) other(s) other(s) other(s) other(s) other(s) other(s) other(s) other(s) other(s) other(s) other(s) other(s) other(s) 0.173
NA20314; NA06989; NA18608; HG00436; HG01357; HG00188; HG00116; NA18974; NA19372; NA19758; HG01191; NA20522; NA18520;
NA20317 NA12044 NA18624 HG00404 HG01461 HG00282 HG00102 NA18978 NA19474 NA19749 HG01048 NA20815 NA19209 and 11 and 10 and 16 and 13 and 10 and 10 and 16 and 17 and 16 and 4 and 7 and 14 and 16 other(s) other(s) other(s) other(s) other(s) other(s) other(s) HG01518 other(s) other(s) other(s) other(s) other(s) other(s) 0.171
NA12827 HG00584 HG00336 0.003
NA19471;
NA19401 NA18868 0.003
NA19121;
NA19175 0.002
NA07346 NA19376 0.002
NA18934;
NA18856 0.002
NA18637 0.001
NA12004 0.001
HG00280 0.001
NA12283 0.001
HG00183 0.001
HG00702 0.001
NA19403 0.001
HG00329 0.001
NA18949 0.001
NA19428 0.001
NA19707 0.001
NA19318 0.001
IJ44
Table llB(ii): A further variant (not listed in TablellB(Q) is the following:-
< h- h- U U
U <
U U ΰ
U
h- <
IID λ
Table 13.2 -I
Table 13.2 - IGHA2
0.00045 3 0.00045 5 0.00045 1 1 0.00045 3 0.00045 13 0.00045 14 0.00045 13 0.00045 2
'Μ
h.type
Table 13.4 - IGHD2-8
Table 13.10 -IGHD6-13
Table 13.11 - IGHD7-27
h.type (5 H «! ϋ Ό
pops
# indvs cum.freq h.type
Table 13.17 -IGHG3
Table 13.17 · IGHG3 s 0.00135 ab 0.00135 ak 0.00135 ag 0.0009 y 0.0009 az 0.0009 aa 0.0009 ap 0.0009 av 0.0009 af 0.0009 at 0.0009 aw 0.0009 ay 0.0009 ar 0.0009 an 0.0009 ah 0.00045 ba 0.00045 ax 0.00045 bb 0.00045 aq 0.00045
be 0.00045 z 0.00045 ao 0.00045 au 0.00045 ad 0.00045 be 0.00045 ac 0.00045 as 0.00045
Table 13.17 -IGHG3
a 0.2813 479 14 1,2,3,4,5,6,7,8,9,10,11,12,13,14 b 0.19955 345 11 1,2,3,4,5,6,7,8,11,12,13 j 0.02345 50 8 1,2,3,4,5,10,12,14 d 0.02095 44 6 1,3,4,8,9,11
c 0.0209 46 10 1,2,3,5,6,7,8,11,12,13 i 0.019 41 10 1,2,3,4,7,8,10,12,13,14 g 0.01735 38 10 2,3,4,5,6,7,9,11,12,13 f 0.01725 36 7 1,2,5,6,7,11,13
h 0.0164 36 11 2,3,4,5,6,7,8,9,11,12,13 e 0.015 33 9 2,4,5,6,7,9,11,12,13 k 0.01315 27 5 1,5,10,12,14
t 0.0126 28 6 1,2,5,10,13,14
q 0.0126 27 3 1,10,14
V 0.0072 16 8 2,3,5,6,7,9,11,12
0 0.00675 15 7 2,5,7,8,11,12,13
r 0.0063 14 5 1,4,10,12,14
m 0.00585 13 5 1,5,10,12,14
n 0.00495 11 4 3,4,9,11
am 0.0045 10 5 1,5,10,12,14
I 0.0036 8 6 2,6,7,8,12,13
P 0.0036 8 2 1,10
u 0.0036 8 4 1,2,6,11
X 0.00315 7 3 2,7,13
ae 0.00225 5 3 1,10,14
ai 0.00225 5 2 1,14
aj 0.0018 4 2 10,14
w 0.0018 4 1 4
bd 0.00135 3 1 9
al 0.00135 3 2 1,14
Table 13.17 -IGHG3 s 0.00135 3 2 7,11 ab 0.00135 3 2 1,14 ak 0.00135 3 2 10,14 ag 0.0009 2 2 1,10 y 0.0009 2 2 2,7 az 0.0009 2 2 2,13 aa 0.0009 2 2 2,6 ap 0.0009 2 2 10,14 av 0.0009 2 1 9 af 0.0009 2 1 14 at 0.0009 2 2 10,14 aw 0.0009 2 2 5,9 ay 0.0009 2 1 11 ar 0.0009 2 2 5,14 an 0.0009 2 1 9 ah 0.00045 1 1 10 ba 0.00045 1 1 13 ax 0.00045 1 1 10 bb 0.00045 1 1 1 aq 0.00045 1 1 5 be 0.00045 1 1 7 z 0.00045 1 1 7 ao 0.00045 1 1 14 au 0.00045 1 1 5 ad 0.00045 1 1 1 be 0.00045 1 1 1 ac 0.00045 1 1 13 as 0.00045 1 1 4
Table 13.18 -IGHG4
Table 13.18 -IGHG4
Table 13.19 -IGHJ1
Table 13.20 -IGHJ2
a 0.01185 23 6 1,6,9,10,11,14 c 0.0045 7 4 1,10,11,14 b 0.00275 6 56,10,11,13,14 d 0.00135 3 34,11,14 e 0.00135 3 32,6,11 f 0.0009 2 2 8,9 g 0.00045 1 1 13 h 0.00045 1 1 10 i 0.00045 1 1 10
pops
# indvs cum.freq h.type
CM > X
.Ω re
Table 13.29 -IGHV1 -3
Table 13.29 -IGHV1 -3
o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o
pops
oo oo CM
CD o
# indvs
oo oo oo
O o CNI CD CD CM o
O O CM o o o o o o O O O O o o o o o o o o o O O O o o o o o o o o O o o o o o cum.freq
h.type
Table 13.33 -IGHV1 -69
Table 13.33 -IGHV1 -69
V 0. .00045 al 0. .00045 ab 0. .00045 ak 0. .00045 q 0. .00045 ap 0. .00045 z 0. .00045 w 0. .00045 av 0. .00045 r 0. .00045
X 0. .00045 au 0. .00045 am 0. .00045 at 0. .00045 aw 0. .00045 ay 0. .00045 ar 0. .00045
P 0. .00045 as 0. .00045 ae 0. .00045 ai 0. .00045
Table 13.34 -IGHV1 -8
a 0.1016 160 9 1,5,7,8,10,11,12,13,14 c 0.00405 8 2 10,13
b 0.0032 6 62,5,6,11,12,13 d 0.0018 4 2 1,14
e 0.00135 3 22,11
f 0.00135 3 27,11
h 0.0009 2 23,5
j 0.00045 1 1 2
g 0.00045 1 1 14
i 0.00045 1 1 13
Table 13.35 - IGHV2-26
Table 13.36 - IGHV2-5
1,2,3,4,5,6,7,8,9,10,11,1
2,13,14
1,10,14
10,14
4,13
6
1
9
3
5
10
12
Table 13.37 -IGHV2-70
Table 13.37 - IGHV2-70
14:107178959 14: 107178965 14: 107178976 14:107179098 14: 107179103 14:107179106 14:1071791 15 14: 107179123 rs184814603 rs2073669 rs148856487 rs191880827 rs185635448 rs10144703 rs182292946 rs187704106
Asp->Gly Leu->Arg Glu->Asp Gly->Ser Glu->Val Arg->Lys Val->Gly Leu->Phe
0.36095 T T 0.31
0.16595
0.06035
0.04295
0.0319
0.00405
0.00225
0.00135
0.00135
0.00135
0.00135
0.0009
0.0009
0.0009 c c T
0.00045 c c T
0.00045 c c T
0.00045 c c T
0.00045 c c T
0.00045 c T
0.00045 c c T
0.00045 c c T
0.00045 c c T
0.00045 c c
0.00045 c c T
0.00045 c c T
0.00045 c c T
0.00045 c c T
0.00045 c c T
< Λ
>A
< Λ
>A
Table 13.39 - IGHV3-13
h.type , σ> E
^— ^—
^— ^—
00" 00" r--" r--" co" co" 0"
^r" ^r" cn" co" o" ^r" co" cn
Table 13.43 - IGHV3-21
Table 13.44 - IGHV3-23
Table 13.44 -IGHV3-23
Table 13.45 - IGHV3-30
h.type CD TO o w
Table 13.47 - IGHV3-35
Table 13.48 - IGHV3-38
Table 13.50 - IGHV3-48
Table 13.53 - IGHV3-64
Table 13.53 - IGHV3-64
a 0.47965 793 14 1,2,3,4,5,6,7,8,9,10,11,12,13,14 b 0.06225 131 13 1,2,3,4,5,6,7,9,10,11,12,13,14 c 0.02785 61 14 1,2,3,4,5,6,7,8,9,10,11,12,13,14 d 0.00275 6 42,4,13,14
e 0.0018 4 2 1,10
f 0.00135 3 1 10
h 0.0009 2 1 12
j 0.00045 1 1 2
g 0.00045 1 1 3
i 0.00045 1 1 8
h.type CD -O O Ό CD
Table 13.56 - IGHV3-73
Table 13.59 - IGHV3-9
Table 13.59 - IGHV3-9
Table 13.60 -IGHV4-28
Table 13.60 - IGHV4-28
ref 0.22145 - a 0.41435 691 14 1,2,3,4,5,6,7,8,9,10,11,12,13,14 b 0.13715 250 14 1,2,3,4,5,6,7,8,9,10,11,12,13,14 c 0.07385 161 14 1,2,3,4,5,6,7,8,9,10,11,12,13,14 d 0.06485 136 13 1,2,3,5,6,7,8,9,10,11,12,13,14 f 0.0195 42 5 1,10,11,12,14
e 0.01685 37 10 1,2,5,6,7,10,11,12,13,14 g 0.01355 29 4 1,5,10,14
i 0.01185 22 6 1,8,10,11,13,14
h 0.01175 25 11 1,2,3,5,7,8,9,10,11,13,14 j 0.00405 9 5 2,6,7,10,13
k 0.00315 7 3 1,10,14
P 0.00225 5 3 1,10,14
s 0.0009 2 2 1,11
n 0.0009 2 2 10,14
u 0.00045 1 1 10
t 0.00045 1 1 11
V 0.00045 1 1 13
q 0.00045 1 1 11
r 0.00045 1 1 1
m 0.00045 1 1 10
I 0.00045 1 1 10
0 0.00045 1 1 14
Table 13.61 - IGHV4-31
Table 13.61 - IGHV4-31
Table 13.62 -IGHV4-34
Table 13.63 - IGHV4-39
Table 13.63 - IGHV4-39
Table 13.64 - IGHV4-4
361
Table 13.65 - IGHV4-59
Table 13.66 - IGHV4-61
Table 13.69 - IGHV7-81
Table 13.70 -IGKJ2
Table 13.71 -IGKJ3
Table 13.72 - IGKJ4
0.9883 - 0.00225 5 0.0018 4 0.00135 3 0.0009 2 0.0009 2 0.0009 2 h 0.0009 2 d 0.00045 e 0.00045 f 0.00045 i 0.00045 m 0.00045
0.00045
Table 13.72 -IGKJ4
Table 13.73 -IGKJ5
Table 13.74 -IGKV1 -16
Table 13.77 -IGKV1 -6
Table 13.78 -IGKV1 -8
-J
Table 13.79 -IGKV1 -9
Table 13.80 -IGKV1D-12
Table 13.81 -IGKV1D-16
Table 13.82 -IGKV1D-17
Table 13.83 -IGKV1D-42
h.type -a TO
Table 13.84 -IGKV1D-43
Table 13.85 -IGKV1D-8
Table 13.86 - IGKV2-24
Table 13.87 - IGKV2-30
Table 13.88 - IGKV2D-24
Table 13.89 - IGKV2D-26
Table 13.90 - IGKV2D-29
Table 13.93 -IGKV3-20
Table 13.93 - IGKV3-20
Table 13.94 - IGKV3-7
Table 13.98 -IGKV4-1
0) O
Table 13.98 -IGKV4-1
Table 13.98 -IGKV4-1
Table 13.99 -IGKV5-2
Table 13.100 -IGKV6-21
Table 13.101 -IGKV6D-21
o
Table 13.104 -IGLJ2
Table 13.105 -IGLJ3
Table 13.106 -IGLJ5
Table 13.107 -IGLJ6
Table 13.108 -IGLJ7
Table 13.111 -IGLV1-36
ENST00000390301
1,2,3,4,5,6,7,8,9,10,11,12,13,14
2,6,7,12,13
1,10,12,14
10,14
10,14
1,4,10
2,6,7
Table 13.112 -IGLV1-40
Table 13.112 -IGLV1-40
Table 13.113 -IGLV1-44
Table 13.114 -IGLV1-47
Table 13.115 -IGLV1-50
pops
CO C
CM
CM
# indvs
r~- CD o o
CM O o o o O o
O q q q o q o O o q q q o o o o cum.freq
h.type
Table 13.117 -IGLV2-11
Table 13.118 -IGLV2-14
Table 13.120 -IGLV2-23
Table 13.120 -IGLV2-23
Table 13.121 -IGLV2-33
Table 13.123 -IGLV3-10
Table 13.124 -IGLV3-12
Table 13.125 -IGLV3-16
Table 13.126 -IGLV3-19
Table 13.126 -IGLV3-19
Table 13.127 -IGLV3-1
Table 13.127 -IGLV3-1
Table 13.127 -IGLV3-1
Table 13.127 -IGLV3-1
Table 13.127 -IGLV3-1
co"
M"
P P P P P P P p p P P P P
P P P P P P P P P P P P IP P
Λ TO
<
I"-
Table 13.128 -IGLV3-21
pops
O CO co O co CN o CO CO CM CM M
UO co cn CO CM CM
m co CM
# indvs
m 00 CO O CO UO UO O r^- 00 CO UO σ> σ> cn UO UO UO U0 UO U0 UO σι Γ-~ CO r-~ σι CM ^— 00 o o o
CO ^— o σι o o C o o o o o o o o o o o Nj CM q o q q q q o q q q o o o o o o o
O CO o O d q q d d d d q d d d o o o o o o o d O d d d o o o o o o o cum.fre
h.type c c E Q. o
a 0.2962 529 14 1,2,3,4,5,6,7,8,9,10,11,12,13,14 b 0.01545 33 7 1,3,4,9,10,12,14
c 0.00825 18 5 3,4,6,9,14
e 0.0027 6 1 10
d 0.0027 6 3 1,10,14
g 0.0018 4 3 3,4,10
h 0.0018 4 2 10,14
f 0.00135 3 3 2,10,12
i 0.00135 3 1 10
j 0.0009 2 1 4
n 0.0009 2 2 10,12
m 0.0009 2 2 1,14
o 0.0009 2 2 10,14
k 0.00045 1 1 11
I 0.00045 1 1 14
Table 13.130 -IGLV3-25
Table 13.130 -IGLV3-25
Table 13.130 -IGLV3-25
a 0.6581 943 14 1,2,3,4,5,6,7,8,9,10,11,12,13,14 b 0.19965 367 14 1,2,3,4,5,6,7,8,9,10,11,12,13,14 c 0.02105 41 6 2,3,4,5,9,11
d 0.00405 9 5 1,2,5,6,10
0.00135 3 3 2,5,14
g 0.0009 2 1 2
I 0.0009 2 2 3,5
j 0.00045 1 1 6
k 0.00045 1 1 5
s 0.00045 1 1 10
q 0.00045 1 1 2
r 0.00045 1 1 7
h 0.00045 1 1 10
f 0.00045 1 1 4
i 0.00045 1 1 6
n 0.00045 1 1 14
m 0.00045 1 1 8
P 0.00045 1 1 10
o 0.00045 1 1 10
Table 13.131 -IGLV3-27
•J\
Table 13.135 -IGLV4-60
Table 13.135 -IGLV4-60
ref 0.0851 - a 0.4868 785 14 1,2,3,4,5,6,7,8,9,10,11,12,13,14 b 0.3607 628 14 1,2,3,4,5,6,7,8,9,10,11,12,13,14 c 0.03615 74 5 1,5,10,12,14
d 0.015 32 4 1,5,10,14
e 0.00635 14 4 1,10,11,14
f 0.00225 5 4 1,3,10,14
g 0.0009 2 2 5,11
n 0.0009 2 2 2,9
o 0.0009 2 2 5,10
j 0.00045 1 1 10
k 0.00045 1 1 5
t 0.00045 1 1 6
s 0.00045 1 1 13
q 0.00045 1 1 13
r 0.00045 1 1 13
h 0.00045 1 1 14
i 0.00045 1 1 10
m 0.00045 1 1 10
I 0.00045 1 1 5
P 0.00045 1 1 10
Table 13.136 - IGLV4-69
Table 13.137 - IGLV5-37
9
•J\
Table 13.138 - IGLV5-45
Table 13.139 - IGLV5-48
pops _
CM
in # indvs
lO <J> > ^— —I
O
cum.freq
10
h.type β
Table 13.141 -IGLV6-57
Table 13.143 - IGLV7-46
pops
,_
O
# indvs
m σ> — o o o o o o o O q q
O o o o cum.freq
h.type (0 Ό ID ϋ
Table 13.145 -IGLV9-49
Table 13.145 -IGLV9-49
Table 14A: Variants Having a Cumulative Frequency Greater than 5% or 10%
IGHV IGHVl-45-a 0.1286 Yes 12
IGHV IGHVl-45-b 0.1126 Yes 12
IGHV IGHVl-58-a 0.4503 Yes 14
IGHV IGHVl-58-b 0.3144 Yes 14
IGHV IGHVl-69-a 0.1689 Yes 14
IGHV IGHVl-69-b 0.1543 Yes 14
IGHV IGHVl-69-c 0.0561 No 13
IGHV IGHV2-26-a 0.06135 No 13
IGHV IGHV2-5-a 0.6657 Yes 14
IGHV IGHV2-70-a 0.31 Yes 14
IGHV IGHV2-70-b 0.16595 Yes 14
IGHV IGHV2-70-d 0.06035 No 13
IGHV IGHV3-13-a 0.15245 Yes 13
IGHV IGHV3-15-a 0.0572 No 11
IGHV IGHV3-16-a 0.11075 Yes 13
IGHV IGHV3-20-a 0.2829 Yes 14
IGHV IGHV3-20-b 0.1209 Yes 13
IGHV IGHV3-23-a 0.09825 No 12
IGHV IGHV3-33-a 0.145 Yes 12
IGHV IGHV3-35-a 0.11765 Yes 14
IGHV IGHV3-35-b 0.09695 No 10
IGHV IGHV3-38-a 0.0723 No 14
IGHV IGHV3-43-a 0.2428 Yes 14
IGHV IGHV3-43-b 0.08365 No 13
IGHV IGHV3-48-a 0.3355 Yes 14
IGHV IGHV3-48-b 0.20455 Yes 14
IGHV IGHV3-49-a 0.38705 Yes 14
IGHV IGHV3-49-b 0.28555 Yes 13
IGHV IGHV3-53-a 0.2535 Yes 14
IGHV IGHV3-53-b 0.2264 Yes 13
IGHV IGHV3-64-a 0.47965 Yes 14
IGHV IGHV3-64-b 0.06225 No 13
IGHV IGHV3-66-a 0.27865 Yes 14
IGHV IGHV3-66-b 0.12575 Yes 14
IGHV IGHV3-66-C 0.0649 No 13
IGHV IGHV4-28-a 0.41435 Yes 14
IGHV IGHV4-28-b 0.13715 Yes 14
IGHV IGHV4-28-C 0.07385 No 14
IGHV IGHV4-28-d 0.06485 No 13
IGHV IGHV4-31-a 0.5475 Yes 14
IGHV IGHV4-31-b 0.2035 Yes 14
IGHV IGHV4-31-C 0.1554 Yes 14
IGHV IGHV4-39-a 0.10295 Yes 14
IGHV IGHV4-39-b 0.0918 No 14
IGHV IGHV4-4-a 0.1136 Yes 14
IGHV IGHV4-4-d 0.0817 No 14
IGHV IGHV4-4-f 0.06675 No 14
IGHV IGHV4-4-b 0.06385 No 13
IGHV IGHV4-4-C 0.0599 No 14
IGHV IGHV4-4-e 0.05215 No 12
IGHV IGHV4-61-a 0.5701 Yes 14
IGHV IGHV4-61-b 0.18115 Yes 14
IGHV IGHV4-61-C 0.13535 Yes 13
IGHV IGHV4-61-f 0.05855 No 14
Kaooa C
IGKC IGKC-a 0.2427 Yes 14
Kaooa V
IGKV IGKVl-17-a 0.08655 No 13
IGKV IGKVl-17-b 0.0545 No 12
IGKV IGKVl-8-a 0.20315 Yes 14
IGKV IGKVl-8-b 0.1334 Yes 14
IGKV IGKVl-9-a 0.1854 Yes 14
IGKV IGKVlD-42-a 0.22345 Yes 14
IGKV IGKVlD-8-a 0.1872 Yes 14
IGKV IGKV2-24-a 0.1708 Yes 13
IGKV IGKV2-30-a 0.24085 Yes 13
IGKV IGKV2D-26-a 0.325 Yes 14
IGKV IGKV2D-29-a 0.30175 Yes 14
IGKV IGKV3-7-a 0.2018 Yes 14
IGKV IGKV3D-ll-a 0.35105 Yes 14
IGKV IGKV3D-15-a 0.2061 Yes 14
IGKV IGKV5-2-a 0.32315 Yes 14
Lambda C
IGLC IGLC7-a 0.0751 No 14
Lambda J
IGU IGU2-a 0.0741 No 13
IGU IGU7-a 0.93225 Yes 14
Lambda V
IGLV IGLV10-54-a 0.50725 Yes 14
IGLV IGLV10-54-b 0.09425 No 14
IGLV IGLVll-55-a 0.4463 Yes 14
IGLV IGLVl-36-a 0.0942 No 14
IGLV IGLVl-47-a 0.8413 Yes 14
IGLV IGLVl-50-a 0.19325 Yes 14
IGLV IGLVl-51-a 0.1177 Yes 11
IGLV IGLV2-14-a 0.48365 Yes 14
IGLV IGLV2-14-C 0.08855 No 14
IGLV IGLV2-14-b 0.0804 No 10
IGLV IGLV2-18-a 0.763 Yes 14
IGLV IGLV2-23-a 0.34655 Yes 14
IGLV IGLV2-8-a 0.1451 Yes 11
IGLV IGLV3-12-a 0.38715 Yes 14
IGLV IGLV3-12-b 0.1116 Yes 14
IGLV IGLV3-12-C 0.0774 No 14
IGLV IGLV3-19-a 0.10015 Yes 12
IGLV IGLV3-21-a 0.31195 Yes 14
IGLV IGLV3-21-b 0.178 Yes 14
IGLV IGLV3-21-C 0.1613 Yes 14
IGLV IGLV3-22-a 0.2962 Yes 14
IGLV IGLV3-25-a 0.6581 Yes 14
IGLV IGLV3-25-b 0.19965 Yes 14
IGLV IGLV4-60-a 0.4868 Yes 14
IGLV IGLV4-60-b 0.3607 Yes 14
IGLV IGLV5-37-a 0.1266 Yes 13
IGLV IGLV5-45-a 0.1706 Yes 12
IGLV IGLV5-48-a 0.0873 No 14
IGLV IGLV6-57-a 0.3734 Yes 14
IGLV IGLV6-57-b 0.2802 Yes 14
IGLV IGLV7-46-a 0.9166 Yes 14
IGLV IGLV8-61-a 0.2193 Yes 12
Table 14B: Variants Having a Cumulative Frequency Greater than 20%
IGHV IGHVl-2-a 0.3268 14
IGHV IGHVl-3-a 0.3564 14
IGHV IGHVl-58-a 0.4503 14
IGHV IGHVl-58-b 0.3144 14
IGHV IGHV2-5-a 0.6657 14
IGHV IGHV2-70-a 0.31 14
IGHV IGHV3-20-a 0.2829 14
IGHV IGHV3-43-a 0.2428 14
IGHV IGHV3-48-a 0.3355 14
IGHV IGHV3-48-b 0.20455 14
IGHV IGHV3-49-a 0.38705 14
IGHV IGHV3-49-b 0.28555 13
IGHV IGHV3-53-a 0.2535 14
IGHV IGHV3-53-b 0.2264 13
IGHV IGHV3-64-a 0.47965 14
IGHV IGHV3-66-a 0.27865 14
IGHV IGHV4-28-a 0.41435 14
IGHV IGHV4-31-a 0.5475 14
IGHV IGHV4-31-b 0.2035 14
IGHV IGHV4-61-a 0.5701 14
Kaooa C
IGKC IGKC-a 0.2427 14
IGKVl-8-a 0.20315 14
Kaooa V
IGKV
IGKV IGKVlD-42-a 0.22345 14
IGKV IGKV2-30-a 0.24085 13
IGKV IGKV2D-26-a 0.325 14
IGKV IGKV2D-29-a 0.30175 14
IGKV IGKV3-7-a 0.2018 14
IGKV IGKV3D-ll-a 0.35105 14
IGKV IGKV3D-15-a 0.2061 14
IGKV IGKV5-2-a 0.32315 14
Lambda J
IGU IGU7-a 0.93225 14
Lambda V
IGLV IGLV10-54-a 0.50725 14
IGLV IGLVll-55-a 0.4463 14
IGLV IGLVl-47-a 0.8413 14
IGLV IGLV2-14-a 0.48365 14
IGLV IGLV2-18-a 0.763 14
IGLV IGLV2-23-a 0.34655 14
IGLV IGLV3-12-a 0.38715 14
IGLV IGLV3-21-a 0.31195 14
IGLV IGLV3-22-a 0.2962 14
IGLV IGLV3-25-a 0.6581 14
IGLV IGLV4-60-a 0.4868 14
IGLV IGLV4-60-b 0.3607 14
IGLV IGLV6-57-a 0.3734 14
IGLV IGLV6-57-b 0.2802 14
IGLV IGLV7-46-a 0.9166 14
IGLV IGLV8-61-a 0.2193 12
Table 14C: Variants Having a Cumulative Frequency Greater than 30%
IGHV IGHV3-64-a 0.47965 14
IGHV IGHV4-28-a 0.41435 14
IGHV IGHV4-31-a 0.5475 14
IGHV IGHV4-61-a 0.5701 14
IGKV IGKV2D-26-a 0.325 14
IGKV IGKV2D-29-a 0.30175 14
IGKV IGKV3D-ll-a 0.35105 14
IGKV IGKV5-2-a 0.32315 14
Lambda J
IGU IGU7-a 0.93225 14
Lambda V
IGLV IGLV10-54-a 0.50725 14
IGLV IGLVll-55-a 0.4463 14
IGLV IGLVl-47-a 0.8413 14
IGLV IGLV2-14-a 0.48365 14
IGLV IGLV2-18-a 0.763 14
IGLV IGLV2-23-a 0.34655 14
IGLV IGLV3-12-a 0.38715 14
IGLV IGLV3-21-a 0.31195 14
IGLV IGLV3-25-a 0.6581 14
IGLV IGLV4-60-a 0.4868 14
IGLV IGLV4-60-b 0.3607 14
IGLV IGLV6-57-a 0.3734 14
Table 14D: Variants Having a Cumulative Frequency Greater than 40%
IGLV IGLVl-47-a 0.8413 14
IGLV IGLV2-14-a 0.48365 14
IGLV IGLV2-18-a 0.763 14
IGLV IGLV3-25-a 0.6581 14
IGLV IGLV4-60-a 0.4868 14
IGLV IGLV7-46-a 0.9166 14
Table 14E: Variants Having a Cumulative Frequency Greater than 50%
IGLV IGLVl-47-a 0.8413 14
IGLV IGLV2-18-a 0.763 14
IGLV IGLV3-25-a 0.6581 14
IGLV IGLV7-46-a 0.9166 14
Table 14F: Variants Having a Cumulative Frequency Greater than 60%
Table 14G: Variants Having a Cumulative Frequency Greater than 70%
Table 14H: Variants Having a Cumulative Frequency Greater than 80%
IGLV
IGLV IGLV7-46-a 0.9166 14
Table 141: Variants Having a Cumulative Frequency Greater than 90%
Table 15: NAIVE HEAVY CHAIN REPERTOIRES
Naive - Long HCDR3 using IGHJ6*02
Average
HCDR3
J D Length Count
IGHJ6*02 IGHD6- 19*01 23 1
IGHJ6*02 IGHD4- 17*01 22 2
IGHJ6*02 IGHD3-9*01 21 11
IGHJ6*02 IGHD3-10*01 21 25
IGHJ6*02 IGHD6- 13*01 20 1
IGHJ6*02 IGHD3 -22*01 20 1
I Naive HCDR3>=20
Average
HCDR3
V J Length Count
IGHV3-21 *03 IGHJ6*02 23 3
IGHV3-13*01 IGHJ6*02 22 1
IGHV3-7*01 IGHJ6*02 22 3
IGHV6-1 *01 IGHJ6*02 21 3
IGHV1-8*01 IGHJ6*02 21 10
IGHVl-2*02 IGHJ6*02 21 3
IGHV7-4-l *01 IGHJ6*02 21 3
IGHV1-3*01 IGHJ6*02 21 4
IGHV1-18*01 IGHJ6*02 21 5
IGHV4-4*02 IGHJ6*02 20 3
IGHV3-9*01 IGHJ6*02 20 2
IGHV3 -23*04 IGHJ6*02 20 1
TABLE 16: IMMUNISED HEAVY CHAIN REPERTOIRES
Immunised - Long HCDR3 using IGHJ6*02
TABLE 16B:
All Immunised - J & D Usage
TABLE 16C:
All Immunised - V & J Usage
TABLE 17: ANTIGEN-SPECIFIC HEAVY CHAIN REPERTOIRES
Immunised - Long HCDR3 using IGHJ6*02
IGHV3-9*01 IGHJ6*02 20 1
IGHV3-11 *01 IGHJ6*02 21 1
IGHV3-20*d01 IGHJ6*02 22 1
Table 18: Sequence Correlation Table
IGHV2-5*01 36 IGHV3-33*01
IGHV2-26*01 37 IGHV3-35*01
IGHV2-70*01 38 IGHV3-38*01
IGHV3-7*01 39 IGHV3-43*01
IGHV3-9*01 40 IGHV3-47*01
IGHV3-11*01 41 IGHV3-48*01
IGHV3-13*01 42 IGHV3-49*01
IGHV3-15*01 43 IGHV3-53*01
IGHV3-16*01 44 IGHV3-64*01
IGHV3-19*01 45 IGHV3-66*01
IGHV3-20*01 46 IGHV3-72*01
IGHV3-21*01 47 IGHV3-73*01
IGHV3-23*01 48 IGHV3-74*01
IGHV3-30*01 49 IGHV3-d*01
IGHV3-h*01 64 IGHV6-1*01
IGHV4-4*01
65 IGHV7-4-l*01
IGHV4-28*01
66 IGHV7-81*01
IGHV4-30-2*01
67 IGHD1-1*01
IGHV4-30-4*01 68 IGHD1-7*01
69 IGHD1-14*01
IGHV4-31*01 70 IGHD1-20*01
71 IGHD1-26*01
IGHV4-34*01
72 IGHD2-2*01
73 IGHD2-8*01
IGHV4-39*01
74 IGHD2-15*01
IGHV4-55*01 75 IGHD2-21*01
76 IGHD3-3*01
IGHV4-59*01 77 IGHD3-9*01
78 IGHD3-10*01
IGHV4-61*01
79 IGHD3-16*01
80 IGHD3-22*01
IGHV4-b*01
81 IGHD4-4*01
82
IGHV5-51*01 IGHD4-11*01
83 IGHD4-17*01
IGHV5-a*01 84 IGHD4-23*01
85 IGHD5-5*01
86 IGHD5-12*01
87 IGHD5-18*01 107 IGKV1-16*01
88 IGHD5-24*01
108 IGKV1D-16*01
89 IGHD6-6*01
90 IGHD6-13*01
109 IGKV1-17*01
91 IGHD6-19*01
92 IGHD6-25*01
110 IGKV1D-17*01
93 IGHD6-25*01
94 JH1*01 111 IGKV1-27*01
95 JH2*01
112 IGKV1-33*01
96 JH3*01
97 JH4*01
113 IGKV1D-33*01
98 JH5*01
99 JH6*01
114 IGKV1-37*01
100 IGKV1-5*01
115 IGKV1D-37*01
101 IGKV1-6*01
116 IGKV1-39*01
102 IGKV1-8*01
117 IGKV1D-39
103 IGKV1D-8*01
118 IGKV1D-42*01
104 IGKV1-9*01
119 IGKV1D-43*01
105 IGKV1-12*01
120 IGKV2-24*01
106 IGKV1-13*01
121 IGKV2D-24*01
122 IGKV2-28*01 137 IGKV3-20*01
123 IGKV2D-28*01 138 IGKV3D-20*01
124 IGKV2-29*01 139 IGKV4-1*01
125 IGKV2D-29*01 140 IGKV5-2*01
126 IGKV2-30*01 141 IGKV6-21*01
127 IGKV2D-30*01 142 IGKV6D-21*01
128 IGKV2-40*01 143 IGKV6D-41*01
129 IGKV2D-40*01 144 IGLV1-36*01
130 IGKV3-7*01 145 IGLV1-40*01
131 IGKV3-7*03 146 IGLV1-41*01
132 IGKV3D-7*01 147 IGLV1-44*01
133 IGKV3-11*01 148 IGLV1-47*01
134 IGKV3D-11*01 149 IGLV1-50*01
135 IGKV3-15*01 150 IGLV1-51*01
136 IGKV3D-15*01 151 IGLV2-8*01
152 IGLV2-11*01 167 IGLV4-3*01
153 IGLV2-14*01
168 IGLV4-60*01
154 IGLV2-18*01
169 IGLV4-69*01
155 IGLV2-23*01
170 IGLV5-37*01
156 IGLV2-33*01
171 IGLV5-45*01
157 IGLV3-1*01
158 IGLV3-10*01 172 IGLV5-48*01
159 IGLV3-12*01
173 IGLV5-52*01
160 IGLV3-16*01
174 IGLV6-57*01
161 IGLV3-19*01
175 IGLV7-43*01
162 IGLV3-21*01
176 IGLV7-46*01
163 IGLV3-22*01
177 IGLV8-61*01
164 IGLV3-25*01
178 IGLV9-49*01
165 IGLV3-27*01
166 IGLV3-32*01 179 IGLV10-54*01
180 IGLV11-55*01 199 IGLV11-55*01
181 IGKJ1*01 200 IGLV2-14*01
182 IGKJ2*01
201 IGLV2-18*01
183 IGKJ3*01
184 IGKJ4*01
202 IGLV2-23*01
185 IGKJ5*01
186 IGU1*01
203 IGLV2-8*01
187 IGU2*01
188 IGU3*01 204 IGLV3-1*01
189 IGU4*01
205 IGLV3-12*01
190 IGU5*01
191 IGU6*01
206 IGLV3-19*01
192 IGU7*01
193 IGKV2D-26*01
207 IGLV3-21*01
194 IGLV1-36*01
208 IGLV3-22*01
195 IGLV1-47*01
209 IGLV3-25*01
196 IGLV1-50*01
210 IGLV4-60*01
197 IGLV1-51*01
211 IGLV5-37*01
198 IGLV10-54*01
212 IGLV5-45*01
213 IGLV5-48*01 220 IGHE
214 IGLV6-57*01
215 IGLV7-46*01
216 IGLV8-61*01
217 IGHG3 221 IGHE
222 IGHA1
218 IGHA2
223 IGHG1
224 IGHG1
219 IGHG2
239 IGHJ1 ref
240 IGHJ2 ref 260 IGHV3-16 ref
241 IGHJ3 ref
261 IGHV3-20 ref
242 IGHJ4 ref
243 IGHJ5 ref
262 IGHV3-21 ref
244 IGHJ6 ref
245 IGHVl-18 ref
263 IGHV3-23 ref
246 IGHV1-2 ref
264 IGHV3-30 ref
247 IGHV1-24 ref
248 IGHV1-3 ref
265 IGHV3-33 ref
249 IGHV1-45 ref
266 IGHV3-35 ref
250 IGHV1-46 ref
267 IGHV3-38 ref
251 IGHV1-58 ref
268 IGHV3-43 ref
252 IGHV1-69 ref
253 IGHV1-8 ref
269 IGHV3-48 ref
254 IGHV2-26 ref
270 IGHV3-49 ref
255 IGHV2-5 ref
256 IGHV2-70 ref
271 IGHV3-53 ref
257 IGHV3-11 ref
272 IGHV3-64 ref
258 IGHV3-13 ref
273 IGHV3-66 ref
259 IGHV3-15 ref
274 IGHV3-7 ref
275 IGHV3-72 ref 292 IGKJ5 ref
293 IGKV1-16 ref
276 IGHV3-73 ref
294 IGKV1-17 ref τη IGHV3-74 ref 295 IGKV1-5 ref
278 IGHV3-9 ref 296 IGKV1-6 ref
297 IGKV1-8 ref
279 IGHV4-28 ref
280 IGHV4-31 ref 298 IGKV1-9 ref
281 IGHV4-34 ref
299 IGKV1D-12 ref
282 IGHV4-39 ref
283 IGHV4-4 ref 300 IGKVlD-16 ref
284 IGHV4-59 ref 301 IGKV1D-17 ref
302 IGKV1D-42 ref
303 IGKV1D-43 ref
285 IGHV4-61 ref 304 IGKV1D-8 ref
286 IGHV5-51 ref 305 IGKV2-24 ref
287 IGHV6-1 ref
288 IGHV7-81 ref 306 IGKV2-30 ref
289 IGKJ2 ref
290 IGKJ3 ref 307 IGKV2D-24 ref
291 IGKJ4 ref
308 IGKV2D-26 ref 323 IGU2 ref
324 IGU3 ref
325 IGU5 ref
309 IGKV2D-29 ref
326 IGU6 ref
310 IGKV2D-30 ref 327 IGU7 ref
328 IGLV10-54 ref
329 IGLV11-55 ref
311 IGKV3-11 ref
330 IGLV1-36 ref
312 IGKV3-20 ref
331 IGLV1-40 ref
313 IGKV3-7 ref
332 IGLV1-44 ref
314 IGKV3D-11 ref
333 IGLV1-47 ref
315 IGKV3D-15 ref
334 IGLV1-50 ref
316 IGKV3D-20 ref
335 IGLV1-51 ref
317 IGKV4-1 ref
336 IGLV2-11 ref
318 IGKV5-2 ref
337 IGLV2-14 ref
319 IGKV6-21 ref
338 IGLV2-18 ref
339 IGLV2-23 ref
320 IGKV6D-21 ref
340 IGLV2-33 ref
321 IGKV6D-41 ref
322 IGU1 ref
341 IGLV2-8 ref 355 IGLV4-69 ref
342 IGLV3-1 ref 356 IGLV5-37 ref
357 IGLV5-45 ref
343 IGLV3-10 ref
358 IGLV5-48 ref
344 IGLV3-12 ref
359 IGLV5-52 ref
345 IGLV3-16 ref 360 IGLV6-57 ref
346 IGLV3-19 ref 361 IGLV7-43 ref
362 IGLV7-46 ref
347 IGLV3-21 ref
363 IGLV8-61 ref
364 IGLV9-49 ref
348 IGLV3-22 ref
349 IGLV3-25 ref
350 IGLV3-27 ref
351 IGLV3-32 ref
352 IGLV3-9 ref
353 IGLV4-3 ref
354 IGLV4-60 ref
365 IGHGl refGENOMIC 369 IGHG2 ref¬
GENOMIC
370 IGHG2 ref-CDS
(ensembi transcript
ID
ENST00000390545)
371 IGHG2-a CDS
372 IGHG2-a GENOMIC
373 IGHG3 ref¬
GENOMIC
366 IGHGl ref-CDS
(ensembi transcript
ID
ENST00000390542)
367 IGHGl ref-CDS
(Ensembi transcript 374 IGHG3 ref-CDS ID (ensembi transcript
ENST00000390549) ID
ENST00000390551)
368 IGHGl ref-CDS
(ensembi transcript 375 IGHG3-a CDS ID
ENST00000390548)
376 IGHG3-a GENOMIC 382 IGHG4-a GENOMIC
383 IGHAl ref GENOMIC
377 IGHG3-b CDS
384 IGHAl ref- CDS
378 IGHG3-b GENOMIC (ensembl transcript
ID
ENST00000390547)
385 IGHAl-a GENOMIC
379 IGHG4 ref - GENOMIC 386 IGHAl-a CDS
387 IGHA2 ref GENOMIC
380 IGHG4 ref - CDS
(ensembl transcript
ID
ENST00000390543)
381 IGHG4-a CDS 388 IGHA2 ref- CDS
(ensembl transcript ID
ENST00000390539)
389 IGHA2-a GENOMIC 393 IGHD ref GENOMIC
390 IGHA2-a CDS
391 IGHA2-b GENOMIC
392 IGHA2-b CDS
394 IGHD ref- CDS
(ensembi transcript ID
ENST00000390556)
395 IGHE ref GENOMIC 401 IGHM-a GENOMIC
402 IGHM-a CDS
403 IGHM-b GENOMIC
396 IGHE ref- CDS
(ensembl transcript
ID
ENST00000390541)
397 IGHE ref- CDS 404 IGHM-b CDS
(ensembl transcript
ID
ENST00000576077)
398 IGHE ref- CDS
(ensembl transcript 405 IGHD7-27 GENOMIC
ID
ENST00000577108) 406 IGHD2-15 GENOMIC
399 IGHM ref GENOMIC 407 IGHD3-16 GENOMIC
408 IGHD6-6 ref
GENOMIC
409 IGHD5-18 ref
GENOMIC
410 IGHD2-2 ref
400 IGHM ref- CDS GENOMIC
(ensembl transcript
ID 411 IGHD4-11 ref
ENST00000390559) GENOMIC
412 IGHD5-12 ref
GENOMIC 428 IGHD3-22 ref
GENOMIC
413 IGHD3-3 ref
GENOMIC 429 IGHD5-5 ref
GENOMIC
414 IGHD2-8 ref
GENOMIC 430 IGHD6-19 ref
GENOMIC
415 IGHD4-4 ref
GENOMIC 431 IGHD1-7 ref
GENOMIC
416 IGHD4-23 ref
GENOMIC 432 Rabbit JH6 (amino acid)
417 IGHD1-14 ref
GENOMIC 433 Rabbit JH6
(nucleotide)
418 IGHD3-10 ref
GENOMIC 434 Sheep JH6 (amino acid)
419 IGHD1-26 ref
GENOMIC 435 Sheep JH6
(nucleotide)
420 IGHD3-9 ref
GENOMIC 436 Bovine JH6 (amino acid)
421 IGHDl-1 ref
GENOMIC 437 Bovine JH6
(nucleotide)
422 IGHD6-25 ref
GENOMIC 438 Dog JH3 (amino acid)
423 IGHD5-24 ref 439 Dog JH3 (nucleotide)
GENOMIC
440 Human JH6*02
424 IGHD2-21 ref (amino acid)
GENOMIC
441 Human JH6*02
425 IGHD1-20 ref (nucleotide)
GENOMIC
442 Leader Sequence
426 IGHD6-13 ref (nucleotide)
GENOMIC 443 Leader Sequence
(amino acid)
427 IGHD4-17 ref 444 PRIMER
GENOMIC 445 PRIMER
Table 19
Table 20
Table 20A: Variants Found In No More Than 3 Human Populations
IGHV IGHV5-51-b 0.0055 0.55% 11 3
IGLV IGLV5-45-C 0.00545 0.55% 12 2
IGHV IGHV4-31-I 0.0054 0.54% 10 3
IGKV IGKV2D-26-b 0.00455 0.46% 9 3
IGLV IGLVl-36-c 0.00455 0.46% 10 2
IGHV IGHVl-24-c 0.00415 0.42% 9 3
IGHV IGHVl-8-c 0.00405 0.41% 8 2
IGLV IGLVl-47-d 0.00405 0.41% 9 3
IGHV IGHV3-43-I 0.00365 0.37% 8 3
IGHV IGHV3-53-h 0.0036 0.36% 8 2
IGLV IGLV10-54-e 0.0036 0.36% 8 3
IGLV IGLVl-36-f 0.0036 0.36% 8 2
IGLV IGLV5-45-d 0.0036 0.36% 8 3
IGHV IGHVl-46-b 0.0032 0.32% 7 3
IGHV IGHV2-26-C 0.0032 0.32% 7 2
IGU IGU6-b 0.0032 0.32% 7 3
IGLV IGLV3-32-a 0.0032 0.32% 7 3
IGLV IGLV9-49-b 0.0032 0.32% 7 2
IGHJ IGHJ6-b 0.00315 0.32% 7 2
IGHV IGHV3-16-d 0.00315 0.32% 7 3
IGHV IGHV4-28-k 0.00315 0.32% 7 3
IGKJ IGKJ2-d 0.00315 0.32% 6 3
IGLV IGLV10-54-f 0.00315 0.32% 7 2
IGLV IGLV2-8-C 0.00315 0.32% 7 3
IGLV IGLV3-10-C 0.00315 0.32% 6 2
IGLV IGLVl-40-c 0.00275 0.28% 6 2
IGLV IGLVl-51-b 0.00275 0.28% 6 3
IGHV IGHVl-69-m 0.0027 0.27% 6 3
IGHV IGHV3-33-e 0.0027 0.27% 6 3
IGHV IGHV3-49-C 0.0027 0.27% 6 3
IGHV IGHV3-66-g 0.0027 0.27% 6 3
IGHV IGHV4-4-U 0.0027 0.27% 6 3
IGKV IGKV1D-42-C 0.0027 0.27% 6 1
IGKV IGKV1D-43-C 0.0027 0.27% 5 3
IGLV IGLV10-54-h 0.0027 0.27% 6 2
IGLV IGLVlO-54-i 0.0027 0.27% 6 2
IGLV IGLVl-36-g 0.0027 0.27% 6 3
IGLV IGLV2-8-d 0.0027 0.27% 6 3
IGLV IGLV3-22-e 0.0027 0.27% 6 1
IGLV IGLV3-22-d 0.0027 0.27% 6 3
IGHJ IGHJ2-b 0.00225 0.23% 4 3
IGHV IGHVl-3-u 0.00225 0.23% 5 2
IGHV IGHVl-3-v 0.00225 0.23% 5 2
IGHV IGHVl-3-ap 0.00225 0.23% 4 3
IGHV IGHVl-46-c 0.00225 0.23% 5 3
IGHV IGHVl-58-f 0.00225 0.23% 5 3
IGHV IGHVl-69-j 0.00225 0.23% 5 3
IGHV IGHV3-13-e 0.00225 0.23% 5 3
IGHV IGHV3-23-f 0.00225 0.23% 5 3
IGHV IGHV3-23-g 0.00225 0.23% 5 3
IGHV IGHV4-28-p 0.00225 0.23% 5 3
IGHV IGHV4-31-j 0.00225 0.23% 5 3
IGKV IGKVl-17-d 0.00225 0.23% 4 1
IGKV IGKV3-20-a 0.00225 0.23% 5 3
IGKV IGKV3-7-C 0.00225 0.23% 5 3
IGKV IGKV3-7-d 0.00225 0.23% 5 3
IGKV IGKV3D-ll-b 0.00225 0.23% 5 3
IGU IGU3-a 0.00225 0.23% 4 2
IGLV IGLVll-55-g 0.00225 0.23% 5 3
IGLV IGLVl-50-c 0.00225 0.23% 5 3
IGLV IGLV2-ll-g 0.00225 0.23% 5 3
IGLV IGLV2-14-n 0.00225 0.23% 5 3
IGLV IGLV2-23-f 0.00225 0.23% 5 2
IGLV IGLV3-19-C 0.00225 0.23% 5 2
IGLV IGLV5-37-C 0.00225 0.23% 4 2
IGLV IGLV5-48-k 0.00225 0.23% 5 3
IGLV IGLV2-14-I 0.00185 0.19% 4 2
IGHJ IGHJ l-a 0.0018 0.18% 3 3
IGHV IGHVl-2-g 0.0018 0.18% 4 3
IGHV IGHVl-3-y 0.0018 0.18% 4 3
IGHV IGHVl-3-ar 0.0018 0.18% 4 3
IGHV IGHVl-3-ai 0.0018 0.18% 4 3
IGHV IGHVl-69-s 0.0018 0.18% 4 3
IGHV IGHVl-8-d 0.0018 0.18% 4 2
IGHV IGHV2-5-d 0.0018 0.18% 4 2
IGHV IGHV3-13-j 0.0018 0.18% 4 2
IGHV IGHV3-21-d 0.0018 0.18% 4 3
IGHV IGHV3-23-n 0.0018 0.18% 4 3
IGHV IGHV3-33-d 0.0018 0.18% 4 3
IGHV IGHV3-64-e 0.0018 0.18% 4 2
IGHV IGHV3-9-g 0.0018 0.18% 4 3
IGHV IGHV4-39-y 0.0018 0.18% 4 3
IGHV IGHV4-39-n 0.0018 0.18% 4 3
IGHV IGHV4-39-0 0.0018 0.18% 4 3
IGHV IGHV7-81-C 0.0018 0.18% 4 3
IGKJ IGKJ2-e 0.0018 0.18% 4 3
IGKV IGKV2D-26-C 0.0018 0.18% 4 1
IGKV IGKV3D-ll-g 0.0018 0.18% 3 2
IGKV IGKV3D-ll-f 0.0018 0.18% 4 3
IGKV IGKV4-1-W 0.0018 0.18% 3 3
IGU IGU l-a 0.0018 0.18% 4 2
IGLV IGLV10-54-k 0.0018 0.18% 4 2
IGLV IGLVll-55-e 0.0018 0.18% 4 3
IGLV IGLVl-36-e 0.0018 0.18% 4 3
IGLV IGLVl-40-f 0.0018 0.18% 4 3
IGLV IGLVl-44-d 0.0018 0.18% 4 3
IGLV IGLVl-44-e 0.0018 0.18% 4 3
IGLV IGLVl-47-g 0.0018 0.18% 4 2
IGLV IGLVl-50-d 0.0018 0.18% 4 2
IGLV IGLVl-51-d 0.0018 0.18% 4 2
IGLV IGLVl-51-c 0.0018 0.18% 4 3
IGLV IGLV2-14-r 0.0018 0.18% 4 1
IGLV IGLV2-33-b 0.0018 0.18% 4 3
IGLV IGLV2-8-e 0.0018 0.18% 4 2
IGLV IGLV3-16-h 0.0018 0.18% 4 3
IGLV IGLV3-21-j 0.0018 0.18% 4 3
IGLV IGLV3-22-g 0.0018 0.18% 4 3
IGLV IGLV3-22-h 0.0018 0.18% 4 2
IGLV IGLV5-48-j 0.0018 0.18% 4 3
IGHJ IGHJ4-d 0.00135 0.14% 3 3
IGHV IGHVl-18-d 0.00135 0.14% 3 3
IGHV IGHVl-18-e 0.00135 0.14% 3 3
IGHV IGHVl-2-h 0.00135 0.14% 3 2
IGHV IGHVl-2-f 0.00135 0.14% 3 3
IGHV IGHVl-3-aa 0.00135 0.14% 3 1
IGHV IGHVl-3-ak 0.00135 0.14% 3 3
IGHV IGHVl-3-w 0.00135 0.14% 3 1
IGHV IGHVl-3-at 0.00135 0.14% 3 2
IGHV IGHVl-69-k 0.00135 0.14% 3 1
IGHV IGHVl-69-ac 0.00135 0.14% 3 3
IGHV IGHVl-8-e 0.00135 0.14% 3 2
IGHV IGHVl-8-f 0.00135 0.14% 3 2
IGHV IGHV2-70-y 0.00135 0.14% 3 3
IGHV IGHV2-70-Z 0.00135 0.14% 3 3
IGHV IGHV2-70-af 0.00135 0.14% 3 2
IGHV IGHV2-70-h 0.00135 0.14% 3 3
IGHV IGHV3-13-g 0.00135 0.14% 3 2
IGHV IGHV3-16-e 0.00135 0.14% 3 2
IGHV IGHV3-20-f 0.00135 0.14% 3 3
IGHV IGHV3-30-d 0.00135 0.14% 3 2
IGHV IGHV3-30-C 0.00135 0.14% 3 3
IGHV IGHV3-33-h 0.00135 0.14% 3 3
IGHV IGHV3-43-k 0.00135 0.14% 3 2
IGHV IGHV3-43-m 0.00135 0.14% 3 3
IGHV IGHV3-53-n 0.00135 0.14% 3 2
IGHV IGHV3-53-m 0.00135 0.14% 3 3
IGHV IGHV3-64-f 0.00135 0.14% 3 1
IGHV IGHV3-73-C 0.00135 0.14% 3 3
IGHV IGHV3-9-h 0.00135 0.14% 2 1
IGHV IGHV4-31-h 0.00135 0.14% 3 2
IGHV IGHV4-39-U 0.00135 0.14% 3 3
IGHV IGHV4-39-t 0.00135 0.14% 3 2
IGHV IGHV4-39-q 0.00135 0.14% 3 3
IGHV IGHV4-4-ao 0.00135 0.14% 3 3
IGHV IGHV4-4-ac 0.00135 0.14% 3 1
IGHV IGHV4-4-ae 0.00135 0.14% 3 2
IGHV IGHV5-51-g 0.00135 0.14% 3 3
IGHV IGHV7-81-e 0.00135 0.14% 3 1
IGKJ IGKJ2-f 0.00135 0.14% 3 2
IGKJ IGKJ 3-d 0.00135 0.14% 3 3
IGKJ IGKJ4-g 0.00135 0.14% 3 3
IGKJ IGKJ5-C 0.00135 0.14% 3 3
IGKJ IGKJ5-b 0.00135 0.14% 3 3
IGKV IGKVl-5-c 0.00135 0.14% 3 3
IGKV IGKVl-9-j 0.00135 0.14% 3 3
IGKV IGKV1D-17-C 0.00135 0.14% 3 2
IGKV IGKVlD-17-b 0.00135 0.14% 3 2
IGKV IGKVlD-42-e 0.00135 0.14% 3 1
IGKV IGKVlD-42-d 0.00135 0.14% 3 2
IGKV IGKV2D-24-b 0.00135 0.14% 3 2
IGKV IGKV2D-30-C 0.00135 0.14% 3 2
IGKV IGKV3-20-d 0.00135 0.14% 3 3
IGKV IGKV3-20-f 0.00135 0.14% 3 2
IGKV IGKV3D-ll-d 0.00135 0.14% 3 2
IGKV IGKV4-l-r 0.00135 0.14% 3 3
IGKV IGKV4-1-X 0.00135 0.14% 3 2
IGKV IGKV4-l-e 0.00135 0.14% 3 3
IGKV IGKV4-1-0 0.00135 0.14% 3 2
IGU IGU6-C 0.00135 0.14% 3 2
IGU IGU7-b 0.00135 0.14% 3 3
IGLV IGLV10-54-g 0.00135 0.14% 3 1
IGLV IGLVll-55-h 0.00135 0.14% 3 2
IGLV IGLVll-55-f 0.00135 0.14% 3 2
IGLV IGLVl-40-g 0.00135 0.14% 3 3
IGLV IGLVl-44-f 0.00135 0.14% 3 2
IGLV IGLVl-47-f 0.00135 0.14% 3 2
IGLV IGLV2-23-e 0.00135 0.14% 3 3
IGLV IGLV3-12-d 0.00135 0.14% 3 3
IGLV IGLV3-16-d 0.00135 0.14% 3 3
IGLV IGLV3-19-d 0.00135 0.14% 3 1
IGLV IGLV3-19-I 0.00135 0.14% 3 2
IGLV IGLV3-l-ag 0.00135 0.14% 3 3
IGLV IGLV3-l-y 0.00135 0.14% 3 3
IGLV IGLV3-1-S 0.00135 0.14% 3 3
IGLV IGLV3-1-X 0.00135 0.14% 3 3
IGLV IGLV3-l-ad 0.00135 0.14% 3 2
IGLV IGLV3-1-I 0.00135 0.14% 3 3
IGLV IGLV3-l-p 0.00135 0.14% 3 2
IGLV IGLV3-21-t 0.00135 0.14% 3 2
IGLV IGLV3-22-f 0.00135 0.14% 3 3
IGLV IGLV3-22-I 0.00135 0.14% 3 1
IGLV IGLV3-25-e 0.00135 0.14% 3 3
IGLV IGLV5-48-t 0.00135 0.14% 3 2
IGLV IGLV5-48-S 0.00135 0.14% 3 3
IGLV IGLV5-52-d 0.00135 0.14% 3 2
IGLV IGLV5-52-C 0.00135 0.14% 3 1
IGLV IGLV7-43-C 0.00135 0.14% 3 2
IGHJ IGHJ5-d 0.0009 0.09% 2 2
IGHJ IGHJ6-e 0.0009 0.09% 2 2
IGHJ IGHJ6-h 0.0009 0.09% 2 2
IGHJ IGHJ6-f 0.0009 0.09% 2 2
IGHV IGHVl-18-f 0.0009 0.09% 2 2
IGHV IGHVl-24-g 0.0009 0.09% 2 1
IGHV IGHVl-2-i 0.0009 0.09% 2 2
IGHV IGHVl-2-m 0.0009 0.09% 2 2
IGHV IGHVl-2-l 0.0009 0.09% 2 2
IGHV IGHVl-3-ag 0.0009 0.09% 2 2
IGHV IGHVl-3-aj 0.0009 0.09% 2 2
IGHV IGHVl-3-aq 0.0009 0.09% 2 1
IGHV IGHVl-3-s 0.0009 0.09% 2 2
IGHV IGHVl-3-q 0.0009 0.09% 2 1
IGHV IGHVl-3-z 0.0009 0.09% 2 1
IGHV IGHVl-3-ad 0.0009 0.09% 2 2
IGHV IGHVl-3-aw 0.0009 0.09% 2 2
IGHV IGHVl-3-ae 0.0009 0.09% 2 2
IGHV IGHVl-3-an 0.0009 0.09% 2 2
IGHV IGHVl-46-k 0.0009 0.09% 2 2
IGHV IGHVl-46-e 0.0009 0.09% 2 2
IGHV IGHVl-46-n 0.0009 0.09% 2 2
IGHV IGHVl-58-g 0.0009 0.09% 2 1
IGHV IGHVl-69-ah 0.0009 0.09% 2 2
IGHV IGHVl-69-t 0.0009 0.09% 2 2
IGHV IGHVl-69-ao 0.0009 0.09% 2 1
IGHV IGHVl-69-af 0.0009 0.09% 2 2
IGHV IGHVl-69-ad 0.0009 0.09% 2 2
IGHV IGHVl-69-n 0.0009 0.09% 2 2
IGHV IGHVl-69-an 0.0009 0.09% 2 2
IGHV IGHV1-69-0 0.0009 0.09% 2 2
IGHV IGHVl-8-h 0.0009 0.09% 2 2
IGHV IGHV2-26-f 0.0009 0.09% 2 2
IGHV IGHV2-5-C 0.0009 0.09% 2 2
IGHV IGHV2-70-g 0.0009 0.09% 2 2
IGHV IGHV2-70-S 0.0009 0.09% 2 2
IGHV IGHV2-70-ab 0.0009 0.09% 2 2
IGHV IGHV3-ll-b 0.0009 0.09% 2 2
IGHV IGHV3-13-f 0.0009 0.09% 2 2
IGHV IGHV3-20-d 0.0009 0.09% 2 2
IGHV IGHV3-21-C 0.0009 0.09% 2 2
IGHV IGHV3-21-h 0.0009 0.09% 2 2
IGHV IGHV3-23-j 0.0009 0.09% 2 1
IGHV IGHV3-23-h 0.0009 0.09% 2 2
IGHV IGHV3-33-f 0.0009 0.09% 2 2
IGHV IGHV3-43-p 0.0009 0.09% 2 2
IGHV IGHV3-64-h 0.0009 0.09% 2 1
IGHV IGHV3-66-h 0.0009 0.09% 2 2
IGHV IGHV3-74-C 0.0009 0.09% 2 2
IGHV IGHV3-9-0 0.0009 0.09% 2 1
IGHV IGHV4-28-S 0.0009 0.09% 2 2
IGHV IGHV4-28-n 0.0009 0.09% 2 2
IGHV IGHV4-31-t 0.0009 0.09% 2 2
IGHV IGHV4-31-m 0.0009 0.09% 2 2
IGHV IGHV4-31-I 0.0009 0.09% 2 2
IGHV IGHV4-34-d 0.0009 0.09% 2 2
IGHV IGHV4-34-g 0.0009 0.09% 2 2
IGHV IGHV4-34-b 0.0009 0.09% 2 2
IGHV IGHV4-39-aa 0.0009 0.09% 2 2
IGHV IGHV4-39-S 0.0009 0.09% 2 2
IGHV IGHV4-39-X 0.0009 0.09% 2 2
IGHV IGHV4-39-p 0.0009 0.09% 2 2
IGHV IGHV4-4-aa 0.0009 0.09% 2 2
IGHV IGHV4-4-af 0.0009 0.09% 2 2
IGHV IGHV4-4-X 0.0009 0.09% 2 2
IGHV IGHV4-4-ad 0.0009 0.09% 2 2
IGHV IGHV4-4-ai 0.0009 0.09% 2 1
IGHV IGHV5-51-d 0.0009 0.09% 2 2
IGHV IGHV5-51-k 0.0009 0.09% 2 2
IGHV IGHV5-51-C 0.0009 0.09% 2 2
IGHV IGHV6-l-a 0.0009 0.09% 2 2
IGHV IGHV6-1-C 0.0009 0.09% 2 1
IGHV IGHV7-81-d 0.0009 0.09% 2 2
IGKJ IGKJ2-g 0.0009 0.09% 2 2
IGKJ IGKJ3-b 0.0009 0.09% 2 2
IGKJ IGKJ4-J 0.0009 0.09% 2 1
IGKJ IGKJ4-C 0.0009 0.09% 2 2
IGKJ IGKJ4-k 0.0009 0.09% 2 2
IGKJ IGKJ4-h 0.0009 0.09% 2 2
IGKV IGKVl-16-d 0.0009 0.09% 2 2
IGKV IGKVl-17-e 0.0009 0.09% 2 2
IGKV IGKVl-5-d 0.0009 0.09% 2 1
IGKV IGKVl-8-h 0.0009 0.09% 2 2
IGKV IGKVl-9-i 0.0009 0.09% 2 2
IGKV IGKV1D-16-C 0.0009 0.09% 2 1
IGKV IGKVlD-16-b 0.0009 0.09% 2 1
IGKV IGKVlD-42-g 0.0009 0.09% 2 2
IGKV IGKVlD-42-f 0.0009 0.09% 2 1
IGKV IGKVlD-43-e 0.0009 0.09% 2 1
IGKV IGKVlD-43-d 0.0009 0.09% 2 2
IGKV IGKVlD-8-d 0.0009 0.09% 2 1
IGKV IGKVlD-8-f 0.0009 0.09% 2 2
IGKV IGKV2D-26-d 0.0009 0.09% 2 2
IGKV IGKV2D-26-f 0.0009 0.09% 2 2
IGKV IGKV2D-29-b 0.0009 0.09% 2 1
IGKV IGKV3-ll-g 0.0009 0.09% 2 1
IGKV IGKV3-ll-f 0.0009 0.09% 2 2
IGKV IGKV3-20-j 0.0009 0.09% 2 2
IGKV IGKV3-20-I 0.0009 0.09% 2 2
IGKV IGKV3-20-e 0.0009 0.09% 2 2
IGKV IGKV3-20-C 0.0009 0.09% 2 2
IGKV IGKV3D-ll-h 0.0009 0.09% 2 1
IGKV IGKV3D-11-I 0.0009 0.09% 2 1
IGKV IGKV3D-20-d 0.0009 0.09% 2 2
IGKV IGKV4-l-y 0.0009 0.09% 2 2
IGKV IGKV4-l-g 0.0009 0.09% 2 2
IGKV IGKV4-l-t 0.0009 0.09% 2 2
IGKV IGKV4-1-I 0.0009 0.09% 2 2
IGKV IGKV4-l-n 0.0009 0.09% 2 2
IGKV IGKV4-1-I 0.0009 0.09% 2 2
IGU IGU2-e 0.0009 0.09% 2 2
IGU IGU2-C 0.0009 0.09% 2 2
IGU IGU5-b 0.0009 0.09% 2 1
IGLV IGLVlO-54-n 0.0009 0.09% 2 2
IGLV IGLV10-54-j 0.0009 0.09% 2 2
IGLV IGLVl-40-h 0.0009 0.09% 2 2
IGLV IGLVl-40-e 0.0009 0.09% 2 2
IGLV IGLVl-47-e 0.0009 0.09% 2 2
IGLV IGLVl-51-g 0.0009 0.09% 2 2
IGLV IGLV2-ll-j 0.0009 0.09% 2 2
IGLV IGLV2-ll-f 0.0009 0.09% 2 2
IGLV IGLV2-11-I 0.0009 0.09% 2 2
IGLV IGLV2-ll-e 0.0009 0.09% 2 1
IGLV IGLV2-14-p 0.0009 0.09% 2 2
IGLV IGLV2-14-q 0.0009 0.09% 2 1
IGLV IGLV2-14-0 0.0009 0.09% 2 1
IGLV IGLV2-23-k 0.0009 0.09% 2 2
IGLV IGLV2-23-0 0.0009 0.09% 2 2
IGLV IGLV2-33-C 0.0009 0.09% 2 1
IGLV IGLV3-19-j 0.0009 0.09% 2 2
IGLV IGLV3-19-k 0.0009 0.09% 2 2
IGLV IGLV3-19-h 0.0009 0.09% 2 1
IGLV IGLV3-19-I 0.0009 0.09% 2 1
IGLV IGLV3-19-p 0.0009 0.09% 2 2
IGLV IGLV3-l-ah 0.0009 0.09% 2 2
IGLV IGLV3-l-d 0.0009 0.09% 2 2
IGLV IGLV3-l-j 0.0009 0.09% 2 1
IGLV IGLV3-l-g 0.0009 0.09% 2 2
IGLV IGLV3-1-Z 0.0009 0.09% 2 2
IGLV IGLV3-l-ac 0.0009 0.09% 2 2
IGLV IGLV3-l-ae 0.0009 0.09% 2 2
IGLV IGLV3-21-k 0.0009 0.09% 2 2
IGLV IGLV3-21-r 0.0009 0.09% 2 1
IGLV IGLV3-21-I 0.0009 0.09% 2 2
IGLV IGLV3-22-j 0.0009 0.09% 2 1
IGLV IGLV3-22-n 0.0009 0.09% 2 2
IGLV IGLV3-22-m 0.0009 0.09% 2 2
IGLV IGLV3-22-0 0.0009 0.09% 2 2
IGLV IGLV3-25-g 0.0009 0.09% 2 1
IGLV IGLV3-25-I 0.0009 0.09% 2 2
IGLV IGLV3-27-a 0.0009 0.09% 2 2
IGLV IGLV3-32-C 0.0009 0.09% 2 2
IGLV IGLV3-9-a 0.0009 0.09% 2 2
IGLV IGLV3-9-b 0.0009 0.09% 2 2
IGLV IGLV4-3-d 0.0009 0.09% 2 2
IGLV IGLV4-60-g 0.0009 0.09% 2 2
IGLV IGLV4-60-n 0.0009 0.09% 2 2
IGLV IGLV4-60-O 0.0009 0.09% 2 2
IGLV IGLV5-45-g 0.0009 0.09% 2 2
IGLV IGLV5-48-U 0.0009 0.09% 2 2
IGLV IGLV5-48-q 0.0009 0.09% 2 2
IGLV IGLV5-48-r 0.0009 0.09% 2 2
IGLV IGLV5-48-n 0.0009 0.09% 2 2
IGLV IGLV5-48-m 0.0009 0.09% 2 1
IGLV IGLV5-48-I 0.0009 0.09% 2 2
IGLV IGLV5-52-b 0.0009 0.09% 2 1
IGLV IGLV7-46-C 0.0009 0.09% 2 2
IGLV IGLV9-49-C 0.0009 0.09% 2 2
Table 20B: Variants Found In No More Than 3 Human Populations & In At Least 10 Individuals
Table 20C: Variants Found In No More Than 3 Human Populations & In At Least 20 Individuals
Table 20D: Variants Found In No More Than 3 Human Populations & In At Least 30 Individuals
525
Table 21
References:
1. Nat Biotechnol. 2005 Sep;23(9):1117-25; Human antibodies from transgenic animals;
Lonberg N.
2. J Clin Invest. 1992 Mar;89(3):729-38; Immunoglobulin light chain variable region gene
sequences for human antibodies to Haemophilus influenzae type b capsular polysaccharide are dominated by a limited number of V kappa and V lambda segments and VJ
combinations; Adderson EE, Shackelford PG, Insel RA, Quinn A, Wilson PM, Carroll WL.
3. J Immunol. 1993 Oct 15;151(8):4352-61; Clonal characterization of the human IgG antibody repertoire to Haemophilus influenzae type b polysaccharide. V. In vivo expression of individual antibody clones is dependent on Ig CH haplotypes and the categories of antigen; Chung GH, Scott MG, Kim KH, Kearney J, Siber GR, Ambrosino DM, Nahm MH.
4. J Immunol. 1998 Dec l;161(ll):6068-73; Decreased frequency of rearrangement due to the synergistic effect of nucleotide changes in the heptamer and nonamer of the recombination signal sequence of the V kappa gene A2b, which is associated with increased susceptibility of Navajos to Haemophilus influenzae type b disease; Nadel B, Tang A, Lugo G, Love V, Escuro G, Feeney AJ.
5. J Clin Invest. 1996 May 15;97(10):2277-82; A defective Vkappa A2 allele in Navajos which may play a role in increased susceptibility to haemophilus influenzae type b disease; Feeney AJ, Atkinson MJ, Cowan MJ, Escuro G, Lugo G.
6. Infect Immun. 1994 Sep;62(9):3873-80; Variable region sequences of a protective human monoclonal antibody specific for the Haemophilus influenzae type b capsular
polysaccharide; Lucas AH, Larrick JW, Reason DC.
7. J Clin Invest. 1993 Jun;91(6):2734-43; Restricted immunoglobulin VH usage and VDJ
combinations in the human response to Haemophilus influenzae type b capsular polysaccharide. Nucleotide sequences of monospecific anti-Haemophilus antibodies and polyspecific antibodies cross-reacting with self antigens; Adderson EE, Shackelford PG, Quinn A, Wilson PM, Cunningham MW, Insel RA, Carroll WL.
8. J Clin Invest. 1993 Mar;91(3):788-96; Variable region expression in the antibody responses of infants vaccinated with Haemophilus influenzae type b polysaccharide-protein conjugates. Description of a new lambda light chain-associated idiotype and the relation between idiotype expression, avidity, and vaccine formulation. The Collaborative Vaccine Study Group; Granoff DM, Shackelford PG, Holmes SJ, Lucas AH.
9. Infect Immun. 1994 May;62(5):1776-86; Variable region sequences and idiotypic expression of a protective human immunoglobulin M antibody to capsular polysaccharides of Neisseria meningitidis group B and Escherichia coli Kl; Azmi FH, Lucas AH, Raff HV, Granoff DM.
J Clin Invest. 1992 Dec;90(6):2197-208; Sequence analyses of three immunoglobulin G antivirus antibodies reveal their utilization of autoantibody-related immunoglobulin Vh genes, but not V lambda genes; Huang DF, Olee T, Masuho Y, Matsumoto Y, Carson DA, Chen PP. Science. 2011 Aug 12;333(6044):834-5, Biochemistry. Catching a moving target, Wang TT, Palese P Science. 2009 Apr 10;324(5924):246-51. Epub 2009 Feb 26; Antibody recognition of a highly conserved influenza virus epitope; Ekiert DC, Bhabha G, Elsliger MA, Friesen H, Jongeneelen M, Throsby M, Goudsmit J, Wilson IA. PLoS One. 2008;3(12):e3942. Epub 2008 Dec 16; Heterosubtypic neutralizing monoclonal antibodies cross-protective against H5N1 and H1N1 recovered from human lgM+ memory B cells; Throsby M, van den Brink E, Jongeneelen M, Poon LL, Alard P, Cornelissen L, Bakker A, Cox F, van Deventer E, Guan Y, Cinatl J, ter Meulen J, Lasters I, Carsetti R, Peiris M, de Kruif J, Goudsmit J. Nat Struct Mol Biol. 2009 Mar;16(3):265-73. Epub 2009 Feb 22,Structural and functional bases for broad-spectrum neutralization of avian and human influenza A viruses, Sui J, Hwang WC, Perez S, Wei G, Aird D, Chen LM, Santelli E, Stec B, Cadwell G, Ali M, Wan H, Murakami A, Yammanuru A, Han T, Cox NJ, Bankston LA, Donis RO, Liddington RC, Marasco WA. Science. 2011 Aug 12;333(6044):843-50. Epub 2011 Jul 7, A highly conserved neutralizing epitope on group 2 influenza A viruses, Ekiert DC, Friesen RH, Bhabha G, Kwaks T,
Jongeneelen M, Yu W, Ophorst C, Cox F, Korse HJ, Brandenburg B, Vogels R, Brakenhoff JP, Kompier R, Koldijk MH, Cornelissen LA, Poon LL, Peiris M, Koudstaal W, Wilson IA, Goudsmit J.
* * *
Claims
CLAIMS:
1. A non-human vertebrate (optionally a mouse or a rat) or vertebrate cell whose genome comprises an immunoglobulin heavy chain locus comprising human gene segment JH6*02, one or more VH gene segments and one or more D gene segments upstream of a constant region; wherein the gene segments in the heavy chain locus are operably linked to the constant region thereof so that the mouse is capable of producing an antibody heavy chain produced by recombination of the human JH6*02 with a D segment and a VH segment.
The vertebrate of claim 1, wherein the vertebrate has been immunised with a target antig and wherein the variable domain of the heavy chain is the product of recombination between a VH, D and JH6*02 and wherein the HCDR3 length is at least 20 amino acids.
3. A non-human vertebrate cell (optionally a mouse cell or a rat cell) whose genome comprises an immunoglobulin heavy chain locus comprising human gene segment JH6*02, one or more VH gene segments and one or more D gene segments upstream of a constant region;
wherein the gene segments in the heavy chain locus are operably linked to the constant region thereof for producing (eg, in a subsequent progeny cell) an antibody heavy chain produced by recombination of the human JH6*02 with a D segment and a VH segment.
4. The cell of claim 3, which is an ES cell capable of differentiation into a progeny antibody- producing cell that expresses said heavy chain.
5. The vertebrate or cell of any preceding claim, wherein the heavy chain locus comprises a human JH6*02 recombination signal sequence (RSS) operably connected 5' to the JH6*02 gene segment.
6. The vertebrate or cell of claim 5, wherein the RSS is SEQ ID NO: 238 or a sequence having an identical 9mer and 7mer sequence flanking a sequence that is at least 70% identical to the 22mer sequence of SEQ ID NO: 238.
7. The vertebrate or cell of claim 6, wherein the RSS and JH6*02 are provided as SEQ ID NO:
237.
8. The vertebrate or cell of any preceding claim, wherein the JH6*02 is the only JH6-type gene segment in the genome.
9. The vertebrate or cell of any preceding claim, wherein the JH6*02 is the closest JH gene segment to the constant region in the locus.
The vertebrate or cell of any preceding claim, wherein the locus comprises one, more or all human D gene segments D3-9; D4-17; D3-10; D2-2; D5-24; D6-19; D3-22; D6-13; D5-12; Dl- 26; Dl-20; D5-18; D3-16; D2-21; Dl-14; D7-27; Dl-1; D6-25; D2-14; and D4-23.
11. The vertebrate or cell of claim 10, wherein the locus comprises one, more or all human D gene segments D3-9, D3-10, D6-19, D4-17, D6-13, D3-22, D2-2, D2-25 and D3-3.
The vertebrate or cell of any preceding claim, wherein the locus comprises a plurality of human D gene segments and the JH6*02 is in human germline configuration with respect to the 3'-most human D gene segment.
The vertebrate or cell of any preceding claim, wherein the locus comprises one, more or all of IGHV gene segments selected from V3-21, V3-13, V3-7, V6-1, Vl-8, Vl-2, V7-4-1, Vl-3, VI- 18, V4-4, V3-9, V3-23, V3-11 and V3-20.
The vertebrate or cell of any preceding claim, wherein the locus comprises one, more or all of human D3-9*01, D3-10*01, D6-19*01, D6-13*01, Dl-26*01, IGHV1-8*01, IGHV4-61*01, IGHV6-1*01, IGHV4-4*02, IGHV1-3*01, IGHV3-66*03, IGHV3-7*01 and IGHV3-9*01.
An antibody-producing cell (eg, a B-cell) that is a progeny of the cell of any one of claims 3 to 14, wherein the antibody-producing cell comprises a heavy chain locus comprising a rearranged variable region produced by recombination of human JH6*02 with a D segment and a VH segment.
The cell of claim 15, which is a B-cell or hybridoma that expresses a target antigen-specific antibody comprising a heavy chain that comprises a rearranged variable region produced by recombination of human JH6*02 with a D segment and a VH segment.
The vertebrate or cell of any preceding claim, wherein the antibody heavy chain specifically binds a target antigen.
The vertebrate or cell of any preceding claim, wherein the antibody heavy chain has a HCDR3 length of at least 20 amino acids.
The vertebrate or cell of any preceding claim, wherein the antibody heavy chain is a product of the recombination of JH6*02 with a human VH gene segment recited in claim 13 or 14 and/or a D gene segment recited in claim 10, 11 or 14.
The vertebrate or cell of any preceding claim, wherein all endogenous non-human vertebrate heavy chain variable region gene segments have been inactivated in the genome.
21. The vertebrate or cell of any preceding claim, wherein the genome is homozygous for said heavy chain locus.
22 A heavy chain (eg, comprised by an antibody) isolated from a vertebrate of any one of claims 1, 2, 5 to 14 and 17 to 21 wherein the heavy chain comprises a HCDR3 of at least 20 amino acids.
23 The heavy chain of claim 22, wherein the HCDR3 is the product of recombination of human JH6*02 with a human VH gene segment recited in claim 13 or 14 and/or a D gene segment recited in claim 10, 11 or 14.
24. A heavy chain (eg, comprised by an antibody) whose VH variable domain is identical to the VH variable domain of the heavy chain of claim 22 or 23, and which comprises a human constant region or a human-mouse chimaeric constant region.
25. The heavy chain of claim 22, 23 or 24, whose VH variable domain is specific for a target antigen.
26. A method for producing a heavy chain, VH domain or an antibody specific to a target
antigen, the method comprising immunizing a non-human vertebrate according to any one
of claims 1, 2, 5 to 14 and 17 to 21 with the antigen and isolating the heavy chain, VH domain or an antibody specific to a target antigen or a cell producing the heavy chain, VH domain or an antibody, wherein the heavy chain, VH domain or an antibody comprises a HCD 3 that is derived from the recombination of human J H6*02 with a VH gene segment and a D gene segment.
A method for producing a human heavy chain or antibody comprising carrying out the method of claim 26, wherein the constant region of the locus is a non-human vertebrate (eg, mouse or rat) constant region, and then replacing the non-human constant region of the isolated heavy chain or antibody with a human constant region.
28. A heavy chain, VH domain or an antibody produced by the method of claim 26 or 27.
29. A B-cell or hybridoma expressing a heavy chain VH domain that is identical to the VH domain of the heavy chain of claim 22, 23 or 28.
30. A nucleic acid encoding the VH domain of the heavy chain of claim 22, 23 or 28, or encoding the heavy chain of claim 22, 23, 24, 25 or 28.
31. A vector (eg, a CHO cell or H EK293 cell vector) comprising the nucleic acid of claim 30;
optionally wherein the vector is in a host cell (eg, a CHO cell or HEK293 cell).
A pharmaceutical composition comprising the antibody, heavy chain or VH domain (eg, comprised by an antibody) of any one of claims 22 to 25 and 28, together with a
pharmaceutically-acceptable excipient, diluent or a medicament (eg, a further antigen- specific variable domain, heavy chain or antibody).
33. The antibody, heavy chain or VH domain (eg, comprised by an antibody) of any one of claims 22 to 25 and 28 for use in medicine.
A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) having a genome comprising at least 3 human variable region gene segments of the same type (eg, at least 3 human VH6-1 gene segments, at least 3 human JH6 gene segments, at least 3 human VK1-39 gene segments, at least 3 human D2-2 gene segments or
at least 3 human JKI gene segments), wherein at least two of the human gene segments are variants that are not identical to each other.
A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) having a genome comprising at least 2 different non-endogenous variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 3 human JH6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments) cis at the same Ig locus.
A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) having a genome comprising at least 2 different human variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human JH6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments) trans at the same Ig locus; and optionally a third human gene segment of the same type, wherein the third gene segment is cis with one of said 2 different gene segments.
A population of non-human vertebrates (eg, mice or rats) comprising a repertoire of human variable region gene segments, wherein the plurality comprises at least 2 human variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human JH6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments), a first of said different gene segments is provided in the genome of a first vertebrate of the population, and a second of said different gene segments being provided in the genome of a second vertebrate of the population, wherein the genome of the first vertebrate does not comprise the second gene segment.
A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) having a genome comprising at least 2 different non-endogenous variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human JH6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments), wherein the gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
39. A method of enhancing the human immunoglobulin gene diversity of a non-human
vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising at least 3 human variable region gene segments of the same type (eg, at
least 3 human VH6-1 gene segments, at least 3 human JH6 gene segments, at least 3 human VK1-39 gene segments, at least 3 human D2-2 gene segments or at least 3 human JKI gene segments), wherein at least two of the human gene segments are variants that are not identical to each other.
A method of enhancing the immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising at least 2 different non-endogenous variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human JH6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments) cis at the same Ig locus.
A method of enhancing the immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising at least 2 different human variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human JH6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments) trans at the same Ig locus; and optionally a third human gene segment of the same type, wherein the third gene segment is cis with one of said 2 different gene segments.
A method of providing an enhanced human immunoglobulin variable region gene segment repertoire, the method comprising providing a population of non-human vertebrates (eg, a mouse or rat) comprising a repertoire of human variable region gene segments, wherein the method comprises providing at least 2 different human variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human JH6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments), wherein a first of said different gene segments is provided in the genome of a first vertebrate of the population, and a second of said different gene segments is provided in the genome of a second vertebrate of the population, wherein the genome of the first vertebrate does not comprise the second gene segment.
A method of enhancing the human immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising at least 2 different non-endogenous variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human JH6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments), wherein the gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
44. The vertebrate, cell or method of any one of claims 34 to 43, wherein at least 2 or 3 of said different gene segments are provided cis at the same Ig locus in said genome.
The vertebrate, cell or method of any one of claims 34 to 44, wherein the gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
The vertebrate, cell or method of any one of claims 34 to 45, wherein the gene segments are derived from the genome sequence of two or more different human individuals; optionally wherein the different human individuals are from different human populations.
The vertebrate, cell or method of claim 46, wherein the individuals are not genetically related.
A method of enhancing the human immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising at least 2 human variable region gene segments of the same type (eg, at least 2 human VH6-1 gene segments, at least 2 human J H6 gene segments, at least 2 human VK1-39 gene segments, at least 2 human D2-2 gene segments or at least 2 human JKI gene segments), wherein the gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations; optionally wherein at least 2 or 3 of said different gene segments are provided at the same Ig locus in said genome.
The method of claim 48, wherein the different human individuals are from different human populations.
50. The method of claim 48, wherein the individuals are not genetically related.
51. The vertebrate, cell or method of preceding claim, wherein at least one of the different segments is a synthetic mutant of a human germline gene segment.
52. The vertebrate, cell or method of any one of claims 34 to 51, wherein each of said gene segments occurs in 10 or more different human populations.
The vertebrate, cell or method of preceding claim, wherein each of said gene segments has human frequency of 5% or greater.
The vertebrate, cell or method of claim 53, wherein each of said gene segments occurs in 10 or more different human populations.
55. The vertebrate, cell or method of any one of claims 34 to 54, wherein each of said gene segments occurs in the 1000 Genomes database in more than 50 individuals.
The vertebrate, cell or method of preceding claim, wherein each of said gene segments (i) has a human frequency of 5% or greater; and (ii) occurs in 10 or more different human populations.
A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) having a genome comprising first and second human Ig locus gene segments of the same type (eg, first and second human JH6 gene segments; or first and second lgG2 gene segments; or first and second human J\7 gene segments), wherein the first gene segment is a gene segment selected from any one of Tables 1 to 7 and 9 to 14 (eg, IGHJ6-a) and the second gene segment is the corresponding reference sequence (eg, IGHJ6 ref; SEQ. ID NO: 244).
58. The vertebrate or cell of claim 57, wherein the genome comprises a third human gene
segment of said type, the third gene segment being different from the first and second gene segments.
59. The vertebrate or cell of claim 57 or 58, wherein the first and second gene segments are cis on the same chromosome; and optionally the third gene segment is also cis on said chromosome.
The vertebrate or cell of claim 59, wherein the gene segments are targeted insertions into an endogenous non-human Ig locus.
The vertebrate or cell of claim 57 or 58, wherein the first and second gene segments are trans on different chromosomes.
The vertebrate or cell of any one of claims 57 to 61, wherein the first gene segment is a gen segment selected any one of Tables 1 to 7 and 9 to 14 and the second gene segment is the corresponding reference sequence.
A population of non-human vertebrates (eg, mice or rats) comprising first and second human Ig locus gene segments of the same type (eg, first and second human JH6 gene segments; or first and second lgG2 gene segments; or first and second human J\7 gene segments), wherein the first gene segment is a gene segment selected from any one of Tables 1 to 7 and 9 to 14 (eg, IGHJ6-a) and the second gene segment is the corresponding reference sequence (eg, SEQ. ID NO: 244), wherein the first gene segment is provided in th genome of a first vertebrate of the population, and the second gene segment is provided i the genome of a second vertebrate of the population.
The population of claim 63, wherein the genome of the first vertebrate does not comprise the second gene segment.
The population of claim 63 or 64, wherein the population comprises a third human gene segment of said type, the third gene segment being different from the first and second gi segments and optionally wherein the first and third gene segments are present in the genome of the first vertebrate.
66. The population of claim 63, 64 or 65, wherein the gene segments are targeted insertions into an endogenous non-human Ig locus in the respective genome.
The population of any one of claims 63 to 66, wherein the first gene segment is a gene segment selected from any one of Tables 1 to 7 and 9 to 14 and the second gene segment is the corresponding reference sequence.
A method of enhancing the human immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising first and second human Ig locus gene segments of the same type (eg,
first and second human JH6 gene segments; or first and second lgG2 gene segments; or first and second human J\7 gene segments), wherein the first gene segment is a gene segment selected from any one of Tables 1 to 7 and 9 to 14 (eg, IGHJ6-a) and the second gene segment is the corresponding reference sequence (eg, SEQ. ID NO: 244).
69. A method of providing an enhanced human immunoglobulin gene segment repertoire, the method comprising providing a population according to any one of claims 63 to 66.
70. A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) according to claim 34, having a genome comprising at least 3 human D gene segments of the same type (eg, D2-2 gene segments), wherein at least two of the human D gene segments are variants that are not identical to each other (eg, D2-2ref and D2-2a).
71. A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) according to claim 35, having a genome comprising at least 2 different non-endogenous D gene segments of the same type type (eg, D2-2ref and D2-2a) cis at the same Ig locus.
72. A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) according to claim 36, having a genome comprising at least 2 different human D gene segments of the same type (eg, D2-2ref and D2-2a) trans at the same Ig locus; and optionally a third human D gene segment (eg, (eg, D2-2ref, D2-2a or D2-2b) of the same type, wherein the third D is cis with one of said 2 different D gene segments.
73. A population of non-human vertebrates (eg, mice or rats) according to claim 37, comprising a repertoire of human D gene segments, wherein the plurality comprises at least 2 different human D gene segments of the same type (eg, D2-2 gene segments), a first of said different D gene segments (eg, D2-2ref) is provided in the genome of a first vertebrate of the population, and a second of said different D gene segment (eg, D2-2a) being provided in the genome of a second vertebrate of the population, wherein the genome of the first vertebrate does not comprise the second D gene segment.
74. A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) according to claim 38, having a genome comprising at least 2 different non-endogenous D gene segments of the same type (eg, human D2-2 gene segments), wherein the D gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
75. A method of enhancing the human immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat) according to claim 39, the method comprising providing the vertebrate with
a genome comprising at least 3 human D gene segments of the same type (eg, D2-2 gene segments), wherein at least two of the human D gene segments are variants that are not identical to each other (eg, D2-2ref and D2-2a).
76. A method of enhancing the immunoglobulin gene diversity of a non-human vertebrate (eg, £ mouse or rat) according to claim 40, the method comprising providing the vertebrate with a genome comprising at least 2 different non-endogenous D gene segments of the same type human D2-2 gene segments) cis at the same Ig locus. 77. A method of enhancing the immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat) according to claim 41, the method comprising providing the vertebrate with a genome comprising at least 2 different human D gene segments of the same type (eg, D2-2ref and D2-2a) trans at the same Ig locus; and optionally a third human D gene segment (eg, D2- 2ref, D2-2a or D2-2b) of the same type, wherein the third D is cis with one of said 2 different D gene segments.
A method of providing an enhanced human immunoglobulin D gene segment repertoire according to claim 42, the method comprising providing a population of non-human vertebrates (eg, a mouse or rat) comprising a repertoire of human D gene segments, wherein the method comprises providing at least 2 different human D gene segments of the same type (eg, D2-2ref and D2-2a), wherein a first of said different D gene segments is provided in the genome of a first vertebrate of the population, and a second of said different D gene segments is provided in the genome of a second vertebrate of the population, wherein the genome of the first vertebrate does not comprise the second D gene segment.
A method of enhancing the human immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat) according to claim 43, the method comprising providing the vertebrate with a genome comprising at least 2 different non-endogenous D gene segments of the same type (eg, D2-2ref and D2-2a), wherein the D gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
80. The vertebrate or cell of claim 70, 71 or 74, or the method of claim 75, 77 or 79, wherein at least 2 or 3 of said different gene segments are provided cis at the same Ig locus in said genome. 81. The vertebrate or cell of claim 70, 71 or 71, or the method of any one of claims 75 to 78 and 80, wherein the D gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
82. The vertebrate or cell of any one of claims 70 to 73, or the method of any one of claims 75 to 78 and 81, wherein the D gene segments are derived from the genome sequence of two or more
different human individuals; optionally wherein the different human individuals are from different human populations.
83. The vertebrate, cell or method of claim 82, wherein the individuals are not genetically related.
84. The vertebrate, cell or method of any one of claims 70 to 83, wherein at least one of the
different D segments is a synthetic mutant of a human germline D gene segment.
85. A method of enhancing the human immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat) according to claim 48, the method comprising providing the vertebrate with a genome comprising at least 2 human D gene segments (eg, D2-2ref and D2-2a), wherein the D gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations; optionally wherein at least 2 or 3 of said different gene segments are provided at the same IgH locus in said genome.
86. The vertebrate or cell of any one of claims 70 to 74 and 80 to 84, wherein the genome comprises a substantially complete functional repertoire of human D gene segment types supplemented with one, two or more variant human D gene segments, wherein said substantially complete functional repertoire and the supplementary D gene segments are not found together in the germline genome of a human individual.
87. The population of claim 73, wherein the population comprises a substantially complete
functional repertoire of human D gene segment types supplemented with one, two or more variant human D gene segments, wherein said substantially complete functional repertoire and the supplementary D gene segments are not found together in the germline genome of a human individual.
88. A non-human vertebrate (eg, a mouse or rat) or a non-human cell (eg, an ES cell or a B-cell) having a genome comprising a substantially complete functional repertoire of human D gene segment types supplemented with one, two or more variant human D gene segments, wherein said substantially complete functional repertoire and the supplementary D gene segments are not found together in the germline genome of a human individual.
89. A population of non-human vertebrates (eg, mice or rats) comprising a substantially complete functional repertoire of human JH gene segment types supplemented with one, two or more variant human D gene segments, wherein said substantially complete functional repertoire and the supplementary D gene segments are not found together in the germline genome of a human individual.
90. The vertebrate or cell of claim 88 or the population of claim 89, comprising first and second D gene segments selected from
D2-2ref and D2-2a; or
D2-21ref and D2-21a; or
D3-10ref and D3-10a; or
D3-16ref and D3-16a; or
D2-8ref and D2-8a; or
D3-3ref and D3-3a; or
D4-23ref and D4-23a; or
D6-13ref and D6-13a; or
D3-9ref and D3-9a; or
D4-4ref and D4-4a; or
D7-27ref and D7-27a; optionally wherein the first and/or second D gene segment is present in two or more copies.
91. The vertebrate, cell or population of claim 90, comprising human gene segments D2-2ref and D2-2a; and D3-3ref and D3-3a; and optionally also D2-15.
92. A non-human vertebrate or vertebrate cell according to claim 71, comprising a genome that comprises VH, D and JH gene repertoires comprising human gene segments, the D gene repertoire comprising one or more of a plurality of D2-2 gene segments provided by at least 2 different D2-2 gene segments in cis at the same Ig locus in said genome;
a plurality of D2-21 gene segments provided by at least 2 different D2-21 gene segments in cis at the same Ig locus in said genome;
a plurality of D3-10 gene segments provided by at least 2 different D3-10 gene segments in cis at the same Ig locus in said genome;
a plurality of D3-16 gene segments provided by at least 2 different D3-16 gene segments in cis at the same Ig locus in said genome;
a plurality of D2-8 gene segments provided by at least 2 different D2-8 gene segments in cis at the same Ig locus in said genome;
a plurality of D3-3 gene segments provided by at least 2 different D3-3 gene segments in cis at the same Ig locus in said genome;
a plurality of D4-23 gene segments provided by at least 2 different D4-23 gene segments in cis at the same Ig locus in said genome;
a plurality of D6-13 gene segments provided by at least 2 different D6-13 gene segments in cis at the same Ig locus in said genome;
a plurality of D3-9 gene segments provided by at least 2 different D3-9 gene segments in cis at the same Ig locus in said genome;
a plurality of D4-4 gene segments provided by at least 2 different D4-4 gene segments in cis at
the same Ig locus in said genome; and
a plurality of D7-27 gene segments provided by at least 2 different D7-27 gene segments in cis at the same Ig locus in said genome; optionally wherein the D gene segments are derived from the genome sequence of two or more different human individuals.
93. A non-human vertebrate or vertebrate cell according to claim 71, comprising a genome that comprises VH, D and JH gene repertoires comprising human gene segments, the D gene repertoire comprising one or more of a plurality of D2-2 gene segments provided by at least 2 different D2-2 gene segments in trans in said genome;
a plurality of D2-21 gene segments provided by at least 2 different D2-21 gene segments in trans in said genome;
a plurality of D3-10 gene segments provided by at least 2 different D3-10 gene segments in trans in said genome;
a plurality of D3-16 gene segments provided by at least 2 different D3-16 gene segments in trans in said genome;
a plurality of D2-8 gene segments provided by at least 2 different D2-8 gene segments in trans in said genome;
a plurality of D3-3 gene segments provided by at least 2 different D3-3 gene segments in trans in said genome;
a plurality of D4-23 gene segments provided by at least 2 different D4-23 gene segments in trans in said genome;
a plurality of D6-13 gene segments provided by at least 2 different D6-13 gene segments in trans in said genome;
a plurality of D3-9 gene segments provided by at least 2 different D3-9 gene segments in trans in said genome;
a plurality of D4-4 gene segments provided by at least 2 different D4-4 gene segments in trans in said genome; and
a plurality of D7-27 gene segments provided by at least 2 different D7-27 gene segments in trans in said genome; optionally wherein the D gene segments are derived from the genome sequence of two or more different human individuals.
94. A non-human vertebrate or vertebrate cell (optionally an ES cell or B-cell), according to claim 70, comprising a genome that comprises VH, D and JH gene repertoires comprising human gene segments, the D gene repertoire comprising one or more of a plurality of D2-2 gene segments provided by at least 3 different D2-2 gene segments;
a plural ty of D2-21 gene segments provided by at least 3 different D2-21 gene segments;
a plural ty of D3-10 gene segments provided by at least 3 different D3-10 gene segments;
a plural ty of D3-16 gene segments provided by at least 3 different D3-16 gene segments;
a plural ty of D2-8 gene segments provided by at least 3 different D2-8 gene segments;
a plural ty of D3-3 gene segments provided by at least 3 different D3-3 gene segments;
a plural ty of D4-23 gene segments provided by at least 3 different D4-23 gene segments;
a plural ty of D6-13 gene segments provided by at least 3 different D6-13 gene segments;
a plural ty of D3-9 gene segments provided by at least 3 different D3-9 gene segments;
a plural ty of D4-4 gene segments provided by at least 3 different D4-4 gene segments; and a plural ty of D7-27 gene segments provided by at least 3 different D7-27 gene segments; optionally wherein the D gene segments are derived from the genome sequence of two or three different human individuals; optionally wherein at least 2 or 3 of said different gene segments are provided in cis at the same
Ig locus in said genome.
95. The vertebrate or cell of claim 92, 93 or 94, wherein the different human individuals are from different human populations.
96. The vertebrate or cell of any one of claims 92 to 95, wherein the individuals are not genetically related.
97. The vertebrate or cell of any one of claims 92 to 96, wherein at least one of the different D segments is a synthetic mutant of a human germline D gene segment.
98. A non-human vertebrate or vertebrate cell (optionally an ES cell or B-cell) according to claim 74, comprising a genome comprising human VH, D and JH gene repertoires, the D gene repertoire comprising of one or more of a plurality of D2-2 gene segments provided by at least 2 different D2-2 gene ; optionally in cis in said genome;
a plurality of D2-21 gene segments provided by at least 2 different D2-21 gene ; optionally in cis in said genome;
a plurality of D3-10 gene segments provided by at least 2 different D3-10 gene ; optionally in cis in said genome;
a plurality of D3-16 gene segments provided by at least 2 different D3-16 gene ; optionally in cis in said genome;
a plurality of D2-8 gene segments provided by at least 2 different D2-8 gene ; optionally in cis in said genome;
a plurality of D3-3 gene segments provided by at least 2 different D3-3 gene ; optionally in cis in said genome;
a plurality of D4-23 gene segments provided by at least 2 different D4-23 gene ; optionally in cis in said genome;
a plurality of D6-13 gene segments provided by at least 2 different D6-13 gene ; optionally in cis in said genome;
a plurality of D3-9 gene segments provided by at least 2 different D3-9 gene ; optionally in cis in said genome;
a plurality of D4-4 gene segments provided by at least 2 different D4-4 gene ; optionally in cis in said genome; and
a plurality of D7-27 gene segments provided by at least 2 different D7-27 gene ; optionally in cis in said genome; wherein the D gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations. 99. The vertebrate or cell of claim 98, wherein the human individuals are from different human populations.
100. The vertebrate, cell or population of any one of claims 70 to 99, wherein one or more of the D gene segments is a variant of a human germline D gene segment, wherein the variant gene segment encodes an amino acid sequence that differs by 1, 2 or 3 amino acids from the corresponding amino acid sequence encoded by the human germline D gene segment, provided in that said amino acid sequence encoded by the variant does not include a stop codon when said corresponding amino acid sequence does not include a stop codon. 101. The vertebrate, cell or population of claim 100, wherein said corresponding amino acid sequence encoded by the human germline D gene segment is a hydrophilic or hydrophobic sequence (according to J Mol Biol. 1997 Jul 25;270(4):587-97; Corbett SJ et a I; Table 2).
102. The vertebrate, cell or population of claim 100 or 101, comprising said variant and said
germline human D gene segments; optionally wherein the variant and germline human D gene segments are cis on the same chromosome.
103. The vertebrate, cell or population of any one of claims 100 to 102, wherein germline human D gene segment is a D2, D3, D5 or D6 family gene segment; optionally a D2-2, D2-15, D3-3, D3-9, D3-10, D3-22, D5-5, D5-18, D6-6, D6-13, D6-19 gene segment.
104. The vertebrate, cell or population of any one of claims 70 to 103, comprising a plurality of D2-2 gene segments, wherein the plurality comprises D2-2 gene segments that vary from each other at one or more nucleotide positions corresponding to positions
106,382,687 and
106,382,711
on human chromosome 14.
105. The vertebrate, cell or population of claim 104, wherein the plurality comprises a human D2- 2 gene segment comprising a thymine at a position corresponding to position 106,382,687 on human chromosome 14; and optionally no further mutation from the sequence of D2-2ref.
106. The vertebrate, cell or population of claim 104 or 105, wherein the plurality comprises a human D2-2 gene segment comprising a cytosine at a position corresponding to position 106,382,687 on human chromosome 14; and optionally no further mutation from the sequence of D2-2a.
107. The vertebrate, cell or population of any one of claims 104 to 106, wherein the plurality comprises a human D2-2 gene segment comprising an adenine at a position corresponding to position 106,382,711 on human chromosome 14; and optionally no further mutation from the sequence of D2-2b.
108. The vertebrate, cell or population of any one of claims 104 to 107, wherein the plurality comprises a human D2-2 gene segment comprising an thymine at a position corresponding to position 106,382,711 on human chromosome 14; and optionally no further mutation from the sequence of D2-2ref.
109. The vertebrate, cell or population of any one of claims 70 to 108, comprising a plurality of D7-27 gene segments, wherein the plurality comprises D7-27 gene segments that vary from each other at a nucleotide position corresponding to position 106,331,767 on human chromosome 14.
110. The vertebrate, cell or population of claim 109, wherein the plurality comprises a human D7- 27 gene segment comprising a cytosine at a position corresponding to position 106,331,767 on human chromosome 14; and optionally no further mutation from the sequence of D7-27ref.
111. The vertebrate, cell or population of claim 109 or 110, wherein the plurality comprises a human D7-27 gene segment comprising a guanine at a position corresponding to position 106,331,767 on human chromosome 14; and optionally no further mutation from the sequence of D7-27a.
112. The vertebrate, cell or population of any one of claims 70 to 111, comprising a plurality of D4-23 gene segments, wherein the plurality comprises D4-23 gene segments that vary from each other at a nucleotide position corresponding to position 106,350,740 on human chromosome 14.
113. The vertebrate, cell or population of claim 112, wherein the plurality comprises a human D4- 23 gene segment comprising an adenine at a position corresponding to position 106,350,740 on human chromosome 14; and optionally no further mutation from the sequence of D4-23ref.
114. The vertebrate, cell or population of claim 112 or 113, wherein the plurality comprises a human D4-23 gene segment comprising an guanine at a position corresponding to position 106,350,740 on human chromosome 14; and optionally no further mutation from the sequence of D4-23a.
115. The vertebrate, cell or population of any one of claims 70 to 113, comprising a plurality of D2-21 gene segments, wherein the plurality comprises D2-21 gene segments that vary from each other at a nucleotide position corresponding to position 106,354,418 on human chromosome 14.
116. The vertebrate, cell or population of claim 115, wherein the plurality comprises a human D2- 21 gene segment comprising an adenine at a position corresponding to position 106,354,418 on human chromosome 14; and optionally no further mutation from the sequence of D2-21ref.
117. The vertebrate, cell or population of claim 115 or 116, wherein the plurality comprises a human D2-21 gene segment comprising a guanine at a position corresponding to position 106,354,418 on human chromosome 14; and optionally no further mutation from the sequence of D2-21a.
118. The vertebrate, cell or population of any one of claims 70 to 117, comprising a plurality of D3-16 gene segments, wherein the plurality comprises D3-16 gene segments that vary from each other at a nucleotide position corresponding to position 106,354,418 on human chromosome 14.
119. The vertebrate, cell or population of claim 118, wherein the plurality comprises a human D3- 16 gene segment comprising a thymine at a position corresponding to position 106,361,515 on human chromosome 14; and optionally no further mutation from the sequence of D3-16ref.
120. The vertebrate, cell or population of claim 118 or 119, wherein the plurality comprises a human D3-16 gene segment comprising a cytosine at a position corresponding to position 106,361,515 on human chromosome 14; and optionally no further mutation from the sequence of D3-16a.
121. The vertebrate, cell or population of any one of claims 70 to 120, comprising a plurality of D6-13 gene segments, wherein the plurality comprises D6-13 gene segments that vary from each other at a nucleotide position corresponding to position 106,367,013 on human chromosome 14.
122. The vertebrate, cell or population of claim 121, wherein the plurality comprises a human D6- 13 gene segment comprising a thymine at a position corresponding to position 106,367,013 on human chromosome 14; and optionally no further mutation from the sequence of D6-13ref.
123. The vertebrate, cell or population of claim 121 or 122, wherein the plurality comprises a human D6-13 gene segment comprising a cytosine at a position corresponding to position 106,367,013 on human chromosome 14; and optionally no further mutation from the sequence of D6-13a. 124. The vertebrate, cell or population of any one of claims 70 to 123, comprising a plurality of
D3-10 gene segments, wherein the plurality comprises D3-10 gene segments that vary from each other at one or more nucleotide positions corresponding to positions
106,370,370 and
106,370,371
on human chromosome 14.
125. The vertebrate, cell or population of claim 124, wherein the plurality comprises a human D3- 10 gene segment comprising a thymine at a position corresponding to position 106,370,370 on human chromosome 14; and optionally no further mutation from the sequence of D3-10ref.
126. The vertebrate, cell or population of claim 124 or 125, wherein the plurality comprises a human D3-10 gene segment comprising a cytosine at a position corresponding to position
106.370.370 on human chromosome 14; and optionally no further mutation from the sequence of D3-10a.
127. The vertebrate, cell or population of claim 124, 125 or 126 wherein the plurality comprises a human D3-10 gene segment comprising an adenine at a position corresponding to position
106.370.371 on human chromosome 14; and optionally no further mutation from the sequence of D3-10ref.
128. The vertebrate, cell or population of any one of claims 124 to 127, wherein the plurality comprises a human D3-10 gene segment comprising a guanine at a position corresponding to position 106,370,371 on human chromosome 14; and optionally no further mutation from the
sequence of D3-10b.
129. The vertebrate, cell or population of any one of claims 70 to 128, comprising a plurality of D3-9 gene segments, wherein the plurality comprises D3-9 gene segments that vary from each other at a nucleotide position corresponding to position 106,370,567 on human chromosome 14.
130. The vertebrate, cell or population of claim 129, wherein the plurality comprises a human D3- 9 gene segment comprising an adenine at a position corresponding to position 106,370,567 on human chromosome 14; and optionally no further mutation from the sequence of D3-9ref.
131. The vertebrate, cell or population of claim 129 or 130, wherein the plurality comprises a human D3-9 gene segment comprising a thymine at a position corresponding to position 106,370,567 on human chromosome 14; and optionally no further mutation from the sequence of D3-9a.
132. The vertebrate, cell or population of any one of claims 70 to 131, comprising a plurality of D2-8 gene segments, wherein the plurality comprises D2-8 gene segments that vary from each other at one or more nucleotide positions corresponding to positions
106,373,085;
106,373,086 and
106,373,089
on human chromosome 14.
133. The vertebrate, cell or population of claim 132, wherein the plurality comprises a human D2- 8 gene segment comprising a cytosine at a position corresponding to position 106,373,085 on human chromosome 14.
134. The vertebrate, cell or population of claim 132 or 133, wherein the plurality comprises a human D2-8 gene segment comprising a thymine at a position corresponding to position
106.373.085 on human chromosome 14; and optionally no further mutation from the sequence of D2-8b.
135. The vertebrate, cell or population of claim 132, 133 or 134 wherein the plurality comprises a human D2-8 gene segment comprising a cytosine at a position corresponding to position
106.373.086 on human chromosome 14; and optionally no further mutation from the sequence of D2-8ref.
136. The vertebrate, cell or population of any one of claims 132 to 135, wherein the plurality comprises a human D2-8 gene segment comprising a thymine at a position corresponding to position 106,373,086 on human chromosome 14; and optionally no further mutation from the sequence of D2-8ref.
137. The vertebrate, cell or population of any one of claims 70 to 136, comprising a plurality of D4-4 gene segments, wherein the plurality comprises D4-4 gene segments that vary from each other at one or more nucleotide positions corresponding to positions
106,379,086; and
106,379,089
on human chromosome 14.
138. The vertebrate, cell or population of claim 137, wherein the plurality comprises a D4-4 gene segment comprising a cytosine at a position corresponding to position 106,379,086 on human chromosome 14; and optionally no further mutation from the sequence of D4-4ref.
139. The vertebrate, cell or population of claim 137 or 138, wherein the plurality comprises a human D4-4 gene segment comprising a thymine at a position corresponding to position 106,379,086 on human chromosome 14; and optionally no further mutation from the sequence of D4-4a.
140. The vertebrate, cell or population of claim 137, 138 or 139 wherein the plurality comprises a human D4-4 gene segment comprising a cytosine at a position corresponding to position 106,379,089 on human chromosome 14; and optionally no further mutation from the sequence of D4-4ref or a cytosine at a position corresponding to position 106,379,086 on human chromosome 14.
141. The vertebrate, cell or population of any one of claims 137 to 140, wherein the plurality comprises a human D4-4 gene segment comprising a thymine at a position corresponding to position 106,373,089 on human chromosome 14; and optionally no further mutation from the sequence of D4-4a.
142. The vertebrate, cell or population of any one of claims 70 to 141, comprising a plurality of D3-3 gene segments, wherein the plurality comprises D3-3 gene segments that vary from each other at one or more nucleotide positions corresponding to positions
106,380,241; and
106,380,246
on human chromosome 14.
143. The vertebrate, cell or population of claim 142, wherein the plurality comprises a D3-3 gene segment comprising a thymine at a position corresponding to position 106,380,241 on human chromosome 14; and optionally no further mutation from the sequence of D3-3ref. 144. The vertebrate, cell or population of claim 142 or 143, wherein the plurality comprises a human D3-3 gene segment comprising a cytosine at a position corresponding to position 106,380,241 on human chromosome 14; and optionally no further mutation from the sequence of D3-3a. 145. The vertebrate, cell or population of claim 142, 143 or 144 wherein the plurality comprises a human D3-3 gene segment comprising an adenine at a position corresponding to position 106,380,246 on human chromosome 14; and optionally no further mutation from the sequence of D3-3ref. 146. The vertebrate, cell or population of any one of claims 142 to 145, wherein the plurality comprises a human D3-3 gene segment comprising a thymine at a position corresponding to position 106,380,246 on human chromosome 14; and optionally no further mutation from the sequence of D3-3a. 147. A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) according to claim 34, having a genome comprising at least 3 human JH gene segments of the same type (JH1, JH2, JH3, JH4, JH5 or JH6), wherein at least two of the human JH gene segments are variants that are not identical to each other. 148. A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) according to claim 35, having a genome comprising at least 2 different non- endogenous JH gene segments of the same type (JH1, JH2, JH3, JH4, JH5 or JH6) cis at the same Ig locus. 149. A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) according to claim 36, having a genome comprising at least 2 different human JH gene segments of the same type (JH1, JH2, JH3, JH4, JH5 or JH6) trans at the same Ig locus; and optionally a third human JH gene segments of the same type, wherein the third JH is cis with one of said 2 different J H gene segments.
150. A population of non-human vertebrates (eg, mice or rats) comprising a repertoire of human JH gene segments according to claim 37, wherein the plurality comprises at least 2 different human JH gene segments of the same type (JH1, JH2, JH3, JH4, JH5 or JH6), a first of said different JH gene segments is provided in the genome of a first vertebrate of the population, and a second of said different JH gene segments being provided in the genome of a second vertebrate of the population, wherein the genome of the first vertebrate does not comprise the second JH gene segment.
151. A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) according to claim 38, having a genome comprising at least 2 different non-
endogenous JH gene segments of the same type (JHl, JH2, JH3, JH4, JH5 or JH6), wherein the JH gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
152. A method of enhancing the human immunoglobulin gene diversity of a non-human
vertebrate (eg, a mouse or rat) according to claim 39, the method comprising providing the vertebrate with a genome comprising at least 3 human JH gene segments of the same type (JHl, JH2, JH3, JH4, JH5 or JH6), wherein at least two of the human JH gene segments are variants that are not identical to each other.
153. A method of enhancing the immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat) according to claim 40, the method comprising providing the vertebrate with a genome comprising at least 2 different non-endogenous JH gene segments of the same type (JHl, JH2, JH3, JH4, JH5 or JH6) cis at the same Ig locus.
154. A method of enhancing the immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat) according to claim 41, the method comprising providing the vertebrate with a genome comprising at least 2 different human JH gene segments of the same type (JHl, JH2, JH3, JH4, JH5 or JH6) trans at the same Ig locus; and optionally a third human JH gene segments of the same type, wherein the third JH is cis with one of said 2 different JH gene segments.
155. A method of providing an enhanced human immunoglobulin JH gene segment repertoire according to claim 42, the method comprising providing a population of non-human vertebrates (eg, a mouse or rat) comprising a repertoire of human JH gene segments, wherein the method comprises providing at least 2 different human JH gene segments of the same type (JHl, JH2, JH3, JH4, JH5 or JH6), wherein a first of said different JH gene segments is provided in the genome of a first vertebrate of the population, and a second of said different JH gene segments is provided in the genome of a second vertebrate of the population, wherein the genome of the first vertebrate does not comprise the second JH gene segment.
156. A method of enhancing the human immunoglobulin gene diversity of a non-human
vertebrate (eg, a mouse or rat) according to claim 43, the method comprising providing the vertebrate with a genome comprising at least 2 different non-endogenous JH gene segments of the same type (JHl, JH2, JH3, JH4, JH5 or JH6), wherein the JH gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
157. The vertebrate or cell of claim 147, 149 or 151, or the method of claim 152, 154, 155 or 156, wherein at least 2 or 3 of said different gene segments are provided cis at the same Ig locus in said genome.
158. The vertebrate or cell of claim 147, 148 or 149, or the method of claim 152, 153, 154 or 155, wherein the JH gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
159. The vertebrate or cell of claim 147, 148 or 149, or the method of claim 152, 153, 154 or 155, wherein the JH gene segments are derived from the genome sequence of two or more different human individuals; optionally wherein the different human individuals are from different human populations.
160. The vertebrate, cell or method of claim 159, wherein the individuals are not genetically related.
161. The vertebrate, cell or method of any one of claims 147 to 160, wherein at least one of the different JH segments is a synthetic mutant of a human germline JH gene segment.
162. A method of enhancing the human immunoglobulin gene diversity of a non-human
vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising at least 2 human JH gene segments of the same type (JH1, JH2, JH3, JH4, JH5 or JH6), wherein the JH gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations; optionally wherein at least 2 or 3 of said different gene segments are provided at the same IgH locus in said genome.
163. The vertebrate or cell of any one of claims 147 to 149 and 151, wherein the genome
comprises a substantially complete functional repertoire of human JH gene segment types supplemented with one, two or more human JH gene segments, wherein said substantially complete functional repertoire and the supplementary JH gene segments are not found together in the germline genome of a human individual.
164. The population of claim 150, wherein the population comprises a substantially complete functional repertoire of human JH gene segment types supplemented with one, two or more human JH gene segments, wherein said substantially complete functional repertoire and the supplementary JH gene segments are not found together in the germline genome of a human individual.
165. A non-human vertebrate (eg, a mouse or rat) or a non-human cell (eg, an ES cell or a B-cell) having a genome comprising a substantially complete functional repertoire of human JH gene segment types supplemented with one, two or more human JH gene segments, wherein said substantially complete functional repertoire and the supplementary JH gene segments are not found together in the germline genome of a human individual.
166. A population of non-human vertebrates (eg, mice or rats) comprising a substantially
complete functional repertoire of human JH gene segment types supplemented with one, two or more human JH gene segments, wherein said substantially complete functional repertoire and the supplementary JH gene segments are not found together in the germline genome of a human individual.
167. The vertebrate of claim 165 or the population of claim 166, wherein at least one of said JH gene segments is SEQ ID NO: 1, 2, 3 or 4.
168. The vertebrate or population of claim 167, wherein at least one of said JH gene segments is SEQ ID NO: 1 and at least one, two or more of said supplementary JH gene segments is a variant according to any one of claims 178 to 196.
169. The vertebrate or population of claim 167 or 168, wherein at least one of said JH gene
segments is SEQ ID NO: 2 and at least one, two or more of said supplementary JH gene segments is a variant according to any one of claims 198 to 209.
170. The vertebrate or population of claim 167, 168 or 169, wherein at least one of said JH gene segments is SEQ ID NO: 2 and at least one, two or more of said supplementary JH gene segments
is a variant according to any one of claims 212 to 217.
171. A non-human vertebrate or vertebrate cell according to claim 148, comprising a genome that comprises VH, D and JH gene repertoires comprising human gene segments, the JH gene repertoire comprising a plurality of JH1 gene segments provided by at least 2 different JH1 gene segments in cis at the same Ig locus in said genome;
a plurality of JH2 gene segments provided by at least 2 different JH2 gene segments in cis at the same Ig locus in said genome;
a plurality of JH3 gene segments provided by at least 2 different JH3 gene segments in cis at the same Ig locus in said genome;
a plurality of JH4 gene segments provided by at least 2 different JH4 gene segments in cis at the same Ig locus in said genome;
a plurality of JH5 gene segments provided by at least 2 different JH5 gene segments in cis at the same Ig locus in said genome; or
a plurality of JH6 gene segments provided by at least 2 different JH6 gene segments in cis at the same Ig locus in said genome; optionally wherein the JH gene segments are derived from the genome sequence of two or more different human individuals.
172. A non-human vertebrate or vertebrate cell (optionally an ES cell or B-cell), according to claim 147, comprising a genome that comprises VH, D and JH gene repertoires comprising human gene segments, the JH gene repertoire comprising a plurality of JH1 gene segments provided by at least 3 different JH1 gene segments;
a plurality of JH2 gene segments provided by at least 3 different JH2 gene segments;
a plurality of JH3 gene segments provided by at least 3 different JH3 gene segments;
a plurality of JH4 gene segments provided by at least 3 different JH4 gene segments;
a plurality of JH5 gene segments provided by at least 3 different JH5 gene segments; or a plurality of JH6 gene segments provided by at least 3 different JH6 gene segments; optionally wherein the JH gene segments are derived from the genome sequence of two or three different human individuals; optionally wherein at least 2 or 3 of said different gene segments are provided in cis at the same Ig locus in said genome.
173. The vertebrate or cell of claim 171 or 172, wherein the different human individuals are from different human populations.
174. The vertebrate or cell of any one of claims 171 to 173, wherein the individuals are not
genetically related.
175. The vertebrate or cell of any one of claims 171 to 174, wherein at least one of the different JH segments is a synthetic mutant of a human germline JH gene segment.
176. A non-human vertebrate or vertebrate cell (optionally an ES cell or B-cell) according to claim 151, comprising a genome comprising human VH, D and JH gene repertoires, the JH gene repertoire comprising
a plurality of JH1 gene segments provided by at least 2 different human JH1 gene segments, optionally in cis at the same Ig locus in said genome;
a plurality of JH2 gene segments provided by at least 2 different human JH2 gene segments, optionally in cis at the same Ig locus in said genome;
a plurality of JH3 gene segments provided by at least 2 different human JH3 gene segments, optionally in cis at the same Ig locus in said genome;
a plurality of JH4 gene segments provided by at least 2 different human JH4 gene segments, optionally in cis at the same Ig locus in said genome;
a plurality of JH5 gene segments provided by at least 2 different human JH5 gene segments, optionally in cis at the same Ig locus in said genome; or
a plurality of JH6 gene segments provided by at least 2 different human JH6 gene segments, optionally in cis at the same Ig locus in said genome; wherein the JH gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
177. The vertebrate or cell of claim 176, wherein the human individuals are from different human populations.
178. The vertebrate, cell or population of any one of claims 147 to 151, 157 to 161 and 163 to 177, comprising a plurality of JH5 gene segments, wherein the plurality comprises a human JH5 gene variant of SEQ ID NO: 1, wherein the variant comprises a nucleotide mutation at one or more positions corresponding to positions
106,330,024
106,330,027
106,330,032
106,330,041
106,330,044
106,330,045
106,330,062
106,330,063
106,330,065
106,330,066
106,330,067
106,330,068 and
106,330,071 on human chromosome 14.
179. The vertebrate, cell or population of claim 178, wherein the plurality comprises a human JH5 gene variant of SEQ ID NO: 1, wherein the variant comprises a guanine at a position
corresponding to position 106,330,067 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
180. The vertebrate, cell or population of claim 179, wherein the variant comprises additionally a mutation at a position corresponding to (i) position 106,330,071 on human chromosome 14 (optionally the additional mutation being a guanine); (ii) position 106,330,066 on human
chromosome 14 (optionally the additional mutation being a guanine); and/or (iii) position 106,330,068 on human chromosome 14 (optionally the additional mutation being a thymine).
181. The vertebrate, cell or population of claim 178, 179 or 180, wherein the plurality comprises a human JH5 gene variant of SEQ ID NO: 1, wherein the variant comprises a guanine at a position corresponding to position 106,330,071 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
182. The vertebrate, cell or population of claim 181, wherein the variant comprises additionally a mutation at a position corresponding to (i) position 106,330,063 on human chromosome 14
(optionally the additional mutation being an adenine); and/or (ii) position 106,330,067 on human chromosome 14 (optionally the additional mutation being a guanine).
183. The vertebrate, cell or population of claim 178 to 182, wherein the plurality comprises a human JH5 gene variant of SEQ ID NO: 1, wherein the variant comprises a cytosine at a position corresponding to position 106,330,045 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
184. The vertebrate, cell or population of claim 178 to 183, wherein the plurality comprises a human JH5 gene variant of SEQ ID NO: 1, wherein the variant comprises an adenine at a position corresponding to position 106,330,044 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
185. The vertebrate, cell or population of claim 184, wherein the variant comprises additionally a mutation at a position corresponding to (i) position 106,330,066 on human chromosome 14
(optionally the additional mutation being a guanine); and/or (ii) position 106,330,068 on human chromosome 14 (optionally the additional mutation being a thymine).
186. The vertebrate, cell or population of claim 178 to 185, wherein the plurality comprises a human JH5 gene variant of SEQ ID NO: 1, wherein the variant comprises a guanine at a position corresponding to position 106,330,066 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
187. The vertebrate, cell or population of claim 186, wherein the variant comprises additionally a mutation at a position corresponding to (i) position 106,330,067 on human chromosome 14
(optionally the additional mutation being a guanine); and/or (ii) position 106,330,068 on human chromosome 14 (optionally the additional mutation being a thymine).
188. The vertebrate, cell or population of claim 178 to 185, wherein the plurality comprises a human JH5 gene variant of SEQ ID NO: 1, wherein the variant comprises a thymine at a position corresponding to position 106,330,068 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
189. The vertebrate, cell or population of claim 188, wherein the variant comprises additionally a mutation at a position corresponding to (i) position 106,330,067 on human chromosome 14
(optionally the additional mutation being a guanine); and/or (ii) position 106,330,066 on human chromosome 14 (optionally the additional mutation being a guanine).
190. The vertebrate, cell or population of claim 178 to 189, wherein the plurality comprises a human JH5 gene variant of SEQ ID NO: 1, wherein the variant comprises a cytosine at a position corresponding to position 106,330,027 on human chromosome 14; and optionally no further
mutation from the sequence of SEQ ID NO: 1.
191. The vertebrate, cell or population of claim 178 to 190, wherein the plurality comprises a human JH5 gene variant of SEQ ID NO: 1, wherein the variant comprises an adenine at a position corresponding to position 106,330,024 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
192. The vertebrate, cell or population of claim 178 to 191, wherein the plurality comprises a human JH5 gene variant of SEQ ID NO: 1, wherein the variant comprises a thymine at a position corresponding to position 106,330,032 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
193. The vertebrate, cell or population of claim 178 to 192, wherein the plurality comprises a human JH5 gene variant of SEQ ID NO: 1, wherein the variant comprises a thymine at a position corresponding to position 106,330,041 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
194. The vertebrate, cell or population of claim 178 to 193, wherein the plurality comprises a human JH5 gene variant of SEQ ID NO: 1, wherein the variant comprises an adenine or thymine at a position corresponding to position 106,330,063 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
195. The vertebrate, cell or population of claim 194, wherein the variant comprises additionally a mutation at a position corresponding to position 106,330,071 on human chromosome 14 (optionally the additional mutation being a guanine).
196. The vertebrate, cell or population of claim 178 to 195, wherein the plurality comprises a human JH5 gene variant of SEQ ID NO: l,wherein the variant comprises a cytosine at a position corresponding to position 106,330,062 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 1.
197. The vertebrate, cell or population of claim 178 to 196, wherein the genome comprises SEQ ID NO:l; optionally in cis at the same Ig locus as one, two or more of the variants.
198. The vertebrate, cell or population of any one of claims 147 to 151, 157 to 161 and 96 to 130, comprising a plurality of JH6 gene segments, wherein the plurality comprises a human JH6 gene variant of SEQ ID NO: 2, wherein the variant comprises a nucleotide mutation at one or more positions corresponding to positions 106,329,411
106,329,413
106,329,414
106,329,417
106,329,419
106,329,426
106,329,434
106,329,435, and
106,329,468
on human chromosome 14.
199. The vertebrate, cell or population of claim 198, comprising a plurality of JH6 gene segments, wherein the plurality comprises a human JH6 gene variant of SEQ ID NO: 2, wherein the variant comprises a guanine at a position corresponding to position 106,329,435 on human
chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 2.
200. The vertebrate, cell or population of claim 199, wherein the variant comprises additionally a mutation at a position corresponding to (i) position 106,329,468 on human chromosome 14 (optionally the additional mutation being a guanine); (ii) position 106,329,419 on human chromosome 14 (optionally the additional mutation being an adenine); (iii) position 106,329,434 on human chromosome 14 (optionally the additional mutation being a cytosine) and/or position 106,329,414 on human chromosome 14 (optionally the additional mutation being a guanine); (iv) position 106,329,426 on human chromosome 14 (optionally the additional mutation being an adenine); (v) position 106,329,413 on human chromosome 14 (optionally the additional mutation being an adenine); (vi) position 106,329,417 on human chromosome 14 (optionally the additional mutation being a thymine); (vii) position 106,329,411 on human chromosome 14 (optionally the additional mutation being a thymine); (viii) position 106,329,451 on human chromosome 14 (optionally the additional mutation being an adenine); (ix) position 106,329,452 on human chromosome 14 (optionally the additional mutation being a cytosine); and/or (x) position 106,329,453 on human chromosome 14 (optionally the additional mutation being a cytosine).
201. The vertebrate, cell or population of claim 200, wherein the variant comprises additionally mutations at positions corresponding to position 106,329,451 on human chromosome 14, the additional mutation being an adenine; position 106,329,452 on human chromosome 14, the additional mutation being a cytosine; and position 106,329,453 on human chromosome 14, the additional mutation being a cytosine.
202. The vertebrate, cell or population of any one of claims 147 to 151, 157 to 161 and 163 to 201, comprising a plurality of JH6 gene segments,, wherein the plurality comprises a human JH6 gene variant of SEQ ID NO: 2, wherein the variant comprises a guanine at a position
corresponding to position 106,329,468 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 2.
203. The vertebrate, cell or population of claim 202, wherein the variant comprises additionally a mutation at a position corresponding to position 106,329,435 on human chromosome 14 (optionally the additional mutation being a guanine).
204. The vertebrate, cell or population of any one of claims 147 to 151, 157 to 161 and 163 to 203, comprising a plurality of JH6 gene segments,, wherein the plurality comprises a human JH6 gene variant of SEQ ID NO: 2, wherein the variant comprises a thymine at a position
corresponding to position 106,329,417 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 2.
205. The vertebrate, cell or population of claim 204, wherein the variant comprises additionally a mutation at a position corresponding to position 106,329,435 on human chromosome 14 (optionally the additional mutation being a guanine).
206. The vertebrate, cell or population of any one of claims 147 to 151, 157 to 161 and 163 to 205, comprising a plurality of JH6 gene segments,, wherein the plurality comprises a human JH6 gene variant of SEQ ID NO: 2, wherein the variant comprises a cytosine at a position corresponding to position 106,329,434 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 2.
207. The vertebrate, cell or population of claim 206, wherein the variant comprises additionally a mutation at a position corresponding to (i) position 106,329,414 on human chromosome 14 (optionally the additional mutation being a guanine); and/or (ii) position 106,329,435 on human chromosome 14 (optionally the additional mutation being a guanine).
208. The vertebrate, cell or population of any one of claims 147 to 151, 157 to 161 and 163 to 207, comprising a plurality of JH6 gene segments, wherein the plurality comprises a human JH6 gene variant of SEQ ID NO: 2, wherein the variant comprises a thymine at a position corresponding to position 106,329,411 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 2.
209. The vertebrate, cell or population of claim 208, wherein the variant comprises additionally a mutation at a position corresponding to position 106,329,435 on human chromosome 14 (optionally the additional mutation being a guanine).
210. The vertebrate, cell or population of any one of claims 147 to 151, 157 to 161 and 163 to 209, comprising a plurality of JH6 gene segments, wherein the plurality comprises a human JH6 gene variant that is an antisense sequence of the variant of any one of claims 107 to 118.
211. The vertebrate, cell or population of any one of claims 198 to 210, wherein the genome comprises SEQ ID NO:2; optionally cis at the same Ig locus as one, two or more of the JH6 variants.
212. The vertebrate, cell or population of any one of claims 147 to 151, 157 to 161 and 163 to 211, comprising a plurality of JH2 gene segments, wherein the plurality comprises a human JH2 gene variant of SEQ ID NO: 3, wherein the variant comprises a nucleotide mutation at one or more positions corresponding to positions
106,331,455
106,331,453, and
106,331,409 on human chromosome 14.
213. The vertebrate, cell or population of claim 212, comprising said plurality of JH2 gene
segments, wherein the plurality comprises a human JH2 gene variant of SEQ ID NO: 3, wherein the variant comprises a guanine at a position corresponding to position 106,331,455 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 3.
214. The vertebrate, cell or population of claim 213, wherein the variant comprises additionally a mutation at a position corresponding to (i) position 106,331,453 on human chromosome 14 (optionally the additional mutation being an adenine); and/or (ii) position 106,331,409 on human chromosome 14 (optionally the additional mutation being an adenine); (iii) position 106,329,434 on human chromosome 14 (optionally the additional mutation being an adenine).
215. The vertebrate, cell or population of any one of claims 147 to 151, 157 to 161 and 163 to 214, comprising a plurality of JH2 gene segments, wherein the plurality comprises a human JH2 gene variant of SEQ ID NO: 3, wherein the variant comprises an adenine at a position corresponding to position 106,331,453 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 3.
216. The vertebrate, cell or population of claim 215, wherein the variant comprises additionally a mutation at a position corresponding to position 106,331,409 on human chromosome 14 (optionally the additional mutation being an adenine).
217. The vertebrate, cell or population of any one of claims 147 to 151, 157 to 161 and 163 to
216, comprising a plurality of JH2 gene segments, wherein the plurality comprises a human JH2 gene variant of SEQ ID NO: 3, wherein the variant comprises an adenine at a position corresponding to position 106,331,409 on human chromosome 14; and optionally no further mutation from the sequence of SEQ ID NO: 3.
218. The vertebrate, cell or population of any one of claims 147 to 151, 157 to 161 and 163 to
217, comprising a plurality of JH2 gene segments, wherein the plurality comprises a human JH2 gene variant that is an antisense sequence of the variant of any one of claims 188 to 193.
219. The vertebrate, cell or population of any one of claims 212 to 218, wherein the genome comprises SEQ ID NO:3; optionally cis at the same Ig locus as one, two or more of the JH2 variants.
220. The vertebrate, cell or population of any one of claims 147 to 151, 157 to 161 and 163 to 219, wherein the genome comprises two or more different JH gene segments selected from SEQ ID NOs: 1 to 3 and variants according to any one of claims 178 to 219; optionally wherein said JH gene segments are cis at the same immunoglobulin Ig locus.
221. A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) according to claim 34, having a genome comprising at least 3 human JL gene segments of the same type (eg, JKI), wherein at least two of the human JL gene segments are variants that are not identical to each other.
222. A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) according to claim 35, having a genome comprising at least 2 different non- endogenous JL gene segments of the same type (eg, J KI) cis at the same Ig locus.
223. A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) according to claim 36, having a genome comprising at least 2 different human JL gene segments of the same type (eg, J KI) trans at the same Ig locus; and optionally a third human JL gene segment of the same type, wherein the third JL is cis with one of said 2 different J L gene segments.
224. A population of non-human vertebrates (eg, mice or rats) comprising a repertoire of human JL gene segments according to claim 37, wherein the plurality comprises at least 2 different human JL gene segments of the same type (eg, JKI), a first of said different JL gene segments is provided in the genome of a first vertebrate of the population, and a second of said different JL gene segments being provided in the genome of a second vertebrate of the population, wherein the genome of the first vertebrate does not comprise the second JL gene segment.
225. A non-human vertebrate (eg, a mouse or rat) or a non-human vertebrate cell (eg, an ES cell or a B-cell) according to claim 38, having a genome comprising at least 2 different non- endogenous JL gene segments of the same type (eg, JKI), wherein the JL gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
226. A method of enhancing the human immunoglobulin gene diversity of a non-human
vertebrate (eg, a mouse or rat) according to claim 39, the method comprising providing the vertebrate with a genome comprising at least 3 human JL gene segments of the same type (eg, JKI), wherein at least two of the human JL gene segments are variants that are not identical to each other.
227. A method of enhancing the immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat) according to claim 40, the method comprising providing the vertebrate with a genome comprising at least 2 different non-endogenous J L gene segments of the same type (eg, JKI) cis at the same Ig locus.
228. A method of enhancing the immunoglobulin gene diversity of a non-human vertebrate (eg, a mouse or rat) according to claim 41, the method comprising providing the vertebrate with a genome comprising at least 2 different human JL gene segments of the same type(eg, JKI) trans at the same Ig locus; and optionally a third human JL gene segment of the same type, wherein the third JL is cis with one of said 2 different J L gene segments.
229. A method of providing an enhanced human immunoglobulin JL gene segment repertoire according to claim 42, the method comprising providing a population of non-human vertebrates (eg, a mouse or rat) comprising a repertoire of human JL gene segments, wherein the method comprises providing at least 2 different human JL gene segments of the same type (eg, JKI), wherein a first of said different J L gene segments is provided in the genome of a first vertebrate of the population, and a second of said different J L gene segments is provided in the genome of a second vertebrate of the population, wherein the genome of the first vertebrate does not comprise the second JL gene segment.
230. A method of enhancing the human immunoglobulin gene diversity of a non-human
vertebrate (eg, a mouse or rat) according to claim 43, the method comprising providing the vertebrate with a genome comprising at least 2 different non-endogenous JL gene segments of the same type (eg, JKI), wherein the JL gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
231. The vertebrate or cell of claim 221, 223 or 225, or the method of claim 226, 228, 229 or 230, wherein at least 2 or 3 of said different gene segments are provided cis at the same Ig locus in said genome.
The vertebrate or cell of claim 221, 222 or 223, or the method of claim 226, 227, 228 or 229, wherein the JL gene segments are derived from the genome sequence of different human
individuals that are not genetically related over at least 3 generations.
233. The vertebrate or cell of claim 221, 222 or 223, or the method of claim 226, 227, 228 or 229, wherein the J L gene segments are derived from the genome sequence of two or more different human individuals; optionally wherein the different human individuals are from different human populations.
234. The vertebrate, cell or method of claim 233, wherein the individuals are not genetically related.
235. The vertebrate, cell or method of any one of claims 221 to 234, wherein at least one of the different J L segments is a synthetic mutant of a human germline JL gene segment.
236. A method of enhancing the human immunoglobulin gene diversity of a non-human
vertebrate (eg, a mouse or rat), the method comprising providing the vertebrate with a genome comprising at least 2 human J L gene segments of the same type (eg, JKI), wherein the J L gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations; optionally wherein at least 2 or 3 of said different gene segments are provided at the same IgL locus in said genome.
237. The vertebrate or cell of any one of claims claim 221 to 223 and 225, wherein the genome comprises a substantially complete functional repertoire of human JK and/or iX gene segment types supplemented with one, two or more human JK and/or iX gene segments respectively, wherein said substantially complete functional repertoire and the supplementary gene segments are not found together in the germline genome of a human individual.
238. The population of claim 224, wherein the population comprises a substantially complete functional repertoire of human J L gene segment types supplemented with one, two or more human JK and/or iX gene segments respectively, wherein said substantially complete functional repertoire and the supplementary gene segments are not found together in the germline genome of a human individual.
239. A non-human vertebrate (eg, a mouse or rat) or a non-human cell (eg, an ES cell or a B-cell) having a genome comprising a substantially complete functional repertoire of human JK and/or iX gene segment types supplemented with one, two or more human JK and/or iX gene segments respectively, wherein said substantially complete functional repertoire and the supplementary gene segments are not found together in the germline genome of a human individual.
240. A population of non-human vertebrates (eg, mice or rats) comprising a substantially
complete functional repertoire of human JK and/or iX gene segment types supplemented with one, two or more human JK and/or iX gene segments respectively, wherein said substantially complete functional repertoire and the supplementary gene segments are not found together in the germline genome of a human individual.
241. A non-human vertebrate or vertebrate cell according to claim 222, comprising a genome that comprises VL and J L gene repertoires comprising human gene segments, the J L gene repertoire comprising a plurality of human JKI gene segments provided by at least 2 different human JKI gene segments in cis at the same Ig locus in said genome;
a plurality of human JK2 gene segments provided by at least 2 different human JKI gene
segments in cis at the same Ig locus in said genome;
a plurality of human JK3 gene segments provided by at least 2 different human JKI gene segments in cis at the same Ig locus in said genome;
a plurality of human JK4 gene segments provided by at least 2 different human JKI gene segments in cis at the same Ig locus in said genome;
a plurality of human JK5 gene segments provided by at least 2 different human JKI gene segments in cis at the same Ig locus in said genome;
a plurality of human J\l gene segments provided by at least 2 different human J\l gene segments in cis at the same Ig locus in said genome;
a plurality of human J\2 gene segments provided by at least 2 different human J\2 gene segments in cis at the same Ig locus in said genome;
a plurality of human J\3 gene segments provided by at least 2 different human J\3 gene segments in cis at the same Ig locus in said genome;
a plurality of human J\4 gene segments provided by at least 2 different human J\4 gene segments in cis at the same Ig locus in said genome;
a plurality of human J\5 gene segments provided by at least 2 different human J\5 gene segments in cis at the same Ig locus in said genome;
a plurality of human J\6 gene segments provided by at least 2 different human J\6 gene segments in cis at the same Ig locus in said genome; or
a plurality of human J\7 gene segments provided by at least 2 different human J\7 gene segments in cis at the same Ig locus in said genome; optionally wherein the J L gene segments are derived from the genome sequence of two or more different human individuals.
242. A non-human vertebrate or vertebrate cell (optionally an ES cell or B-cell), according to claim 221, comprising a genome that comprises VL and J L gene repertoires comprising human gene segments, the JL gene repertoire comprising a plurality of human JKI gene segments provided by at least 3 different human JKI gene segments;
a plurality of human JK2 gene segments provided by at least 3 different human JKI gene segments;
a plurality of human JK3 gene segments provided by at least 3 different human JKI gene segments;
a plurality of human JK4 gene segments provided by at least 3 different human JKI gene segments;
a plurality of human JK5 gene segments provided by at least 3 different human JKI gene segments;
a plurality of human J\l gene segments provided by at least 3 different human J\l gene segments;
a plurality of human J\2 gene segments provided by at least 3 different human J\2 gene segments;
a plurality of human J\3 gene segments provided by at least 3 different human J\3 gene segments;
a plurality of human J\4 gene segments provided by at least 3 different human J\4 gene segments;
a plurality of human J\5 gene segments provided by at least 3 different human J\5 gene segments;
a plurality of human J\6 gene segments provided by at least 3 different human J\6 gene segments; or
a plurality of human J\7 gene segments provided by at least 3 different human J\7 gene segments; optionally wherein the J L gene segments are derived from the genome sequence of two or three different human individuals; optionally wherein at least 2 or 3 of said different gene segments are provided in cis at the same Ig locus in said genome. 243. The vertebrate or cell of claim 241 or 242, wherein the different human individuals are from different human populations.
244. The vertebrate or cell of any one of claims 241 to 243, wherein the individuals are not genetically related.
245. The vertebrate or cell of any one of claims 241 to 244, wherein at least one of the different J L segments is a synthetic mutant of a human germline J L gene segment.
246. A non-human vertebrate or vertebrate cell (optionally an ES cell or B-cell) according to claim 225, comprising a genome comprising human VL and JL gene repertoires, the J L gene repertoire comprising a plurality of human JKI gene segments provided by at least 2 different human JKI gene segments, optionally in cis at the same Ig locus in said genome;
a plurality of human JK2 gene segments provided by at least 2 different human JKI gene segments, optionally in cis at the same Ig locus in said genome;
a plurality of human JK3 gene segments provided by at least 2 different human JKI gene segments, optionally in cis at the same Ig locus in said genome;
a plurality of human JK4 gene segments provided by at least 2 different human JKI gene segments, optionally in cis at the same Ig locus in said genome;
a plurality of human JK5 gene segments provided by at least 2 different human JKI gene segments, optionally in cis at the same Ig locus in said genome;
a plurality of human J\l gene segments provided by at least 2 different human J\l gene segments, optionally in cis at the same Ig locus in said genome;
a plurality of human J\2 gene segments provided by at least 2 different human J\2 gene segments, optionally in cis at the same Ig locus in said genome;
a plurality of human J\3 gene segments provided by at least 2 different human J\3 gene segments, optionally in cis at the same Ig locus in said genome;
a plurality of human J\4 gene segments provided by at least 2 different human J\4 gene segments, optionally in cis at the same Ig locus in said genome;
a plurality of human J\5 gene segments provided by at least 2 different human J\5 gene segments, optionally in cis at the same Ig locus in said genome;
a plurality of human J\6 gene segments provided by at least 2 different human J\6 gene segments, optionally in cis at the same Ig locus in said genome; or
a plurality of human J\7 gene segments provided by at least 2 different human J\7 gene segments, optionally in cis at the same Ig locus in said genome; wherein the J L gene segments are derived from the genome sequence of different human individuals that are not genetically related over at least 3 generations.
247. The vertebrate or cell of claim 246, wherein the human individuals are from different human populations.
248. A method of producing an antibody heavy chain, the method comprising
(a) providing an antigen-specific heavy chain variable domain; and
(b) combining the variable domain with a human heavy chain constant region to produce an antibody heavy chain comprising (in N- to C-terminal direction) the variable domain and the constant region; wherein the human heavy chain constant region is an IGHAref, IGHAla, IGHA2a, IGHA2b, IGHGlref, IGHG2ref, IGHG2a, IGHG3ref, IGHG3a, IGHG3b, IGHG4ref, IGHG4a, IGHDref, IGHEref, IGHMref, IGHMa or IGHMb constant region.
249. The method of claim 248, wherein the variable domain is a human variable domain.
250. The method of any claim 248 or 249, wherein the variable domain has previously been selected from a non-human vertebrate that has been immunised with the antigen.
251. The method of any one of claims 248 to 250, comprising providing an expression vector comprising a nucleotide sequence encoding the constant region; inserting a nucleotide sequence encoding the variable domain into the vector 5' of the constant region sequence; inserting the vector into a host cell and expressing the heavy chain by the host cell; the method further comprising isolating a heavy chain (eg, as part of an antibody) comprising the variable domain and the human constant region.
252. The method of any one of claims 248 to 251, further comprising obtaining a nucleotide sequence encoding the heavy chain.
253. An antibody comprising a human heavy chain, the heavy chain comprising a variable domain that is specific for an antigen and a constant region that is an IGHAref, IGHAla, IGHA2a, IGHA2b, IGHGlref, IGHG2ref, IGHG2a, IGHG3ref, IGHG3a, IGHG3b, IGHG4ref, IGHG4a, IGHDref, IGHEref, IGHMref, IGHMa or IGHMb constant region.
254. A polypeptide comprising (in N- to C- terminal direction) a leader sequence, a human
variable domain that is specific for an antigen and a human constant region that is an IGHAref, IGHAla, IGHA2a, IGHA2b, IGHGlref, IGHG2ref, IGHG2a, IGHG3ref, IGHG3a, IGHG3b, IGHG4ref, IGHG4a, IGHDref, IGHEref, IGHMref, IGHMa or IGHMb constant region; wherein (i) the leader sequence is not the native human variable domain leader sequence; and/or (ii) the variable domain comprises mouse AID-pattern somatic mutations or mouse terminal deoxynucleotidyl transferase (TdT)- pattern junctional mutations.
255. A nucleotide sequence encoding (in 5' to 3' direction) a leader sequence and a human antibody heavy chain, the heavy chain comprising a variable domain that is specific for an antigen and a constant region that is an IGHAref, IGHAla, IGHA2a, IGHA2b, IGHGlref, IGHG2ref, IGHG2a, IGHG3ref, IGHG3a, IGHG3b, IGHG4ref, IGHG4a, IGHDref, IGHEref, IGHMref, IGHMa or IGHMb constant region; and the leader sequence being operable for expression of the heavy chain and wherein the leader sequence is not the native human variable domain leader sequence.
256. A nucleotide sequence encoding (in 5' to 3' direction) a promoter and a human antibody heavy chain, the heavy chain comprising a variable domain that is specific for an antigen and a constant region that is an IGHAref, IGHAla, IGHA2a, IGHA2b, IGHGlref, IGHG2ref, IGHG2a, IGHG3ref, IGHG3a, IGHG3b, IGHG4ref, IGHG4a, IGHDref, IGHEref, IGHMref, IGHMa or IGHMb constant region; and the promoter being operable for expression of the heavy chain and wherein the promoter is not the native human promoter.
257. The antibody, polypeptide or nucleotide sequence of any one of claims 253 to 256, wherein the variable domain comprises mouse AID-pattern somatic mutations or mouse terminal deoxynucleotidyl transferase (TdT)- pattern junctional mutations. 258. A vector (eg, a CHO cell or HEK293 cell vector) comprising the nucleic acid of claim 255, 256 or 257; optionally wherein the vector is in a host cell (eg, a CHO cell or HEK293 cell).
259. A pharmaceutical composition comprising the antibody or polypeptide of any one of claims 253, 254 and 257, together with a pharmaceutically-acceptable excipient, diluent or a medicament (eg, a further antigen-specific variable domain, antibody chain or antibody).
260. The antibody or polypeptide of any one of claims 253, 254 and 257 for use in treating and/or preventing a medical condition in a human patient.
261. Use of the antibody or polypeptide of any one of claims 253, 254 and 257 for the
manufacture of a medicament for treating and/or preventing a medical condition in a human patient.
262. The antibody, polypeptide or use of claim 260 or 261, wherein the human is a member of a human population selected from population numbers 1-14, wherein the populations are numbered as follows (population labels being according to 1000 Genomes Project
nomenclature)
1= ASW;
2= CEU;
3=CHB;
4=CHS;
5=CLM;
6=FIN;
7=GB ;
8=IBS;
9=JPT;
10=LWK;
11=MXL;
12=PUR;
13=TSI;
14=Y I.
263. The antibody, polypeptide or use of claim 262, wherein the constant region is a
(i) IGHAla constant region and the human population is selected from any population number 1-14;
(ii) IGHA2a constant region and the human population is selected from any population number
1-14;
(ill) IGHA2b constant region and the human population is selected from any population number 1-14;
(iV) IGHG2a constant region and the human population is selected from any population number 1-9 and 11-13;
(v) IGHG3a constant region and the human population is selected from any population number 1-14;
(vi) IGHG3b constant region and the human population is selected from any population number 1-8 and 11-13;
(vii) IGHG4a constant region and the human population is selected from any population number
1-9 and 11-13;
(viii) IGHMa constant region and the human population is selected from any population number 1-14; or
(ix) IGHMb constant region and the human population is selected from any population number 1-14;
Wherein the populations are numbered as follows (population labels being according to 1000
Genomes Project nomenclature)
1= ASW;
2= CEU;
3=CHB;
4=CHS;
5=CLM;
6=FIN;
7=GBR;
8=IBS;
9=1 PT;
10=LWK;
11=MXL;
12=PUR;
13=TSI;
14=Y I.
265. A vector (eg, a CHO cell or HEK293 cell vector) comprising a IGHGlref, IGHG2ref, IGHG2a, IGHG3ref, IGHG3a, IGHG3b, IGHG4ref or IGHG4a constant region nucleotide sequence that is 3' of a cloning site for the insertion of a human antibody heavy chain variable domain nucleotide sequence, such that upon insertion of such a variable domain sequence the vector comprises (in 5' to 3' direction) a promoter, a leader sequence, the variable domain sequence and the constant region sequence so that the vector is capable of expressing a human antibody heavy chain when present in a host cell.
A non-human vertebrate or vertebrate cell (optionally an ES cell or antibody-producing cell) comprising a genome having a superhuman immunoglobulin heavy chain human VH and/or D and/or J gene repertoire.
266. The vertebrate or cell of claim 265, wherein the genome comprises a transgenic
immunoglobulin heavy chain locus comprising a plurality of human immunoglobulin VH gene segments, one or more human D gene segments and one or more human J gene segments, wherein the plurality of VH gene segments consists of more than the natural human repertoire of functional VH gene segments; optionally wherein the genome is homozygous for said transgenic heavy chain locus.
267. The vertebrate or cell of claim 266, wherein VH gene repertoire consists of a plurality of VH gene segments derived from the genome sequence of a first human individual, supplemented with one or more different VH gene segments derived from the genome sequence of a second, different human individual; optionally wherein the individuals are not related; optionally wherein the D and J segments are derived from the genome sequence of the first human individual; and optionally wherein the VH gene segments from the genome sequence of the second individual are selected from the VH gene segments listed in Table 1.
268. The vertebrate or cell of claim 267, wherein the transgenic locus comprises more than 26 functional human VH gene segments; optionally wherein the locus comprises at least
27or28functional human VH gene segments (eg, wherein the locus comprises the full functional VH repertoire of said first individual supplemented with one or more VH gene segments derived from the genome sequence of the second human individual and optionally with one or more VH gene segments derived from the genome sequence of a third human individual).
269. The vertebrate of cell of claim 267 or 268, wherein the transgenic locus comprises a first VH gene segment derived from the genome sequence of the first individual and a second VH gene segment derived from the genome sequence of the second individual, wherein the second VH gene segment is a polymorphic variant of the first VH gene segment; optionally wherein the locus comprises a further polymorphic variant of the first VH gene segment (eg, a variant derived from the genome sequence of a third human individual).
270. The vertebrate or cell of any one of claims 265 to 269, wherein the genome comprises a (or said) transgenic immunoglobulin heavy chain locus comprising a plurality of human
immunoglobulin VH gene segments, a plurality of human D gene segments and one or more human J gene segments, wherein the plurality of D gene segments consists of more than the natural human repertoire of functional D gene segments; optionally wherein the genome is homozygous for said transgenic heavy chain locus.
271. The vertebrate or cell of claim 270, wherein D gene repertoire consists of a plurality of D gene segments derived from the genome sequence of a (or said) first human individual, supplemented with one or more different D gene segments derived from the genome sequence of a (or said) second, different human individual; optionally wherein the individuals are not related; optionally wherein J segments are derived from the genome sequence of the first human individual; and optionally wherein the D gene segments from the genome sequence of the second individual are selected from the D gene segments listed in Table 2.
272. The vertebrate or cell of claim 271, wherein the transgenic locus comprises more than 26 functional human D gene segments; optionally wherein the locus comprises at least 27or 28functional human D gene segments (eg, wherein the locus comprises the full functional D repertoire of said first individual supplemented with one or more D gene segments derived from the genome sequence of the second human individual and optionally with one or more D gene segments derived from the genome sequence of a third human individual).
273. The vertebrate of cell of claim 271 or 272, wherein the transgenic locus comprises a first D gene segment derived from the genome sequence of the first individual and a second D gene segment derived from the genome sequence of the second individual, wherein the second D gene segment is a polymorphic variant of the first D gene segment; optionally wherein the locus comprises a further polymorphic variant of the first D gene segment (eg, a variant derived from the genome sequence of a third human individual). 274. The vertebrate or cell of any one of claims 265 to 273, wherein the genome comprises a (or said) transgenic immunoglobulin heavy chain locus comprising a plurality of human
immunoglobulin VH gene segments, one or more human D gene segments and a plurality of human JH gene segments, wherein the plurality of J gene segments consists of more than the natural human repertoire of functional J gene segments; optionally wherein the genome is homozygous for said transgenic heavy chain locus.
275. The vertebrate or cell of claim 274, wherein the J gene repertoire consists of a plurality of J gene segments derived from the genome sequence of a (or said) first human individual, supplemented with one or more different J gene segments derived from the genome sequence of a (or said) second, different human individual; optionally wherein the individuals are not related; optionally wherein D segments are derived from the genome sequence of the first human individual; and optionally wherein the J gene segments from the genome sequence of the second individual are selected from the J gene segments listed in Table 3.
276. The vertebrate or cell of claim 275, wherein the transgenic locus comprises more than 26 functional human J gene segments; optionally wherein the locus comprises at least 27 or 28 functional human J gene segments (eg, wherein the locus comprises the full functional J repertoire of said first individual supplemented with one or more J gene segments derived from the genome sequence of the second human individual and optionally with one or more J gene segments derived from the genome sequence of a third human individual).
277. The vertebrate of cell of claim 275 or 276, wherein the transgenic locus comprises a first J gene segment derived from the genome sequence of the first individual and a second J gene segment derived from the genome sequence of the second individual, wherein the second J gene segment is a polymorphic variant of the first J gene segment; optionally wherein the locus comprises a further polymorphic variant of the first J gene segment (eg, a variant derived from the genome sequence of a third human individual). 278. A non-human vertebrate or vertebrate cell (optionally an ES cell or antibody-producing cell) comprising a genome having a superhuman immunoglobulin light chain human VL gene repertoire; optionally wherein the vertebrate or cell is according to any one of claims 265 to 277.
279. The vertebrate or cell of claim 278, wherein the genome comprises
(i) a transgenic immunoglobulin kappa light chain locus comprising a plurality of human immunoglobulin VK gene segments and one or more human J gene segments, wherein the plurality of VK gene segments consists of more than the natural human repertoire of functional VK gene segments; optionally wherein the genome is homozygous for said transgenic kappa light chain locus; and/or
(ii) a transgenic immunoglobulin lambda light chain locus comprising a plurality of human immunoglobulin VX gene segments and one or more human J gene segments, wherein the plurality of V\ gene segments consists of more than the natural human repertoire of functional V\ gene segments; optionally wherein the genome is homozygous for said transgenic lambda light chain locus.
280. The vertebrate or cell of claim 279, wherein (i) the VK gene repertoire consists of a plurality of VK gene segments derived from the genome sequence of a first human individual, supplemented with one or more VK gene segments derived from the genome sequence of a second, different human individual; optionally wherein the individuals are not related; optionally wherein the J segments are derived from the genome sequence of the first human individual; and optionally wherein the VK gene segments from the genome sequence of the second individual are selected from the VK gene segments listed in
Table 4; and
(i) the V\ gene repertoire consists of a plurality of V\ gene segments derived from the genome sequence of a first human individual, supplemented with one or more V\ gene segments derived from the genome sequence of a second, different human individual; optionally wherein the
individuals are not related; optionally wherein the J segments are derived from the genome sequence of the first human individual; and optionally wherein the V\ gene segments from the genome sequence of the second individual are selected from the V\ gene segments listed in Table 5.
281. The vertebrate or cell of claim 280, wherein the kappa light transgenic locus comprises more than 26 functional human VK gene segments; optionally wherein the locus comprises at least 27 or 28 functional human VK gene segments (eg, wherein the locus comprises the full functional VK repertoire of said first individual supplemented with one or more VK gene segments derived from the genome sequence of the second human individual and optionally with one or more VK gene segments derived from the genome sequence of a third human individual); and the lambda light transgenic locus comprises more than 26 functional human V\ gene segments; optionally wherein the locus comprises at least 27 or 28 functional human V\ gene segments (eg, wherein the locus comprises the full functional V\ repertoire of said first individual supplemented with one or more V\ gene segments derived from the genome sequence of the second human individual and optionally with one or more V\ gene segments derived from the genome sequence of a third human individual);
282. The vertebrate of cell of claim 280 or 281, wherein the kappa light transgenic locus comprises a first VK gene segment derived from the genome sequence of the first individual and a second VK gene segment derived from the genome sequence of the second individual, wherein the second VK gene segment is a polymorphic variant of the first VK gene segment; optionally wherein the locus comprises a further polymorphic variant of the first VK gene segment (eg, a variant derived from the genome sequence of a third human individual); and the lambda light transgenic locus comprises a first V\ gene segment derived from the genome sequence of the first individual and a second V\ gene segment derived from the genome sequence of the second individual, wherein the second VX gene segment is a polymorphic variant of the first V\ gene segment; optionally wherein the locus comprises a further polymorphic variant of the first V\ gene segment (eg, a variant derived from the genome sequence of a third human individual).
283. The vertebrate or cell of any one of claims 278 to 282, wherein the genome comprises a (or said) transgenic immunoglobulin light chain locus comprising a plurality of human
immunoglobulin VL gene segments and a plurality of human JL gene segments, wherein the plurality of J gene segments consists of more than the natural human repertoire of functional J gene segments; optionally wherein the genome is homozygous for said transgenic heavy chain locus.
284. The vertebrate or cell of claim 283, wherein
(i) the JK gene repertoire consists of a plurality of JK gene segments derived from the genome sequence of a (or said) first human individual, supplemented with one or more J K gene segments derived from the genome sequence of a (or said) second, different human individual; optionally wherein the individuals are not related; optionally wherein the VK segments are derived from the genome sequence of the first human individual; optionally wherein the J K gene segments from the genome sequence of the second individual are selected from the J K gene segments listed in Table 6; and
(ii) the JK gene repertoire consists of a plurality of iX gene segments derived from the genome sequence of a (or said) first human individual, supplemented with one or more iX gene segments derived from the genome sequence of a (or said) second, different human individual; optionally wherein the individuals are not related; optionally wherein the V\ segments are derived from the genome sequence of the first human individual; optionally wherein the iX gene segments from the genome sequence of the second individual are selected from the iX gene segments listed in Table 7.
285. The vertebrate or cell of claim 284, wherein
(i) the transgenic light chain locus comprises more than 26 functional human J K gene segments; optionally wherein the locus comprises at least 27 or 28functional human J K gene segments (eg, wherein the locus comprises the full functional JK repertoire of said first individual
supplemented with one or more JK gene segments derived from the genome sequence of the second human individual and optionally with one or more JK gene segments derived from the genome sequence of a third human individual); and/or
(i) the transgenic light chain locus comprises more than 26 functional human iX gene segments; optionally wherein the locus comprises at least 27 or 28 functional human iX gene segments (eg, wherein the locus comprises the full functional iX repertoire of said first individual
supplemented with one or more iX gene segments derived from the genome sequence of the second human individual and optionally with one or more iX gene segments derived from the genome sequence of a third human individual).
286. The vertebrate or cell of claim 284 or 285, wherein
(i) the kappa light transgenic locus comprises a first JK gene segment derived from the genome sequence of the first individual and a second JK gene segment derived from the genome sequence of the second individual, wherein the second JK gene segment is a polymorphic variant of the first JK gene segment; optionally wherein the locus comprises a further polymorphic variant of the first JK gene segment (eg, a variant derived from the genome sequence of a third human individual); and
(ii) the lambda light transgenic locus comprises a first iX gene segment derived from the genome sequence of the first individual and a second iX gene segment derived from the genome
sequence of the second individual, wherein the second JK gene segment is a polymorphic variant of the first iX gene segment; optionally wherein the locus comprises a further polymorphic variant of the first iX gene segment (eg, a variant derived from the genome sequence of a third human individual).
287. A library of antibody-producing transgenic cells whose genomes collectively encode a
repertoire of antibodies, wherein
(a) a first transgenic cell expresses a first antibody having a chain encoded by a first
immunoglobulin gene, the gene comprising a first variable domain nucleotide sequence produced following recombination of a first human unrearranged immunoglobulin gene segment;
(b) a second transgenic cell expresses a second antibody having a chain encoded by a second immunoglobulin gene, the second gene comprising a second variable domain nucleotide sequence produced following recombination of a second human unrearranged immunoglobulin gene segment, the first and second antibodies being non-identical;
(c) the first and second gene segments are different and derived from the genome sequences of first and second human individuals respectively, wherein the individuals are different; and optionally not related;
(d) wherein the cells are non-human vertebrate (eg, mouse or rat) cells. 288. The library of claim 23, wherein in step (c) the individuals or not related.
289. The vertebrate, cell or library of any one of claims 265 to 288, wherein the first and second human individuals are members of first and second ethnic populations respectively, wherein the populations are different; optionally wherein the ethnic populations are selected from those identified in the 1000 genomes database.
290. The vertebrate, cell or library of claim 289, wherein the human immunoglobulin gene
segment derived from the genome sequence of the second individual is low-frequency
(optionally rare) within the second ethnic population.
291. The library of claim 289 or 290, wherein the first variable region nucleotide sequence is produced by recombination of the first human immunoglobulin gene segment with a first J gene segment and optionally a first D gene segment, wherein the first human immunoglobulin gene segment is a V gene segment and the V, D and J segments are derived from the first human population, optionally from the genome of one individual of the first human population.
292. The library of claim 291, wherein the second variable region nucleotide sequence is
produced by recombination of the second human immunoglobulin gene segment with a second J gene segment and optionally a second D gene segment, wherein the second human
immunoglobulin gene segment is a V gene segment derived from the second population and the
D and/or J segments are derived from the first human population, optionally the D and J gene segments being from the genome of one individual of the first human population.
293. The library of claim 292, wherein all of the D and J segments that have been recombined with the first and second V gene segments are D and J segments derived from the first human population, optionally the D and J gene segments being from the genome of one individual of the first human population.
294. The vertebrate, cell or library of any one of claims 289 to 293, wherein the first and second ethnic populations are selected from the group consisting of an ethnic population with European ancestry, an ethnic population with East Asian, an ethnic population with West African ancestry, an ethnic population with Americas ancestry and an ethnic population with South Asian ancestry. 295. The vertebrate, cell or library of claim 294, wherein the first and second ethnic populations are selected from the group consisting of an ethnic population with Northern European ancestry; or an ethnic population with Western European ancestry; or an ethnic population with Toscani ancestry; or an ethnic population with British ancestry; or an ethnic population with Icelandic ancestry; or an ethnic population with Finnish ancestry; or an ethnic population with Iberian ancestry; or an ethnic population with Japanese ancestry; or an ethnic population with
Chinese ancestry; or an ethnic population Vietnamese ancestry; or an ethnic population with Yoruba ancestry; or an ethnic population with Luhya ancestry; or an ethnic population with Gambian ancestry; or an ethnic population with Malawian ancestry; or an ethnic population with Native American ancestry; or an ethnic population with Afro-Caribbean ancestry; or an ethnic population with Mexican ancestry; or an ethnic population with Puerto ican ancestry; or an ethnic population with Columbian ancestry; or an ethnic population with Peruvian ancestry; or an ethnic population with Ahom ancestry; or an ethnic population with Kayadtha ancestry; or an ethnic population with Reddy ancestry; or an ethnic population with Maratha; or an ethnic population with Punjabi ancestry.
296. The library of claim 287, wherein the second human immunoglobulin gene segment is a polymorphic variant of the first human immunoglobulin gene segment; optionally wherein the second gene segment is selected from the group consisting of a gene segment in any of Tables 1 to 7 and 9 to 14, eg, the second gene segment is a polymorphic variant of VH1-69.
297. The library of any one of claims 287 to 296, wherein the first and second human
immunoglobulin gene segments are both (i) VH gene segments; (ii) D segments; (iii) J segments (optionally both JH segments, both JK segments or both ϋλ segments); (iv) constant regions (optionally both a gamma constant region, optionally both a C gamma-1 constant region); (v) CHI regions; (vi) CH2 regions; or (vii) CH3 regions.
298. The library of any one of claims 287 to 297, wherein the library is naive and optionally has a library size of from 102 to 109 cells.
299. The library of any one of claims 287 to 298, wherein the library has been selected against a predetermined antigen optionally has a library size of from 102 to 109 cells.
300. The library of any one of claims 287 to 299, wherein said first and second cells are progeny of first and second ancestor non-human vertebrate cells respectively, wherein the first ancestor cell comprises a genome comprising said first human immunoglobulin gene segment; and the second ancestor cell comprises a genome comprising said second human immunoglobulin gene segment. 301. A library of antibody-producing transgenic cells whose genomes collectively encode a
repertoire of antibodies, wherein the library comprises the first and second ancestor cells recited in claim 300.
302. A library of hybridoma cells produced by fusion of the library of any one of claims 265 to 301 with fusion partner cells; and optionally the hybridoma library has a size of from 102 to 109 cells
303. An isolated antibody having
(a) a heavy chain encoded by a nucleotide sequence produced following recombination in a transgenic non-human vertebrate cell of an unrearranged human immunoglobulin V gene segment with a human D and human J segment, optionally with affinity maturation in said cell, wherein one of the gene segments is derived from the genome of an individual from a first human ethnic population; and the other two gene segments are derived from the genome of an individual from a second, different, human ethnic population, and wherein the antibody comprises heavy chain constant regions of said non-human vertebrate (eg, rodent, mouse or rat heavy chain constant regions); and/or
(b) a light chain encoded by a nucleotide sequence produced following recombination in a transgenic non-human vertebrate cell of an unrearranged human immunoglobulin V gene segment with a human J segment, optionally with affinity maturation in said cell, wherein one of the gene segments is derived from the genome of an individual from a first human ethnic population (optionally the same as the first population in (a)); and the other gene segment is derived from the genome of an individual from a second, different, human ethnic population (optionally the same as the second population in (a)), and wherein the antibody comprises light chain constant regions of said non-human vertebrate (eg, rodent, mouse or rat heavy light constant regions);
(c) Optionally wherein each variable domain of the antibody is a human variable domain. (d) Optionally wherein the heavy chain constant regions are gamma-type constant regions.
304. An isolated nucleotide sequence encoding the antibody of claim 303, optionally wherein the sequence is provided in an antibody expression vector, optionally in a host cell.
305. A method of producing a human antibody, the method comprising replacing the non-human vertebrate constant regions of the antibody of claim 303 with human antibody constant regions.
306. A pharmaceutical composition comprising an antibody according to claim 303, or an
antibody produced according to the method of claim 305 and a diluent, excipient or carrier; optionally wherein the composition is provided in a container connected to an IV needle or syringe or in an IV bag.
307. An antibody-producing cell that expresses the second antibody recited in any one of claims 287 to 302 or the isolated antibody of claim 303.
308. A non-human vertebrate or vertebrate cell (optionally an ES cell or antibody-producing cell) whose genome comprises a transgenic immunoglobulin locus (eg, a heavy chain locus or a light chain locus), said locus comprising immunoglobulin gene segments according to the first and second human immunoglobulin gene segments (optionally V segments) recited in any one of claims 287 to 302 operably connected upstream of an immunoglobulin constant region;
optionally wherein the genome is homozygous for said transgenic immunoglobulin locus; optionally wherein the immunoglobulin locus comprises more than the natural human complement of functional V gene segments; and/or optionally wherein the immunoglobulin locus comprises more than the natural human complement of functional D gene segments; and/or optionally wherein the immunoglobulin locus comprises more than the natural human complement of functional J gene segments.
309. A transgenic non-human vertebrate (eg, a mouse or rat) or vertebrate cell (optionally an ES cell or antibody-producing cell) whose genome comprises a transgenic immunoglobulin locus comprising a plurality of human immunoglobulin gene segments operably connected upstream of a non-human vertebrate constant region for the production of a repertoire of chimaeric antibodies, or chimaeric light or heavy chains, having a non-human vertebrate constant region and a human variable region; wherein the transgenic locus comprises one or more human immunoglobulin V gene segments, one or more human J gene segments and optionally one or more human D gene segments, a first (optionally a V segment) of said gene segments and a second (optionally a V segment) of said gene segments being different and derived from the genomes of first and second human individuals respectively, wherein the individuals are different; and optionally not related; optionally wherein the immunoglobulin locus comprises more than the natural human complement of functional V gene segments; and/or optionally wherein the immunoglobulin locus comprises more than the natural human complement of functional D gene segments; and/or
optionally wherein the immunoglobulin locus comprises more than the natural human complement of functional J gene segments.
310. A transgenic non-human vertebrate (eg, a mouse or rat) or vertebrate cell (optionally an ES cell or antibody-producing cell) whose genome comprises first and second transgenic immunoglobulin loci, each locus comprising a plurality of human immunoglobulin gene segments operably connected upstream of a non-human vertebrate constant region for the production of a repertoire of chimaeric antibodies, or chimaeric light or heavy chains, having a non-human vertebrate constant region and a human variable region; wherein (i) the first transgenic locus comprises one or more human immunoglobulin V gene segments, one or more human J gene segments and optionally one or more human D gene segments, (ii) the second transgenic locus comprises one or more human immunoglobulin V gene segments, one or more human J gene segments and optionally one or more human D gene segments; and (iii) wherein a first (optionally a V) gene segment of said first locus and a second (optionally a V) gene segment of said second gene locus are different and derived from the genomes of first and second human individuals respectively, wherein the individuals are different; and optionally not related optionally wherein the first and second loci are on different chromosomes (optionally chromosomes with the same chromosome number) in said genome; optionally wherein each immunoglobulin locus comprises more than the natural human complement of functional V gene segments; and/or optionally wherein each immunoglobulin locus comprises more than the natural human complement of functional D gene segments; and/or optionally wherein each immunoglobulin locus comprises more than the natural human complement of functional J gene segments.
311. The non-human vertebrate or cell of claim 309 or 310, wherein the immunoglobulin gene segments are as recited in any one of claims 23 to 37.
312. The non-human vertebrate or cell of claim 308, 309, 310 or 311, wherein the genome
comprises a third immunoglobulin gene segment (optionally a V segment), the third gene segment being derived from a human individual that is different from the individual from which the first (and optionally also the second) gene segment is derived; optionally wherein the first, second and third gene segments are polymorphic variants of a human immunoglobulin gene segment.
313. The non-human vertebrate or cell of any one of claims 308 to 312, wherein the genome of the vertebrate or cell is homozygous for the first, second and optional third gene segment,
wherein a copy of the first, second and optional third gene segments are provided together on the same chromosome operably connected upstream of a common non-human vertebrate constant region. 314. The non-human vertebrate or cell of any one of claims 308 to 313, wherein each first,
second and optional third gene segment is a V gene segment.
315. The library of any one of claims 287 to 302, wherein the library is provided by a collection of non-human vertebrates (optionally a collection of rodents, mice or rats); optionally, wherein a first member of said collection produces said first antibody but not said second antibody, and a second member of the collection produces said second antibody (but optionally not said first antibody).
316. A repertoire of antibodies expressed from a library of cells according to any one of claims 287 to 302 and 315.
317. A method of constructing a cell (eg, an ES cell) according to any one of claims 265 to 286, the method comprising
(a) identifying functional V and J (and optionally D) gene segments of the genome sequence of a (or said) first human individual;
(b) identifying one or more functional V and/or D and/or J gene segments of the genome sequence of a (or said) second human individual, wherein these additional gene segments are not found in the genome sequence of the first individual;
(c) and constructing a transgenic immunoglobulin locus in the cell, wherein the gene segments of (a) and (b) are provided in the locus operably connected upstream of a constant region.
318. The method of claim 317, wherein the cell comprises a heavy chain locus constructed
according to steps (a) to (c) and/or a light chain locus (kappa and/or lambda loci) constructed according to steps (a) to (c).
319. The method of claim 317 or 318, wherein the cell is homozygous for the or each transgenic locus; optionally wherein antibody expression from loci endogenous to said cell has been inactivated. 320. The method of any one of claims 317 to 319, wherein the gene segment(s) in step (b) are identified from an immunoglobulin gene database selected from the 1000 genomes, Ensembl, Genbank and IMGT databases.
321. The method of any one of claims 317 to 320, wherein the first and second human individuals are members of first and second ethnic populations respectively, wherein the populations are different, optionally wherein the human immunoglobulin gene segment derived from the genome sequence of the second individual is low-frequency (optionally rare) within the second ethnic population.
322. A method of making a transgenic non-human vertebrate (eg, a mouse or rat), the method comprising
(a) constructing an ES cell (eg, a mouse C57BL/6N, C57BL/6J, 129S5 or 129Sv strain ES cell) by carrying out the method of any one of claims 317 to 321;
(b) injecting the ES cell into a donor non-human vertebrate blastocyst (eg, a mouse C57BL/6N,
C57BL/6J, 129S5 or 129Sv strain blastocyst);
(c) implanting the blastocyst into a foster non-human vertebrate mother (eg, a C57BL/6N, C57BL/6J, 129S5 or 129Sv strain mouse); and
(d) obtaining a child from said mother, wherein the child genome comprises a transgenic immunoglobulin locus.
323. A transgenic non-human vertebrate (eg, a mouse or rat) made by the method of claim 322 or a progeny thereof. 324. A population of non-human vertebrates according to claim 323.
325. A method of isolating an antibody that binds a predetermined antigen (eg, a bacterial or viral pathogen antigen), the method comprising
(a) providing a vertebrate (optionally a mouse or rat) according to any one of claims 265 to 286, 289, 290, 294, 295, 308 to 314 and 323;
(b) immunising (eg, using a standard prime-boost method) said vertebrate with said antigen (optionally wherein the antigen is an antigen of an infectious disease pathogen);
(c) removing B lymphocytes from the vertebrate and selecting one or more B lymphocytes expressing antibodies that bind to the antigen;
(d) optionally immortalising said selected B lymphocytes or progeny thereof, optionally by producing hybridomas therefrom; and
(e) isolating an antibody (eg, and IgG-type antibody) expressed by the B lymphocytes; and
(f) optionally producing a derivative or variant of the antibody. 326. The method of claim 325, further comprising after step (e) the step of isolating from said B lymphocytes nucleic acid encoding said antibody that binds said antigen; optionally exchanging the heavy chain constant region nucleotide sequence of the antibody with a nucleotide sequence encoding a human or humanised heavy chain constant region and optionally affinity maturing the variable region of said antibody; and optionally inserting said nucleic acid into an expression vector and optionally a host.
327. A non-human vertebrate (eg, a mouse or rat) or cell (eg, a mouse cell or rat cell) comprising a genome that comprises a transgenic heavy chain immunoglobulin locus, wherein the locus comprises at least 42 (optionally at least 43, 44, 45, 46, 47, 48, 49, 50) functional human VH gene segments, one or more functional human D gene segments, one or more functional human JH gene segments operably connected upstream of a non-human vertebrate constant region (eg, a mouse constant region, eg, a Cmu and/or a C gamma).
328. The vertebrate or cell of claim 327, wherein the locus comprises at least 23 functional
human D gene segments and/or at least 6 functional human JH gene segments, optionally at
least a full human repertoire of functional VH, D and JH segments (optionally derived from the genome sequence of the same human individual).
329. A non-human vertebrate (eg, a mouse or rat) or cell (eg, a mouse cell or rat cell) comprising a genome that comprises a transgenic heavy chain immunoglobulin locus, wherein the locus comprises a full human repertoire of functional VH, D and JH segments derived from the genome sequence of the same human individual, supplemented with one or more additional functional human VH, D and/or JH gene segment that is not found in the genome sequence of said human individual.
330. The vertebrate or cell of claim 329, wherein each additional VH, D and JH segment is
selected from the group consisting of (i) a gene segment derived from a second, different individual, optionally wherein the first and second individuals are members of different ethnic populations; (ii) a mutant of a human gene segment (optionally a human germline gene segment having up to 5, 10 or 15 mutations); and (iii) a hybrid human gene segment comprising a first and second nucleotide sequences derived from genome sequences of different human individuals or different polymorphic variants of a human immunoglobulin gene segment (eg, variants of a germline human VH, D or JH gene segment).
331. The vertebrate or cell of any one of claims 328 to 330, wherein the genome is homozygous for said heavy chain transgene and optionally endogenous immunoglobulin heavy chain expression has been inactivated.
332. A non-human vertebrate (eg, a mouse or rat) or cell (eg, a mouse cell or rat cell) comprising a genome that comprises a transgenic kappa light chain immunoglobulin locus, wherein the locus comprises at least 39 functional human Vk gene segments and one or more functional human Jk gene segments operably connected upstream of a non-human vertebrate constant region (eg, a mouse constant region).
333. The vertebrate or cell of claim 332, wherein the locus comprises at least a full human
repertoire of functional Vk and Jk segments (optionally derived from the genome sequence of the same human individual).
334. A non-human vertebrate (eg, a mouse or rat) or cell (eg, a mouse cell or rat cell) comprising a genome that comprises a transgenic kappa light chain immunoglobulin locus, wherein the locus comprises a full human repertoire of functional Vk and Jk segments derived from the genome sequence of the same human individual, supplemented with one or more additional functional human Vk and/or Jk gene segment that is not found in the genome sequence of said human individual. 335. The vertebrate or cell of claim 334, wherein each additional Vk and Jk segment is selected from the group consisting of (i) a gene segment derived from a second, different individual, optionally wherein the first and second individuals are members of different ethnic populations; (ii) a mutant of a human gene segment (optionally a human germline gene segment having up to 5, 10 or 15 mutations); and (iii) a hybrid human gene segment comprising a first and second nucleotide sequences derived from: genome sequences of different human individuals or
different polymorphic variants of a human immunoglobulin gene segment (eg, variants of a germline human Vk or Jk gene segment).
336. The vertebrate or cell of any one of claims 332 to 335, wherein the genome is homozygous for said kappa light chain transgene and optionally endogenous immunoglobulin kappa light chain expression has been inactivated.
337. A non-human vertebrate (eg, a mouse or rat) or cell (eg, a mouse cell or rat cell) comprising a genome that comprises a transgenic lambda light chain immunoglobulin locus, wherein the locus comprises at least 32 functional human V lambda gene segments and one or more functional human J lambda gene segments operably connected upstream of a non-human vertebrate constant region (eg, a mouse constant region).
338. The vertebrate or cell of claim 337, wherein the locus comprises at least a full human
repertoire of functional V lambda and J lambda segments (optionally derived from the genome sequence of the same human individual).
339. A non-human vertebrate (eg, a mouse or rat) or cell (eg, a mouse cell or rat cell) comprising a genome that comprises a transgenic lambda light chain immunoglobulin locus, wherein the locus comprises a full human repertoire of functional V lambda and J lambda segments derived from the genome sequence of the same human individual, supplemented with one or more additional functional human V lambda and/or J lambda gene segment that is not found in the genome sequence of said human individual.
340. The vertebrate or cell of claim 339, wherein each additional V lambda and J lambda segment is selected from the group consisting of (i) a gene segment derived from a second, different individual, optionally wherein the first and second individuals are members of different ethnic populations; (ii) a mutant of a human gene segment (optionally a human germline gene segment having up to 5, 10 or 15 mutations); and (iii) a hybrid human gene segment comprising a first and second nucleotide sequences derived from genome sequences of different human individuals or different polymorphic variants of a human immunoglobulin gene segment (eg, variants of a germline human V lambda or J lambda gene segment).
341. The vertebrate or cell of any one of claims 337 to 340, wherein the genome is homozygous for said lambda light chain transgene and optionally endogenous immunoglobulin lambda light chain expression has been inactivated.
342. A transgenic immunoglobulin locus comprising a synthetic immunoglobulin gene haplotype, the haplotype comprising first and second human gene segments (each being a V, D or J), a switch region and a constant region, wherein a) the second gene segment is a polymorphic variant of the first gene segment; or
b) the first and second gene segments are derived respectively from genome sequence of individuals from different, first and second, ethnic populations (eg, according to the 1000 Genomes database) and the second gene segment is not found in the first population (eg,
according to the 1000 Genomes database), optionally wherein the second gene segment occurs at low-frequency (or is rare) in the second population; and
Wherein the constant region, and optionally the switch region, are non-human vertebrate (eg, mouse or rat) constant and switch regions (eg, mouse or rat Cmu; mouse or rat Smu; mouse or rat C gamma; or mouse or rat S gamma).
343. The transgenic immunoglobulin locus of claim 342 wherein the transgene comprises a third human immunoglobulin gene segment (a V, D or J) which is (a) a polymorphic variant of the first and second gene segments; or (b) derived from a genome sequence of the second population
(and optionally is a low-frequency or rare gene in that population) or is from a third human ethnic population, wherein the third gene segment is not found in the first population (eg, according to the 1000 Genomes database).
344. A non-human vertebrate or cell comprising the transgene of claim 342 or 343; optionally wherein the vertebrate or cell is homozygous for said transgene.
345. An isolated antibody for administration to a Chinese patient, the antibody
comprising a human heavy chain, the heavy chain comprising a variable domain that is specific for an antigen and a constant region, wherein the constant region is a human constant region selected from a constant region (eg, an IGHG constant region) inTable 13 found in a Chinese population and with a cumulative frequency of at least 5%;, and wherein (i) the variable domain is derived from the recombination of said human gene segments in a non-human vertebrate (eg, in a mouse or a rat); or ( ii) the variable domain comprises non- human vertebrate (eg, mouse or rat) AID-pattern mutations and non-human vertebrate (eg, mouse or rat) terminal deoxynucleotidyl transferase (TdT)-pattern mutations. 346. The antibody of claim 345 wherein the constant region is a IGHGla, IGHG2a,
IGHG3a, IGHG3b or IGHG4a constant region.
347. The antibody of claim 345 or 346, wherein the variable domain is derived from the recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the VH gene segment being selected from a VH in Table 13 found in a
Chinese population and with a cumulative frequency of at least 5%.
348. The antibody of claim 345, 346 or 347, wherein the variable domain is derived from the recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the D gene segment being selected from a D in Table 13 found in a
Chinese population and with a cumulative frequency of at least 5%.
349. The antibody of claim 345, 346, 347 or 348 wherein the variable domain is derived from the recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the JH gene segment being selected from a JH in Table 13 found in
a Chinese population and with a cumulative frequency of at least 5%.
350. An isolated VH domain identical to a variable domain as recited in any one of claims
347 to 349, optionally fused at its C-terminus to a polypeptide (eg, an antibody Fc).
351. A pharmaceutical composition comprising the antibody or variable domain of any one of claims 345 to 350 together with a pharmaceutically-acceptable excipient, diluent or a medicament (eg, a further antigen-specific variable domain, antibody chain or antibody).
352. An isolated antibody for administration to a Chinese patient, the antibody
comprising a human heavy chain, the heavy chain comprising a variable domain that is specific for an antigen and a constant region, wherein the variable domain is derived from the recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the VH gene segment being selected from a VH in Table 13 found in a Chinese population and with a cumulative frequency of at least 5%; and wherein
(i) the variable domain is derived from the recombination of said human gene segments in a non-human vertebrate (eg, in a mouse or a rat); or ( ii) the variable domain comprises non- human vertebrate (eg, mouse or rat) AID-pattern mutations and non-human vertebrate (eg, mouse or rat) terminal deoxynucleotidyl transferase (TdT)-pattern mutations.
353. The antibody of claim 352, wherein the variable domain is derived from the
recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the D gene segment being selected from a D in Table 13 found in a Chinese population and with a cumulative frequency of at least 5%.
354. The antibody of claim 352 or 353, wherein the variable domain is derived from the recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the JH gene segment being selected from a JH in Table 13 found in a Chinese population and with a cumulative frequency of at least 5%.
355. An isolated VH domain identical to a variable domain as recited in any one of claims 352 to 354, optionally fused at its C-terminus to a polypeptide (eg, an antibody Fc).
356. A pharmaceutical composition comprising the antibody or variable domain of any one of claims 352 to 355 together with a pharmaceutically-acceptable excipient, diluent or a medicament (eg, a further antigen-specific variable domain, antibody chain or antibody).
357. An antibody heavy chain or VH domain (eg, provided as part of an antibody) for therapy and/or prophylaxis of a disease or medical condition in a Chinese patient, wherein the heavy chain is a heavy chain produced by the following steps (or is a copy of such a heavy chain):-
(a) Selection of an antigen-specific antibody heavy chain or VH domain from a non- human vertebrate (eg, a mouse or a rat), wherein the heavy chain or VH domain is derived
from the recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the VH gene segment being selected from a VH in Table 13 found in a Chinese population and with a cumulative frequency of at least 5%; (b) Optional humanisation of the heavy chain by combining the variable domain of the heavy chain with a human constant region; or optional humanisation of the selected VH domain by combining with a human constant region.
358. The antibody heavy chain or VH domain of claim 357, wherein the human constant region is as recited in claim 345 or 346.
359. An antibody heavy chain or VH domain as recited in claim 357 or 358 for use in a medicament for therapy and/or prophylaxis of a disease or medical condition in a Chinese patient.
360. A method of treating and/or preventing a disease or medical condition in a Chinese patient, the method comprising administering to the patient a therapeutically or prophylactically-effective amount of the antibody heavy chain or VH domain as recited in claim 357 or 358.
361. An isolated antibody for administration to a patient of European, East Asian, West African, South Asian or Americas ancestry, the antibody comprising a human heavy chain, the heavy chain comprising a variable domain that is specific for an antigen and a constant region, wherein the constant region is a human constant region selected from a constant region (eg, an IGHG constant region) in Table 13 found in a population of European, East
Asian, West African, South Asian or Americas ancestry respectively and with a cumulative frequency of at least 5%;, and wherein
(i) the variable domain is derived from the recombination of said human gene segments in a non-human vertebrate (eg, in a mouse or a rat); or ( ii) the variable domain comprises non- human vertebrate (eg, mouse or rat) AID-pattern mutations and non-human vertebrate (eg, mouse or rat) terminal deoxynucleotidyl transferase (TdT)-pattern mutations.
362. The antibody of claim 361 wherein the constant region is a IGHGla, IGHG2a,
IGHG3a, IGHG3b or IGHG4a constant region and the patient is of European ancestry.
363. The antibody of claim 361 or 362, wherein the variable domain is derived from the recombination of a human VH gene segment with a human D gene segment and a human JH gene segment, the VH gene segment being selected from a VH in Table 13 found in said population and with a cumulative frequency of at least 5%.
364. The antibody of claim 361, 362 or 363, wherein the variable domain is derived from the recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the D gene segment being selected from a D in Table 13 found in
said population and with a cumulative frequency of at least 5%.
365. The antibody of claim 361, 362, 363 or 364 wherein the variable domain is derived from the recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the JH gene segment being selected from a JH in Table 13 found in said population and with a cumulative frequency of at least 5%.
366. An isolated VH domain identical to a variable domain as recited in any one of claims 363 to 365, optionally fused at its C-terminus to a polypeptide (eg, an antibody Fc).
367. A pharmaceutical composition comprising the antibody or variable domain of any one of claims 361 to 366 together with a pharmaceutically-acceptable excipient, diluent or a medicament (eg, a further antigen-specific variable domain, antibody chain or antibody). 368. An isolated antibody for administration to a patient of European, East Asian, West
African or Americas ancestry, the antibody comprising a human heavy chain, the heavy chain comprising a variable domain that is specific for an antigen and a constant region, wherein the variable domain is derived from the recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the VH gene segment being selected from a VH in Table 13 found in a population of European, East Asian, West African, South
Asian or Americas ancestry respectively and with a cumulative frequency of at least 5%; and wherein
(i) the variable domain is derived from the recombination of said human gene segments in a non-human vertebrate (eg, in a mouse or a rat); or ( ii) the variable domain comprises non- human vertebrate (eg, mouse or rat) AID-pattern mutations and non-human vertebrate (eg, mouse or rat) terminal deoxynucleotidyl transferase (TdT)-pattern mutations.
369. The antibody of claim 368, wherein the variable domain is derived from the
recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the D gene segment being selected from a D in Table 13 found in said population and with a cumulative frequency of at least 5%.
370. The antibody of claim 368 or 369, wherein the variable domain is derived from the recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the JH gene segment being selected from a JH in Table 13 found in said population and with a cumulative frequency of at least 5%.
371. An isolated VH domain identical to a variable domain as recited in any one of claims 368 to 370, optionally fused at its C-terminus to a polypeptide (eg, an antibody Fc).
372. A pharmaceutical composition comprising the antibody or variable domain of any one of claims 368 to 371 together with a pharmaceutically-acceptable excipient, diluent or a medicament (eg, a further antigen-specific variable domain, antibody chain or antibody).
373. An antibody heavy chain or VH domain (eg, provided as part of an antibody) for therapy and/or prophylaxis of a disease or medical condition in a patient of European, East Asian, West African, South Asian or Americas ancestry, wherein the heavy chain is a heavy chain produced by the following steps (or is a copy of such a heavy chain):-
(a) Selection of an antigen-specific antibody heavy chain or VH domain from a non- human vertebrate (eg, a mouse or a rat), wherein the heavy chain or VH domain is derived from the recombination of a human VH gene segment with a human D gene segment and a human JH gene segment , the VH gene segment being selected from a VH in Table 13 found in said population and with a cumulative frequency of at least 5%;
(b) Optional humanisation of the heavy chain by combining the variable domain of the heavy chain with a human constant region; or optional humanisation of the selected VH domain by combining with a human constant region.
374. The antibody heavy chain or VH domain of claim 373, wherein the human constant region is as recited in claim 361 or 362.
375. An antibody heavy chain or VH domain as recited in claim 373 or 374 for use in a medicament for therapy and/or prophylaxis of a disease or medical condition in a patient of said ancestry.
376. A method of treating and/or preventing a disease or medical condition in a patient of European, East Asian, West African, South Asian or Americas ancestry, the method comprising administering to the patient a therapeutically or prophylactically-effective amount of the antibody heavy chain or VH domain as recited in claim 373 or 374.
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| ES12772122.3T ES2612935T3 (en) | 2011-09-19 | 2012-09-18 | Antibodies, variable domains and chains adapted for use in humans |
| CA2846319A CA2846319A1 (en) | 2011-09-19 | 2012-09-18 | Antibodies, variable domains & chains tailored for human use |
| EP16189625.3A EP3128009B1 (en) | 2011-09-19 | 2012-09-18 | Antibodies, variable domains & chains tailored for human use |
| NZ623756A NZ623756B2 (en) | 2011-09-19 | 2012-09-18 | Antibodies, variable domains & chains tailored for human use |
| EP20188009.3A EP3839049A3 (en) | 2011-09-19 | 2012-09-18 | Antibodies, variable domains & chains tailored for human use |
| CN201280056727.0A CN104080916A (en) | 2011-09-19 | 2012-09-18 | Antibodies, variable domains & chains tailored for human use |
| AU2012311286A AU2012311286B2 (en) | 2011-09-19 | 2012-09-18 | Antibodies, variable domains and chains tailored for human use |
| BR112014006390A BR112014006390A2 (en) | 2011-09-19 | 2012-09-18 | antibodies, variable domains and chains made especially for human use |
| JP2014531302A JP5813880B2 (en) | 2011-09-19 | 2012-09-18 | Antibodies, variable domains and chains made for human use |
| EP12772122.3A EP2758535B1 (en) | 2011-09-19 | 2012-09-18 | Antibodies, variable domains&chains tailored for human use |
| US14/052,259 US20140041067A1 (en) | 2011-09-19 | 2013-10-11 | Antibodies, variable domains & chains tailored for human use |
| HK14108036.3A HK1194757A1 (en) | 2011-09-19 | 2014-08-05 | Antibodies, variable domains & chains tailored for human use |
| US15/786,281 US20180030121A1 (en) | 2011-09-19 | 2017-10-17 | Antibodies, variable domains & chains tailored for human use |
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| GB201116122A GB201116122D0 (en) | 2011-09-19 | 2011-09-19 | Synthetically-extended & ethnically diverse superhuman immunoglobulin gene repertoires |
| GB201116120A GB201116120D0 (en) | 2011-09-19 | 2011-09-19 | Manipulation of immunoglobulin gene diversity and multi antibody therapeutics, especially for infectious diseases |
| GB1116120.5 | 2011-09-19 | ||
| GB1116122.1 | 2011-09-19 | ||
| GBGB1203257.9A GB201203257D0 (en) | 2012-02-24 | 2012-02-24 | Animals, repertoires & methods |
| GB1203257.9 | 2012-02-24 | ||
| GB1204592.8 | 2012-03-15 | ||
| GBGB1204592.8A GB201204592D0 (en) | 2012-03-15 | 2012-03-15 | Animals, repertoires & methods |
| GBGB1205702.2A GB201205702D0 (en) | 2012-03-29 | 2012-03-29 | Animals,repertoires & methods |
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| GB1208749.0 | 2012-05-18 | ||
| GBGB1208749.0A GB201208749D0 (en) | 2012-05-18 | 2012-05-18 | Synthetically-extended & ethnically-diverse superhuman immunoglobulin gene repertoires |
| GB1211692.7 | 2012-07-02 | ||
| GB201211692A GB201211692D0 (en) | 2012-07-02 | 2012-07-02 | Animals, repertories & methods |
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