Papers by CÍNTIA ANDRADE ALVES
Forensic Science International
The Spanish and Portuguese ISFG Working Group (GEP-ISFG) carried out a collaborative exercise in ... more The Spanish and Portuguese ISFG Working Group (GEP-ISFG) carried out a collaborative exercise in order to asses the performance of two Y chromosome STR tetraplexes, which include the loci DYS461, GATA C4, DYS437 and DYS438 (GEPY I), and DYS460, GATA A10, GATA H4 and DYS439 (GEPY II). The groups that reported correct results in all the systems were also asked to analyse a population sample in order to evaluate the informative content of these STRs in different populations. A total of 1020 males out of 13 population samples from Argentina, Brazil, Costa Rica, Macao, Mozambique, Portugal and Spain were analysed for all the loci included in the present study. Haplotype and allele frequencies of these eight Y-STRs were estimated in all samples. The lowest haplotype diversity was found in the Lara (Argentina) population (95.44%) and the highest (99.90%) in Macao (China). Pairwise haplotype analysis showed the relative homogeneity of the Iberian origin samples, in accordance with what was ...
The 17 Y-chromosomal short tandem repeats (STRs) included in the AmpFlSTR YFiler Amplification Ki... more The 17 Y-chromosomal short tandem repeats (STRs) included in the AmpFlSTR YFiler Amplification Kit (AB Applied Biosystems) (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4.1) were typed in 250 samples from Portugal. A total of 231 different haplotypes were found, where 17 haplotypes were shared by two individuals and one haplotype by three. The overall haplotype diversity (HD) was 0.9994. DYS458 non-consensus alleles found in 5 samples (out of 85) are all associated with paragroup J*(xJ1,2). Population comparisons with available Yfiler loci data in European samples were undertaken, namely with Northern Portuguese data (N = 174) where no significant differences were observed with our sample (Rst = 0.0000; P = 0.8649 AE 0.0310). Since both Portuguese databases can be joined (N = 424; HD = 0.9997; 394 distinct haplotypes), a study on the best loci for HD increment in this sample was also undertaken: by fixing the haplotypes generated from the minimal haplotype and SWGDAM core set (www.yhrd.org) and adding the other Yfiler loci one by one, the order in which the loci contribute more is DYS458, DYS456, GATA H4.1, DYS437 or DYS635, and finally DYS448. Therefore, at least in this population sample, all Yfiler loci are contributing for haplotype discrimination. #
Forensic Science International: Genetics Supplement Series, 2009
Insertion/deletion polymorphisms (indels) have considerable potential in the field of identificat... more Insertion/deletion polymorphisms (indels) have considerable potential in the field of identification, since they combine desirable characteristics of both SNPs and STRs: (i) the use of reduced amplicon sizes comparable to those of forensic SNP assays thus improving amplification success of degraded samples and (ii) the simplicity of analysis through PCR and capillary electrophoresis, in the same way as STRs. We
Forensic Science International: Genetics Supplement Series, 2011
Forensic Science International: Genetics Supplement Series, 2008
We analyzed 17 Y-chromosomal STR loci in a population sample of 126 unrelated Portuguese Gypsies.... more We analyzed 17 Y-chromosomal STR loci in a population sample of 126 unrelated Portuguese Gypsies. Fifty three different haplotypes were found, three represented with considerable high frequencies (!8.7%). The percentage of unique haplotypes (71.2%) was rather low as well as haplotype diversity (94.37%). In the comparison with available Portuguese population data and with those from other Gypsy and general population samples from Bulgaria, Lithuania and Spain, our sample showed significant differences in comparison with the general population data from Portugal, Spain and Bulgaria. Significant differences were observed with Bulgarian Gypsies, but not with the Spanish or Lithuanian groups. The Gypsy populations from Portugal, Spain and Bulgaria were found to be more closely related to each other than with the general population from their own countries. #
Forensic Science International: Genetics, 2015
PLoS ONE, 2011
Previous genetic, anthropological and linguistic studies have shown that Roma (Gypsies) constitut... more Previous genetic, anthropological and linguistic studies have shown that Roma (Gypsies) constitute a founder population dispersed throughout Europe whose origins might be traced to the Indian subcontinent. Linguistic and anthropological evidence point to Indo-Aryan ethnic groups from North-western India as the ancestral parental population of Roma. Recently, a strong genetic hint supporting this theory came from a study of a private mutation causing primary congenital glaucoma. In the present study, complete mitochondrial control sequences of Iberian Roma and previously published maternal lineages of other European Roma were analyzed in order to establish the genetic affinities among Roma groups, determine the degree of admixture with neighbouring populations, infer the migration routes followed since the first arrival to Europe, and survey the origin of Roma within the Indian subcontinent. Our results show that the maternal lineage composition in the Roma groups follows a pattern of different migration routes, with several founder effects, and low effective population sizes along their dispersal. Our data allowed the confirmation of a North/West migration route shared by Polish, Lithuanian and Iberian Roma. Additionally, eleven Roma founder lineages were identified and degrees of admixture with host populations were estimated. Finally, the comparison with an extensive database of Indian sequences allowed us to identify the Punjab state, in North-western India, as the putative ancestral homeland of the European Roma, in agreement with previous linguistic and anthropological studies.
Molecular Phylogenetics and Evolution, 2003
Partial sequences from two mitochondrial DNA genes, cytochrome b and 12S rRNA, were used to asses... more Partial sequences from two mitochondrial DNA genes, cytochrome b and 12S rRNA, were used to assess the phylogenetic relationships of populations of Lacerta dugesii from the volcanic Atlantic islands of Madeira, the Desertas, Porto Santo, and the Selvagens. All four-island groups are genetically distinguishable and populations within each contain similar degrees of genetic diversity. Molecular clock estimates suggest that the islands were colonized much later after their emergence compared to other Atlantic islands, possibly due to their greater geographical isolation. Mismatch analysis of all populations is consistent with exponential growth, as expected after colonization of empty niches. The Selvagens contain genetic substructuring between the islets.
Journal of Clinical Microbiology, 2005
Five new microsatellite loci were described and characterized for use as molecular markers for th... more Five new microsatellite loci were described and characterized for use as molecular markers for the identification and genetic differentiation of Candida albicans strains. Following the typing of 72 unrelated clinical isolates, the analysis revealed that they were all polymorphic, presenting from 5 to 30 alleles and 8 to 46 different genotypes. The discriminatory power obtained by combining the information generated by three microsatellites used in a multiplex PCR amplification strategy was 0.99, the highest ever reported. The multiplex PCR was later used to test a total of 114 C. albicans strains, including multiple isolates from the same patient collected from different body locations and along episodes of vulvovaginal infections. Three different scenarios for strain relatedness were identified: (i) different isolates that were revealed to be the same strain, (ii) isolates that were the same strain but that apparently underwent a process of microevolution, and (iii) isolates that corresponded to different strains. Analysis of the microevolutionary changes between isolates from recurrent infections indicated that the genotype alterations observed could be the result of events that lead to the loss of heterozygosity (LOH). In one case of recurrent infection, LOH was observed at the CAI locus, and this could have been related to exposure to fluconazole, since such strains were exposed to this antifungal during treatment. The analysis of microsatellites by a multiplex PCR strategy was found to be a highly efficient tool for the rapid and accurate differentiation of C. albicans strains and adequate for the identification of fine microevolutionary events that could be related to strain microevolution in response to environmental stress conditions. on August 24, 2015 by guest https://jcm.asm.org/ Downloaded from clinical isolates to test its efficiency for strain differentiation. The potential capacity of this system to identify fine microevolutionary events was also evaluated.
Journal of Clinical Microbiology, 2003
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International Journal of Legal Medicine, 2009
In a collaborative work carried out by the Spanish and Portuguese ISFG Working Group (GEP-ISFG), ... more In a collaborative work carried out by the Spanish and Portuguese ISFG Working Group (GEP-ISFG), a polymerase chain reaction multiplex was optimized in order to type ten X-chromosome short tandem repeats (STRs) in a single reaction, including: DXS8378, DXS9902, DXS7132, DXS9898, DXS6809, DXS6789, DXS7133, GATA172D05, GATA31E08, and DXS7423. Using this X-decaplex, each 17 of the participating laboratories typed a population sample of approximately 200 unrelated individuals (100 males and 100 females). In this work, we report the allele frequencies for the ten X-STRs in 15 samples from Argentina (Buenos Aires, Int J Legal Med (
International Journal of Legal Medicine, 2012
Kinship investigations such as paternity are currently solved using sets of (commercially availab... more Kinship investigations such as paternity are currently solved using sets of (commercially available) highly polymorphic autosomal short tandem repeats (STRs), which lead to powerful likelihood ratios (LR). Still, some difficult cases arise whenever the kinship is much more remote or if the alternative hypotheses are not correctly formulated due to the lack of information (for e.g. there is an unknown relationship between the alleged and the true fathers). In these situations, beyond the routinely used marker set, laboratories usually enlarge the number and/or the type of markers analysed. Among these, autosomal indels and X-chromosome STRs have gained popularity. The aim of this study was to compare the results obtained after complementing an initial set of autosomal STRs with indels or with X-chromosome-specific STRs in simulated paternity cases where the alleged father is a close relative of the real one. Results show that in paternity cases where a low number of incompatibilities are observed, the best strategy is to increase the number of autosomal STRs under analysis. Nevertheless, if these are not available, our study globally shows that in father-daughter duos, a set of 12 X-STRs is more advantageous than 38 highly diverse autosomal biallelic markers. Additionally, the usefulness of X-STRs was also evaluated in cases where only a close relative of the alleged parent (father or mother) is available for testing. For those situations where these markers have the power to exclude, strong LR values are obtained. In the remaining cases, LRs are usually weak and sometimes the results are more likely under the wrong kinship hypothesis.
International Journal of Legal Medicine, 2003
A deviation from the stepwise mutation model (SMM) has been suggested for the trinucleotide Y-STR... more A deviation from the stepwise mutation model (SMM) has been suggested for the trinucleotide Y-STR locus DYS392, based upon its bimodal allele frequency distribution in various populations. The same type of distribution is also observed for the pentanucleotide Y-STR DYS438. In order to verify whether a departure from an SMM is likely for these two loci, we studied a large number of Portuguese male DNA samples typed for the two loci and in addition, for the Y-STR loci DYS19, DYS389I/II, DYS390, DYS391 and DYS393. The compatibility of the observed allele frequency spectrum with an SMM was assessed by an apportionment of the molecular variance among, and consideration of the molecular distances between, haplotype groups defined according to their allelic state at each of the two markers of interest. For haplotypes carrying either modal alleles 11 or 13 of DYS392, 18.6% of the molecular variance of the remaining Y-STR background could be attributed to variation between the two groups. When all pairwise Phi(st) values between haplotype groups were compared, group 12 was found to be closer to 11 than to 13, and group 14 was much closer to 13 than to 12 and 11. It may therefore be concluded that DYS392 allele 13 represents an evolutionary lineage with little or no relationship to 11 and 12. Furthermore, allele 14 is a one-step neighbour of 13 and is therefore likely to represent an offshoot from group 13. For haplotypes carrying either modal allele 10 or modal allele 12 of DYS438, 27.7% of the molecular variance of the Y-STR background was found to be due to variation between the two groups. Comparison of the other pairwise Phi(st) values indicated that group 10 was closer to 9 and 11 than to 12, and that group 12 was closer to 11 and 13 than to 10. The lineages defined by the two modal alleles of DYS438 therefore also seem to be phylogenetically distant. When the two loci were analysed in combination, using the standardised linkage disequilibrium measure (D'), a strong association was noted between alleles DYS392*11 and DYS438*10 (D'=0.70) and between DYS392*13 and DYS438*12 (D'=0.72). Taken together, these results show that the bimodal allele frequency distributions of DYS392 and DYS438 are explicable in terms of (probably the same) historical and demographic causes, rather than a mutational mechanism other than SMM. The loci do therefore not appear to warrant any special attention when applied in population genetic or forensic studies.
International Journal of Legal Medicine, 2008
A collaborative work was carried out by the Spanish and Portuguese International Society for Fore... more A collaborative work was carried out by the Spanish and Portuguese International Society for Forensic Genetics Working Group in order to extend the existing data on Y-short tandem repeat (STR) mutations at the 17 Y chromosome STR loci included in the AmpFlSTR YFiler kit (Applied Biosystems): DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, and GATA H4.1. In a sample of 701 father/son pairs, 26 mutations were observed among 11,917 allele transfers across the 17 loci. After summing previously reported mutation data with our sample, mutation rates varied between 4.25×10 −4 (95% CI 0.05×10 −3 -1.53×10 −3 ) at DYS438 and 6.36×10 −3 (95% CI 2.75×10 −3 -12.49× 10 −3 ) at DYS458. All mutations were single step, and mutations in the same father/son pair were found twice.
International Congress Series, 2006
21 autosomal STRs are used in our laboratory in routine casework by using two commercially availa... more 21 autosomal STRs are used in our laboratory in routine casework by using two commercially available STR kits (Applied Biosystems' Identifiler and Promega's Powerplex 16) and also an in-house multiplex system, used especially in deficient paternity cases, which amplifies four more loci (CD4, F13A01, FES and MBPB). Northern Portuguese population data are presented here extensively, including D2S1338 and D19S433 for the first time. Deviations from Hardy-Weinberg equilibrium were detected in D8S1179 and Penta D loci, but applying the Bonferroni correction for the number of loci analysed, the departure in both loci was not significant (0.05/21 = 0.0024). Both commercial STR kits share 13 loci but use different primer pairs, and so genotype inconsistencies may occur. For individuals genotyped as homozygotes with one kit and as heterozygotes with the other, the latter genotype was the one considered. The overall matching probability for the 21 STRs in our population sample is of 1 in 1.56 Â 10 24 individuals and combined power of exclusion of 0.9999999914. D
International Congress Series, 2006
Twenty Y-chromosome biallelic polymorphisms were analysed in samples from Angolares, Forros and T... more Twenty Y-chromosome biallelic polymorphisms were analysed in samples from Angolares, Forros and Tongas, three population groups from the African archipelago of São Tomé e Príncipe. Although most male lineages belonged to Sub-Saharan haplogroups, the component of European origin reached 23.9% in the archipelago as a whole. This value contrasts with the previously reported absence of European female lineages in the São Tomean mtDNA pool and reflects the strong sex-biased admixture process between Europeans and Africans that characterized the demographic history of the archipelago. The lowest diversity levels as well as the smallest proportion of putative male European ancestry were registered among the Angolares, representing clear genetic signs of their past relative isolation from other São Tomé e Príncipe's inhabitants. D
International Congress Series, 2006
In this work, 90 individuals living in Karamoja region were typed for 17 autosomal STRs and 40 ma... more In this work, 90 individuals living in Karamoja region were typed for 17 autosomal STRs and 40 males were also typed for 12 Y-STRs. Hardy-Weinberg equilibrium was tested for each autosomal locus and no deviations from equilibrium were observed. For autosomal STRs, our sample shows a combined matching probability of 1 in 6.5 Â 10 19 individuals and a combined power of exclusion of 0.999999988. Haplotype diversity for Y-STRs was 0.9859 and 32 different haplotypes were detected. Our sample was compared with available autosomal data from sub-Saharan African samples and significant differences were found with Mozambique; Cabinda (Angola); Equatorial Guinea; and with Rwanda. Comparisons with the Y-STR data, revealed large genetic distances between our sample and Mozambique, Cabinda and Equatorial Guinea. D
Forensic Science International: Genetics, 2014
Forensic Science International: Genetics, 2014
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Papers by CÍNTIA ANDRADE ALVES