From b5d8f7d01568e28549ad29ed71d8e9927f085bc2 Mon Sep 17 00:00:00 2001 From: Avery Wang Date: Wed, 20 Sep 2023 07:01:42 -0700 Subject: [PATCH 1/4] docs for nci-cgc pipeline generated studies --- docs/supported-projects-and-programs.md | 62 +++++++++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 docs/supported-projects-and-programs.md diff --git a/docs/supported-projects-and-programs.md b/docs/supported-projects-and-programs.md new file mode 100644 index 0000000000..5f5706c3e0 --- /dev/null +++ b/docs/supported-projects-and-programs.md @@ -0,0 +1,62 @@ +# GDC Sourced cBioPortal Studies +The following is a list of studies generated using the NCI-CRDC Pipeline. The list includes the cBioPortal study id and a link to the equivalent project hosted in the GDC portal. Raw data is sourced from the GDC and hosted in [ISB-CGC BigQuery tables](https://isb-cgc.appspot.com/bq_meta_search/). + +## TCGA + +- **Cancer type mapping:** Each study corresponds to one TCGA project. The suffix of the TCGA project is taken and converted to an OncoTree code, which is used for the name of the study. + - **Example:** For the TCGA project `TCGA-LAML`, the `LAML` suffix is taken and converted to the Oncotree code `AML`. The resulting cBioPortal study is `aml_tcga`. + - [Mapping file](../resources/tcga_mappings.txt) + +### List of TCGA cBioPortal Studies +- `acc_tcga_gdc`: [TCGA-ACC](https://portal.gdc.cancer.gov/projects/TCGA-ACC), Adenocortical Carcinoma +- `aml_tcga_gdc`: [TCGA-LAML](https://portal.gdc.cancer.gov/projects/TCGA-LAML), Acute Myeloid Leukemia +- `blca_tcga_gdc`: [TCGA-BLCA](https://portal.gdc.cancer.gov/projects/TCGA-BLCA), Bladder Urothelial Carcinoma +- `brca_tcga_gdc`: [TCGA-BRCA](https://portal.gdc.cancer.gov/projects/TCGA-BRCA), Breast Invasive Carcinoma +- `ccrcc_tcga_gdc`: [TCGA-KIRC](https://portal.gdc.cancer.gov/projects/TCGA-KIRC), Kidney Renal Clear Cell Carcinoma +- `cesc_tcga_gdc`: [TCGA-CESC](https://portal.gdc.cancer.gov/projects/TCGA-CESC), Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma +- `chol_tcga_gdc`: [TCGA-CHOL](https://portal.gdc.cancer.gov/projects/TCGA-CHOL), Cholangiocarcinoma +- `chrcc_tcga_gdc`: [TCGA-KICH](https://portal.gdc.cancer.gov/projects/TCGA-KICH), Kidney Chromophobe +- `coad_tcga_gdc`: [TCGA-COAD](https://portal.gdc.cancer.gov/projects/TCGA-COAD), Colon Adenocarcinoma +- `difg_tcga_gdc`: [TCGA-LGG](https://portal.gdc.cancer.gov/projects/TCGA-LGG), Brain Lower Grade Glioma +- `dlbclnos_tcga_gdc`: [TCGA-DLBC](https://portal.gdc.cancer.gov/projects/TCGA-DLBC), Lymphoid Neoplasm Diffuse Large B-cell Lymphoma +- `esca_tcga_gdc`: [TCGA-ESCA](https://portal.gdc.cancer.gov/projects/TCGA-ESCA), Esophageal Carcinoma +- `gbm_tcga_gdc`: [TCGA-GBM](https://portal.gdc.cancer.gov/projects/TCGA-GBM), Glioblastoma Multiforme +- `hcc_tcga_gdc`: [TCGA-LIHC](https://portal.gdc.cancer.gov/projects/TCGA-LIHC), Liver Hepatocellular Carcinoma +- `hgsoc_tcga_gdc`: [TCGA-OV](https://portal.gdc.cancer.gov/projects/TCGA-OV), Ovarian Serous Cystadenocarcinoma +- `hnsc_tcga_gdc`: [TCGA-HNSC](https://portal.gdc.cancer.gov/projects/TCGA-HNSC), Head and Neck Squamous Cell Carcinoma +- `luad_tcga_gdc`: [TCGA-LUAD](https://portal.gdc.cancer.gov/projects/TCGA-LUAD), Lung Adenocarcinoma +- `lusc_tcga_gdc`: [TCGA-LUSC](https://portal.gdc.cancer.gov/projects/TCGA-LUSC), Lung Squamous Cell Carcinoma +- `mnet_tcga_gdc`: [TCGA-PCPG](https://portal.gdc.cancer.gov/projects/TCGA-PCPG), Pheochromocytoma and Paraganglioma +- `nsgct_tcga_gdc`: [TCGA-TGCT](https://portal.gdc.cancer.gov/projects/TCGA-TGCT), Testicular Germ Cell Tumors +- `paad_tcga_gdc`: [TCGA-PAAD](https://portal.gdc.cancer.gov/projects/TCGA-PAAD), Pancreatic Adenocarcinoma +- `plmeso_tcga_gdc`: [TCGA-MESO](https://portal.gdc.cancer.gov/projects/TCGA-MESO), Mesothelioma +- `prad_tcga_gdc`: [TCGA-PRAD](https://portal.gdc.cancer.gov/projects/TCGA-PRAD), Prostate Adenocarcinoma +- `prcc_tcga_gdc`: [TCGA-KIRP](https://portal.gdc.cancer.gov/projects/TCGA-KIRP), Kidney Renal Papillary Cell Carcinoma +- `read_tcga_gdc`: [TCGA-READ](https://portal.gdc.cancer.gov/projects/TCGA-READ), Rectum Adenocarcinoma +- `skcm_tcga_gdc`: [TCGA-SKCM](https://portal.gdc.cancer.gov/projects/TCGA-SKCM), Skin Cutaneous Melanoma +- `soft_tissue_tcga_gdc`: [TCGA-SARC](https://portal.gdc.cancer.gov/projects/TCGA-SARC), Sarcoma +- `stad_tcga_gdc`: [TCGA-STAD](https://portal.gdc.cancer.gov/projects/TCGA-STAD), Stomach Adenocarcinoma +- `thpa_tcga_gdc`: [TCGA-THCA](https://portal.gdc.cancer.gov/projects/TCGA-THCA), Thyroid Carcinoma +- `thym_tcga_gdc`: [TCGA-THYM](https://portal.gdc.cancer.gov/projects/TCGA-THYM), Thymoma +- `ucec_tcga_gdc`: [TCGA-UCEC](https://portal.gdc.cancer.gov/projects/TCGA-UCEC), Uterine Corpus Endometrial Carcinoma +- `ucs_tcga_gdc`: [TCGA-UCS](https://portal.gdc.cancer.gov/projects/TCGA-UCS), Uterine Carcinosarcoma +- `um_tcga_gdc`: [TCGA-UVM](https://portal.gdc.cancer.gov/projects/TCGA-UVM), Uveal Melanoma + +## CPTAC + +- **Cancer type mapping:** CPTAC is comprised of the CPTAC-2 and CPTAC-3 projects, both of which encompass multiple cancer types. Each study corresponds to a subset of these projects with a particular OncoTree code. The code is determined by looking at `disease_type` and `primary_site` in the BigQuery tables. + - **Example:** The `luad_cptac` study is generated from all samples with primary site `Bronchus and lung` and disease type `Adenomas and Adenocarcinomas`. + - [Mapping file](../resources/cptac_mappings.txt) + +### List of cBioPortal studies + +- `brain_cptac_gdc`: [Brain Cancer](https://portal.gdc.cancer.gov/repository?facetTab=cases&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.primary_site%22%2C%22value%22%3A%5B%22brain%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22CPTAC%22%5D%7D%7D%5D%7D) +- `breast_cptac_gdc`: [Breast Cancer](https://portal.gdc.cancer.gov/repository?facetTab=cases&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.primary_site%22%2C%22value%22%3A%5B%22breast%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22CPTAC%22%5D%7D%7D%5D%7D) +- `coad_cptac_gdc`: [Colon Cancer](https://portal.gdc.cancer.gov/repository?facetTab=cases&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.primary_site%22%2C%22value%22%3A%5B%22colon%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22CPTAC%22%5D%7D%7D%5D%7D) +- `luad_cptac_gdc`: [Lung Adenocarcinoma](https://portal.gdc.cancer.gov/repository?facetTab=cases&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.disease_type%22%2C%22value%22%3A%5B%22adenomas%20and%20adenocarcinomas%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.primary_site%22%2C%22value%22%3A%5B%22bronchus%20and%20lung%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22CPTAC%22%5D%7D%7D%5D%7D) +- `lusc_cptac_gdc`: [Lung Squamous Cell Carcinoma](https://portal.gdc.cancer.gov/repository?facetTab=cases&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.disease_type%22%2C%22value%22%3A%5B%22squamous%20cell%20neoplasms%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.primary_site%22%2C%22value%22%3A%5B%22bronchus%20and%20lung%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22CPTAC%22%5D%7D%7D%5D%7D) +- `ohnca_cptac_gdc`: [Head and Neck Cancer](https://portal.gdc.cancer.gov/repository?facetTab=cases&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.primary_site%22%2C%22value%22%3A%5B%22other%20and%20ill-defined%20sites%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22CPTAC%22%5D%7D%7D%5D%7D) +- `ovary_cptac_gdc`: [Ovarian Cancer](https://portal.gdc.cancer.gov/repository?facetTab=cases&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.primary_site%22%2C%22value%22%3A%5B%22other%20and%20unspecified%20female%20genital%20organs%22%2C%22ovary%22%2C%22rectum%22%2C%22retroperitoneum%20and%20peritoneum%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22CPTAC%22%5D%7D%7D%5D%7D) +- `pancreas_cptac_gdc`: [Pancreatic Cancer](https://portal.gdc.cancer.gov/repository?facetTab=files&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.primary_site%22%2C%22value%22%3A%5B%22pancreas%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22CPTAC%22%5D%7D%7D%5D%7D) +- `rcc_cptac_gdc`: [Renal Cancer](https://portal.gdc.cancer.gov/repository?facetTab=cases&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.disease_type%22%2C%22value%22%3A%5B%22Adenomas%20and%20Adenocarcinomas%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.primary_site%22%2C%22value%22%3A%5B%22Kidney%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22CPTAC%22%5D%7D%7D%5D%7D) +- `uec_cptac_gdc`: [Endometrial Cancer](https://portal.gdc.cancer.gov/repository?facetTab=cases&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.disease_type%22%2C%22value%22%3A%5B%22Adenomas%20and%20Adenocarcinomas%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.primary_site%22%2C%22value%22%3A%5B%22Uterus%2C%20NOS%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22CPTAC%22%5D%7D%7D%5D%7D) From ec53e0abbc0b899bad077e712f290712c96350dd Mon Sep 17 00:00:00 2001 From: averyniceday Date: Wed, 20 Sep 2023 07:06:37 -0700 Subject: [PATCH 2/4] Update supported-projects-and-programs.md --- docs/supported-projects-and-programs.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/supported-projects-and-programs.md b/docs/supported-projects-and-programs.md index 5f5706c3e0..b46102dbb3 100644 --- a/docs/supported-projects-and-programs.md +++ b/docs/supported-projects-and-programs.md @@ -1,5 +1,5 @@ # GDC Sourced cBioPortal Studies -The following is a list of studies generated using the NCI-CRDC Pipeline. The list includes the cBioPortal study id and a link to the equivalent project hosted in the GDC portal. Raw data is sourced from the GDC and hosted in [ISB-CGC BigQuery tables](https://isb-cgc.appspot.com/bq_meta_search/). +The following is a list of studies generated using the NCI-CRDC Pipeline. Source data is from the GDC and can be found inside ISB-CGC BigQuery tables, [here](https://isb-cgc.appspot.com/bq_meta_search/). The list includes both the cBioPortal study identifier as well as a link to the corresponding GDC portal project. ## TCGA From 767cc4cf8af521627f0e8b7f2654ab2e55521877 Mon Sep 17 00:00:00 2001 From: averyniceday Date: Wed, 20 Sep 2023 07:09:18 -0700 Subject: [PATCH 3/4] Update supported-projects-and-programs.md --- docs/supported-projects-and-programs.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/supported-projects-and-programs.md b/docs/supported-projects-and-programs.md index b46102dbb3..1aa43c2904 100644 --- a/docs/supported-projects-and-programs.md +++ b/docs/supported-projects-and-programs.md @@ -5,7 +5,7 @@ The following is a list of studies generated using the NCI-CRDC Pipeline. Source - **Cancer type mapping:** Each study corresponds to one TCGA project. The suffix of the TCGA project is taken and converted to an OncoTree code, which is used for the name of the study. - **Example:** For the TCGA project `TCGA-LAML`, the `LAML` suffix is taken and converted to the Oncotree code `AML`. The resulting cBioPortal study is `aml_tcga`. - - [Mapping file](../resources/tcga_mappings.txt) + - [Mapping file](https://github.com/cBioPortal/nci-crdc-pipeline/blob/main/resources/tcga_mappings.txt) ### List of TCGA cBioPortal Studies - `acc_tcga_gdc`: [TCGA-ACC](https://portal.gdc.cancer.gov/projects/TCGA-ACC), Adenocortical Carcinoma @@ -46,7 +46,7 @@ The following is a list of studies generated using the NCI-CRDC Pipeline. Source - **Cancer type mapping:** CPTAC is comprised of the CPTAC-2 and CPTAC-3 projects, both of which encompass multiple cancer types. Each study corresponds to a subset of these projects with a particular OncoTree code. The code is determined by looking at `disease_type` and `primary_site` in the BigQuery tables. - **Example:** The `luad_cptac` study is generated from all samples with primary site `Bronchus and lung` and disease type `Adenomas and Adenocarcinomas`. - - [Mapping file](../resources/cptac_mappings.txt) + - [Mapping file](https://github.com/cBioPortal/nci-crdc-pipeline/blob/main/resources/cptac_mappings.txt)) ### List of cBioPortal studies From d3b81feb5189a45db4be8fc084a6aa2d98a3eefa Mon Sep 17 00:00:00 2001 From: James Ko Date: Thu, 14 Dec 2023 14:20:19 -0500 Subject: [PATCH 4/4] Add target studies to docs --- ...rojects-and-programs.md => gdc-studies.md} | 26 ++++++++++++++++--- 1 file changed, 22 insertions(+), 4 deletions(-) rename docs/{supported-projects-and-programs.md => gdc-studies.md} (85%) diff --git a/docs/supported-projects-and-programs.md b/docs/gdc-studies.md similarity index 85% rename from docs/supported-projects-and-programs.md rename to docs/gdc-studies.md index 1aa43c2904..27d42b8120 100644 --- a/docs/supported-projects-and-programs.md +++ b/docs/gdc-studies.md @@ -4,10 +4,11 @@ The following is a list of studies generated using the NCI-CRDC Pipeline. Source ## TCGA - **Cancer type mapping:** Each study corresponds to one TCGA project. The suffix of the TCGA project is taken and converted to an OncoTree code, which is used for the name of the study. - - **Example:** For the TCGA project `TCGA-LAML`, the `LAML` suffix is taken and converted to the Oncotree code `AML`. The resulting cBioPortal study is `aml_tcga`. - - [Mapping file](https://github.com/cBioPortal/nci-crdc-pipeline/blob/main/resources/tcga_mappings.txt) + - **Example:** For the TCGA project `TCGA-LAML`, the `LAML` suffix is taken and converted to the Oncotree code `AML`. The resulting cBioPortal study is `aml_tcga_gdc`. + - [Mapping file](https://github.com/cBioPortal/nci-crdc-pipeline/blob/main/resources/oncotree_mappings/tcga.txt) ### List of TCGA cBioPortal Studies + - `acc_tcga_gdc`: [TCGA-ACC](https://portal.gdc.cancer.gov/projects/TCGA-ACC), Adenocortical Carcinoma - `aml_tcga_gdc`: [TCGA-LAML](https://portal.gdc.cancer.gov/projects/TCGA-LAML), Acute Myeloid Leukemia - `blca_tcga_gdc`: [TCGA-BLCA](https://portal.gdc.cancer.gov/projects/TCGA-BLCA), Bladder Urothelial Carcinoma @@ -46,9 +47,9 @@ The following is a list of studies generated using the NCI-CRDC Pipeline. Source - **Cancer type mapping:** CPTAC is comprised of the CPTAC-2 and CPTAC-3 projects, both of which encompass multiple cancer types. Each study corresponds to a subset of these projects with a particular OncoTree code. The code is determined by looking at `disease_type` and `primary_site` in the BigQuery tables. - **Example:** The `luad_cptac` study is generated from all samples with primary site `Bronchus and lung` and disease type `Adenomas and Adenocarcinomas`. - - [Mapping file](https://github.com/cBioPortal/nci-crdc-pipeline/blob/main/resources/cptac_mappings.txt)) + - [Mapping file](https://github.com/cBioPortal/nci-crdc-pipeline/blob/main/resources/oncotree_mappings/cptac.txt)) -### List of cBioPortal studies +### List of CPTAC cBioPortal Studies - `brain_cptac_gdc`: [Brain Cancer](https://portal.gdc.cancer.gov/repository?facetTab=cases&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.primary_site%22%2C%22value%22%3A%5B%22brain%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22CPTAC%22%5D%7D%7D%5D%7D) - `breast_cptac_gdc`: [Breast Cancer](https://portal.gdc.cancer.gov/repository?facetTab=cases&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.primary_site%22%2C%22value%22%3A%5B%22breast%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22CPTAC%22%5D%7D%7D%5D%7D) @@ -60,3 +61,20 @@ The following is a list of studies generated using the NCI-CRDC Pipeline. Source - `pancreas_cptac_gdc`: [Pancreatic Cancer](https://portal.gdc.cancer.gov/repository?facetTab=files&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.primary_site%22%2C%22value%22%3A%5B%22pancreas%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22CPTAC%22%5D%7D%7D%5D%7D) - `rcc_cptac_gdc`: [Renal Cancer](https://portal.gdc.cancer.gov/repository?facetTab=cases&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.disease_type%22%2C%22value%22%3A%5B%22Adenomas%20and%20Adenocarcinomas%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.primary_site%22%2C%22value%22%3A%5B%22Kidney%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22CPTAC%22%5D%7D%7D%5D%7D) - `uec_cptac_gdc`: [Endometrial Cancer](https://portal.gdc.cancer.gov/repository?facetTab=cases&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.disease_type%22%2C%22value%22%3A%5B%22Adenomas%20and%20Adenocarcinomas%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.primary_site%22%2C%22value%22%3A%5B%22Uterus%2C%20NOS%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22CPTAC%22%5D%7D%7D%5D%7D) + +## TARGET + +- **Cancer type mapping:** Each study corresponds to one or more TARGET projects. The name of the project is derived from the OncoTree code defined in the mapping file. + - **Example:** The `bll_target_gdc` study has OncoTree code `BLL` and is sourced from the GDC projects `TARGET-ALL-P1` and `TARGET-ALL-P2`. + - [Mapping file](https://github.com/cBioPortal/nci-crdc-pipeline/blob/main/resources/oncotree_mappings/target.txt) + +### List of TARGET cBioPortal Studies + +- `alal_target_gdc`: [TARGET-ALL-P3](https://portal.gdc.cancer.gov/projects/TARGET-ALL-P3), Acute Lymphoblastic Leukemia - Phase III +- `aml_target_gdc`: [TARGET-AML](https://portal.gdc.cancer.gov/projects/TARGET-AML), Acute Myeloid Leukemia +- `bll_target_gdc`: [TARGET-ALL-P1](https://portal.gdc.cancer.gov/projects/TARGET-ALL-P1) and [TARGET-ALL-P2](https://portal.gdc.cancer.gov/projects/TARGET-ALL-P2), Acute Lymphoblastic Leukemia - Phases I and II +- `ccsk_target_gdc`: [TARGET-CCSK](https://portal.gdc.cancer.gov/projects/TARGET-CCSK), Clear Cell Sarcoma of the Kidney +- `mrt_target_gdc`: [TARGET-RT](https://portal.gdc.cancer.gov/projects/TARGET-RT), Rhabdoid Tumor +- `nbl_target_gdc`: [TARGET-NBL](https://portal.gdc.cancer.gov/projects/TARGET-NBL), Neuroblastoma +- `os_target_gdc`: [TARGET-OS](https://portal.gdc.cancer.gov/projects/TARGET-OS), Osteosarcoma +- `wt_target_gdc`: [TARGET-WT](https://portal.gdc.cancer.gov/projects/TARGET-WT), High-Risk Wilms Tumor