{"id":"gdc-cptac-3","title":"CPTAC-Brain, Head and Neck, Kidney, Lung, Pancreas, Uterus","short_title":"CPTAC-3","aliases":["CPTAC-3"],"summary":"CPTAC-3 is the genomic half of a cohort whose proteomic half lives in a different repository. That split is the single most important practical fact about it: the GDC record carries exome on 1,844 cases, whole genome on 1,827, RNA sequencing on 1,824 and methylation on 1,817, while proteome, phosphoproteome and the scarcer modification layers are distributed through the Proteomic Data Commons under different study identifiers.\nIts clinical annotation is unusually strong for a multi-cancer cohort. Vital status is informative for 95.8%, progression or recurrence for 77.9%, and last known disease status for 77.2% - which makes recurrence-based endpoints genuinely available, not just nominally present.","one_liner":"1,866 tumors across six cancer types with genomics in the GDC and proteomics in the PDC - the largest prospectively collected proteogenomic cohort, with recurrence recorded for 78% of cases.","identifiers":[{"scheme":"gdc_project_id","value":"CPTAC-3","url":"https://portal.gdc.cancer.gov/projects/CPTAC-3","is_primary":true,"evidence":[{"method":"api","source_url":"https://api.gdc.cancer.gov/projects/CPTAC-3?expand=summary,summary.data_categories,summary.experimental_strategies,program","source_label":"GDC API /projects","retrieved_at":"2026-09-18T02:32:25.909822Z","snippet":null,"locator":null,"confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"scheme":"gdc_program","value":"CPTAC","url":null,"is_primary":false,"evidence":[{"method":"api","source_url":"https://api.gdc.cancer.gov/projects/CPTAC-3?expand=summary,summary.data_categories,summary.experimental_strategies,program","source_label":"GDC API /projects","retrieved_at":"2026-09-18T02:32:25.909822Z","snippet":null,"locator":null,"confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"scheme":"dbgap_phs","value":"phs001287","url":"https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001287","is_primary":false,"evidence":[{"method":"api","source_url":"https://api.gdc.cancer.gov/projects/CPTAC-3?expand=summary,summary.data_categories,summary.experimental_strategies,program","source_label":"GDC API /projects","retrieved_at":"2026-09-18T02:32:25.909822Z","snippet":null,"locator":null,"confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]}],"repository":{"name":"NCI Genomic Data Commons","short_name":"GDC","url":"https://portal.gdc.cancer.gov","is_nci_crdc_node":true,"is_nih_repository":true},"additional_repositories":[],"program_name":"CPTAC","program_url":"https://portal.gdc.cancer.gov/analysis_page?app=Projects","nci_program":"CPTAC","generating_institutions":[],"data_generation_funding_role":"generation","version":null,"release_date":"2020-01-01","last_upstream_update":null,"retrieved_at":"2026-09-18T02:35:37.301850Z","landing_page_url":"https://portal.gdc.cancer.gov/projects/CPTAC-3","cancer_types":[{"label":"Not Applicable","ontology":null,"code":null,"url":null},{"label":"Transitional Cell Papillomas and Carcinomas","ontology":null,"code":null,"url":null},{"label":"Ductal and Lobular Neoplasms","ontology":null,"code":null,"url":null},{"label":"Adenomas and Adenocarcinomas","ontology":null,"code":null,"url":null},{"label":"Gliomas","ontology":null,"code":null,"url":null},{"label":"Epithelial Neoplasms, NOS","ontology":null,"code":null,"url":null},{"label":"Complex Epithelial Neoplasms","ontology":null,"code":null,"url":null},{"label":"Complex Mixed and Stromal Neoplasms","ontology":null,"code":null,"url":null},{"label":"Lipomatous Neoplasms","ontology":null,"code":null,"url":null},{"label":"Squamous Cell Neoplasms","ontology":null,"code":null,"url":null},{"label":"Myeloid Leukemias","ontology":null,"code":null,"url":null},{"label":"Nevi and Melanomas","ontology":null,"code":null,"url":null}],"primary_sites":["Stomach","Other and ill-defined sites in lip, oral cavity and pharynx","Unknown","Colon","Other and unspecified urinary organs","Floor of mouth","Other and unspecified parts of mouth","Gum","Bronchus and lung","Oropharynx","Other and unspecified parts of tongue","Base of tongue","Breast","Other and ill-defined sites","Larynx","Lip","Uterus, NOS","Hematopoietic and reticuloendothelial systems","Kidney","Brain","Skin","Pancreas","Tonsil"],"subject":{"scope":"pan_cancer","tissues":[],"evidence":[{"method":"derived","source_url":null,"source_label":"cds.subjects","retrieved_at":null,"snippet":null,"locator":"cancer_types: Not Applicable, Transitional Cell Papillomas and Carcinomas, Ductal and Lobular Neoplasms, Adenomas and Adenocarcinomas, Gliomas, Epithelial Neoplasms, NOS, Complex Epithelial Neoplasms, Complex Mixed and Stromal Neoplasms, Lipomatous Neoplasms, Squamous Cell Neoplasms, Myeloid Leukemias, Nevi and Melanomas; primary_sites: Stomach, Other and ill-defined sites in lip, oral cavity and pharynx, Unknown, Colon, Other and unspecified urinary organs, Floor of mouth, Other and unspecified parts of mouth, Gum, Bronchus and lung, Oropharynx, Other and unspecified parts of tongue, Base of tongue, Breast, Other and ill-defined sites, Larynx, Lip, Uterus, NOS, Hematopoietic and reticuloendothelial systems, Kidney, Brain, Skin, Pancreas, Tonsil","confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Four or more repository-stated tissues make this pan-cancer."}]},"is_pediatric":null,"model_systems":[],"cohort":{"n_cases":1866,"n_samples":null,"n_aliquots":null,"n_files":110077,"total_bytes":816871963467036,"n_tumor_cases":null,"n_normal_cases":null,"has_matched_normal":null,"demographics":{"sex":{"male":1003,"female":863},"race":{"white":1496,"asian":244,"not reported":57,"unknown":46,"black or african american":22,"american indian or alaska native":1},"ethnicity":{"not reported":1432,"not hispanic or latino":371,"hispanic or latino":34,"unknown":29},"age_at_diagnosis_years":{"n":1781.0,"min":18.3,"q1":56.7,"median":64.7,"q3":71.2,"max":90.0},"vital_status":{"alive":1087,"dead":700,"not 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