{"id":"cbio-skcm-broad","title":"Skin Cutaneous Melanoma (Broad, Cell 2012)","short_title":"skcm_broad","aliases":["skcm_broad"],"summary":"Whole-exome sequencing of 121 melanoma samples with matched normals.","one_liner":null,"identifiers":[{"scheme":"cbioportal_study_id","value":"skcm_broad","url":"https://www.cbioportal.org/study/summary?id=skcm_broad","is_primary":true,"evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/skcm_broad","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-18T02:48:40.878054Z","snippet":null,"locator":null,"confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]}],"repository":{"name":"cBioPortal for Cancer Genomics","short_name":"cBioPortal","url":"https://www.cbioportal.org","is_nci_crdc_node":false,"is_nih_repository":false},"additional_repositories":[],"program_name":"Investigator-initiated cohort (harmonized in cBioPortal)","program_url":"https://www.cbioportal.org/study/summary?id=skcm_broad","nci_program":null,"generating_institutions":[],"data_generation_funding_role":"generation","version":null,"release_date":null,"last_upstream_update":null,"retrieved_at":"2026-09-18T02:48:40.878054Z","landing_page_url":"https://www.cbioportal.org/study/summary?id=skcm_broad","cancer_types":[{"label":"Cutaneous Melanoma","ontology":"cBioPortal","code":"skcm","url":null}],"primary_sites":["mel"],"subject":{"scope":"single","tissues":["SKIN"],"evidence":[{"method":"derived","source_url":null,"source_label":"cds.subjects","retrieved_at":null,"snippet":null,"locator":"cancer_types: Cutaneous Melanoma; primary_sites: mel","confidence":"high","reviewer":null,"reviewed_at":null,"note":"OncoTree code rolled up to its pinned tissue."}]},"is_pediatric":null,"model_systems":[],"cohort":{"n_cases":121,"n_samples":121,"n_aliquots":null,"n_files":null,"total_bytes":null,"n_tumor_cases":null,"n_normal_cases":null,"has_matched_normal":null,"demographics":{"sex":{"Male":67,"Female":54},"race":{},"ethnicity":{},"age_at_diagnosis_years":{},"vital_status":{},"country_or_region":{},"evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/skcm_broad","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:26:13.751586Z","snippet":null,"locator":"POST /clinical-data-counts/fetch","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},"evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/skcm_broad","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-18T02:48:40.878054Z","snippet":null,"locator":"field: allSampleCount","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},"assays":[{"modality":"targeted_dna","label":"Mutation calls (panel, exome or genome)","platform":null,"n_cases":null,"n_samples":121,"n_files":null,"data_levels":["processed matrix"],"access_tier":"open","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/skcm_broad","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-18T02:48:40.878054Z","snippet":null,"locator":"field: sequencedSampleCount","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]}],"clinical_variables":[{"name":"cbioportal:ONCOTREE_CODE","harmonized_name":"diagnoses.primary_diagnosis","label":"Oncotree Code","category":"diagnosis","n_nonmissing":121,"n_not_reported":0,"n_informative":121,"n_total":121,"coverage_pct":100.0,"populated_pct":100.0,"is_repeated":false,"example_values":["SKCM"],"unit":"samples","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/skcm_broad","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:26:13.542587Z","snippet":null,"locator":"POST /clinical-data-counts/fetch, attribute ONCOTREE_CODE; denominator is 121 samples","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"cbioportal:PRIMARY_SITE","harmonized_name":"diagnoses.tissue_or_organ_of_origin","label":"Primary Tumor Site","category":"diagnosis","n_nonmissing":84,"n_not_reported":0,"n_informative":84,"n_total":121,"coverage_pct":69.4,"populated_pct":69.4,"is_repeated":false,"example_values":["Trunk","Extremities","Back","Lower Leg","Back, Trunk Posterior Upper (Except Midline)","Thigh"],"unit":"samples","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/skcm_broad","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:26:13.542587Z","snippet":null,"locator":"POST /clinical-data-counts/fetch, attribute PRIMARY_SITE; denominator is 121 samples","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"cbioportal:SEX","harmonized_name":"demographic.sex_at_birth","label":"Sex","category":"demographic","n_nonmissing":121,"n_not_reported":0,"n_informative":121,"n_total":121,"coverage_pct":100.0,"populated_pct":100.0,"is_repeated":false,"example_values":["Male","Female"],"unit":"patients","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/skcm_broad","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:26:13.542587Z","snippet":null,"locator":"POST /clinical-data-counts/fetch, attribute SEX; denominator is 121 patients","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]}],"longitudinal":{"has_followup":null,"has_survival_endpoint":false,"survival_endpoints":[],"median_followup_months":null,"max_followup_months":null,"n_cases_with_followup":null,"has_serial_samples":null,"timepoints":[],"n_cases_with_serial":null,"has_treatment_response":false,"response_criteria":[],"evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/skcm_broad","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:26:13.751586Z","snippet":null,"locator":"derived from no time attribute","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},"access":{"tier":"open","open_components":["harmonized mutation, copy-number, expression and clinical files"],"controlled_components":[],"mechanism":"Processed data download from the cBioPortal study page or its public REST API; no account required. Primary raw data remain wherever the original investigators deposited them.","dua_url":null,"data_access_committee":null,"typical_turnaround":null,"embargo_until":null,"login_required":false,"citation_requirement":"Cite the original publication, and cite cBioPortal if the portal's harmonized files were used.","license":"Per-study terms; cBioPortal asks that the original study be cited","publication_policy_url":"https://www.cbioportal.org/faq","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/skcm_broad","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-18T02:48:40.878054Z","snippet":null,"locator":null,"confidence":"medium","reviewer":null,"reviewed_at":null,"note":null}]},"useful_for":[],"limitations":[],"inappropriate_uses":[],"primary_publications":[{"pmid":"22817889","pmcid":null,"doi":null,"title":null,"journal":null,"year":null,"authors_short":"Hodis et al. Cell 2012","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/22817889/","is_open_access":null,"citation_count":null,"evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/skcm_broad","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-18T02:48:40.878054Z","snippet":null,"locator":"field: pmid","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]}],"reuse":[],"reuse_metrics":{"n_candidates_screened":0,"n_by_tier":{},"n_by_tier_raw":{},"accession_precision":null,"n_citations_to_primary_publication":2084,"citation_to_reuse_ratio":null,"has_citable_accession":false,"n_verified_reuse":null,"n_reuse_examined":0,"n_independent_reuse":0,"n_nci_funded_reuse":0,"first_reuse_year":null,"latest_reuse_year":null,"years_since_release":null,"expected_reuse":null,"reuse_gap_index":null,"reuse_gap_percentile":null,"search_strategy_id":"epmc-index-v3","searched_at":"2026-09-20T18:07:48.729159Z","no_reuse_identified":false,"evidence":[{"method":"derived","source_url":null,"source_label":"reuse index","retrieved_at":"2026-09-20T18:07:48.729159Z","snippet":null,"locator":null,"confidence":"low","reviewer":null,"reviewed_at":null,"note":"This dataset has no accession specific enough to search for in the literature, so citation-based reuse cannot be measured. Absence of a count here is not evidence of absence of reuse."}]},"underexplored":{"is_underexplored":false,"basis":["Not assessed: this dataset has no accession specific enough for citation-based reuse tracing, so a shortfall cannot be measured."],"index_value":null,"percentile":null,"comparator_set":"rgi-huber-v2","evidence":[]},"grants":[{"core_project_num":"U24CA143845","project_num":null,"title":"The Cancer Genome Atlas Data Analysis Center","pi_names":["LYNDA CHIN","GAD A GETZ"],"agency_ic":"NCI","activity_code":"U24","fiscal_years":[2009,2010,2011,2012,2013,2014,2016],"award_amount_usd":15987999,"org_name":"BROAD INSTITUTE, INC.","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U24CA143845","role":"generation","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-18T02:48:44.992046Z","snippet":null,"locator":"PMID 22817889 reported under U24CA143845","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]},{"core_project_num":"T32CA009172","project_num":null,"title":"Physician Scientist Training in Cancer Research","pi_names":["Jennifer R Brown","James A. DeCaprio","ROBERT J MAYER","EMIL FREI"],"agency_ic":"NCI","activity_code":"T32","fiscal_years":[1985,1986,1987,1988,1989,1990,1991,1992,1993,1994,1995,1996,1997,1998,1999,2000,2001,2002,2003,2004,2005,2006,2007,2008,2009,2010,2011,2012,2013,2014,2015,2017,2018,2019,2020,2021,2022,2023,2024,2025,2026],"award_amount_usd":23693301,"org_name":"DANA-FARBER CANCER INST","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=T32CA009172","role":"generation","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-18T02:48:44.992046Z","snippet":null,"locator":"PMID 22817889 reported under T32CA009172","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]},{"core_project_num":"R33CA126674","project_num":null,"title":"High-throughput oncogene mutation detection in human cancer","pi_names":["Levi A. Garraway"],"agency_ic":"NCI","activity_code":"R33","fiscal_years":[2010,2011],"award_amount_usd":607563,"org_name":"DANA-FARBER CANCER INST","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=R33CA126674","role":"generation","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-18T02:48:44.992046Z","snippet":null,"locator":"PMID 22817889 reported under R33CA126674","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]},{"core_project_num":"R01CA093947","project_num":null,"title":"The genetic Basis of Melanoma Metastasis","pi_names":["LYNDA CHIN"],"agency_ic":"NCI","activity_code":"R01","fiscal_years":[2002,2003,2004,2005,2006,2007,2008,2009,2010,2011],"award_amount_usd":3587298,"org_name":"DANA-FARBER CANCER INST","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=R01CA093947","role":"generation","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-18T02:48:44.992046Z","snippet":null,"locator":"PMID 22817889 reported under R01CA093947","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]},{"core_project_num":"P50CA093459","project_num":null,"title":"The University of Texas M. D. Anderson Cancer Center SPORE in Melanoma","pi_names":["ELIZABETH A GRIMM","PATRICK HWU","JEFFREY E GERSHENWALD","MENASHE BARELI","JEFFREY E LEE","Amy Beth Heimberger","DONALD A BERRY","Rongfu Wang"],"agency_ic":"CA","activity_code":"P50","fiscal_years":[2004,2005,2006,2007,2008,2009,2010,2011,2012,2013,2014],"award_amount_usd":46465731,"org_name":"UNIVERSITY OF TX MD ANDERSON CAN CTR","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=P50CA093459","role":"generation","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-18T02:48:44.992046Z","snippet":null,"locator":"PMID 22817889 reported under P50CA093459","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]},{"core_project_num":"P30CA016672","project_num":null,"title":"Cancer Center Support Grant","pi_names":["PETER W PISTERS","Fernando J Benavides","FUNDA MERIC-BERNSTAM","Shannon Neville Westin","Kristy Brock","Vicki Huff"],"agency_ic":"NCI","activity_code":"P30","fiscal_years":[2025],"award_amount_usd":14035344,"org_name":"UNIVERSITY OF TX MD ANDERSON CAN CTR","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=P30CA016672","role":"generation","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-18T02:48:44.992046Z","snippet":null,"locator":"PMID 22817889 reported under P30CA016672","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]}],"access_steps":[{"order":1,"action":"Open the study in cBioPortal","detail":"Harmonized molecular and clinical files are open. Cite the original publication, and cite cBioPortal if the portal's harmonized files were used.","url":"https://www.cbioportal.org/study/summary?id=skcm_broad","requires":[],"est_time":"5 minutes","cli_snippet":null,"audience":"human","evidence":[{"method":"derived","source_url":"https://www.cbioportal.org/study/summary?id=skcm_broad","source_label":"cBioPortal access documentation","retrieved_at":"2026-09-21T12:30:59.433769Z","snippet":null,"locator":null,"confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Generated by applying the repository's documented access policy to this dataset's identifiers. It is not a reviewer's account of this dataset."}]},{"order":2,"action":"Download the whole study as a zip","detail":"The datasets page carries the staging files used by the portal.","url":"https://www.cbioportal.org/datasets","requires":[],"est_time":"minutes","cli_snippet":null,"audience":"human","evidence":[{"method":"derived","source_url":"https://www.cbioportal.org/datasets","source_label":"cBioPortal access documentation","retrieved_at":"2026-09-21T12:30:59.433772Z","snippet":null,"locator":null,"confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Generated by applying the repository's documented access policy to this dataset's identifiers. It is not a reviewer's account of this dataset."}]},{"order":3,"action":"Or pull the staging files with git-lfs","detail":"Study folders are named by study id under public/.","url":"https://github.com/cBioPortal/datahub","requires":[],"est_time":null,"cli_snippet":"git clone https://github.com/cBioPortal/datahub.git && cd datahub\ngit -c lfs.fetchexclude=\"\" lfs pull -I public/skcm_broad","audience":"human","evidence":[{"method":"derived","source_url":"https://github.com/cBioPortal/datahub","source_label":"cBioPortal access documentation","retrieved_at":"2026-09-21T12:30:59.433774Z","snippet":null,"locator":null,"confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Generated by applying the repository's documented access policy to this dataset's identifiers. It is not a reviewer's account of this dataset."}]},{"order":4,"action":"Read the study straight from the REST API","detail":"No key is required; pace requests when sweeping many studies.","url":"https://docs.cbioportal.org/web-api-and-clients/","requires":[],"est_time":null,"cli_snippet":"curl -s 'https://www.cbioportal.org/api/studies/skcm_broad/clinical-data?clinicalDataType=PATIENT&projection=SUMMARY'","audience":"agent","evidence":[{"method":"derived","source_url":"https://docs.cbioportal.org/web-api-and-clients/","source_label":"cBioPortal access documentation","retrieved_at":"2026-09-21T12:30:59.433776Z","snippet":null,"locator":null,"confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Generated by applying the repository's documented access policy to this dataset's identifiers. It is not a reviewer's account of this dataset."}]}],"analysis_examples":[],"agent_package":{"json_url":"/data/datasets/cbio-skcm-broad.json","jsonld_url":"/data/jsonld/cbio-skcm-broad.jsonld","croissant_url":"/data/croissant/cbio-skcm-broad.json","instructions_url":"/data/agent/cbio-skcm-broad.md","bundle_url":null,"mcp_resource_uri":null},"related_dataset_ids":[],"related_underexplored_ids":[],"review":{"status":"machine_only","reviewer":null,"reviewer_affiliation":null,"reviewed_at":null,"sections_reviewed":[],"open_questions":[],"notes":null},"verification":{"last_verified_at":null,"link_checks":[],"n_links_ok":0,"n_links_broken":0,"upstream_version_seen":null,"upstream_version_changed":false,"upstream_counts_seen":{},"upstream_drift":{},"notes":[]},"is_showcase":false,"completeness_score":35.7,"tags":["cbioportal","investigator-cohort","harmonized-for-reuse","nci-funded"],"search_text":null}