{"id":"gdc-tcga-skcm","title":"Skin Cutaneous Melanoma","short_title":"TCGA-SKCM","aliases":["tcga_skcm"],"summary":"Melanoma is a cancer in a type of skin cells called melanocytes. Melanocyes are the cells that produce melanin, which colors the skin. When exposed to sun, these cells make more melanin, causing the skin to darken or tan. Melanoma can occur anywhere on the body and risk factors include fair complexion, family history of melanoma, and being exposed to natural or artificial sunlight over long periods of time. Melanoma is most often discovered because it has metastasized, or spread, to another organ, such as the lymph nodes. In many cases, the primary skin melanoma site is never found. Because of this challenge, TCGA is studying primarily metastatic cases (in contrast to other cancers selected for study, where metastatic cases are excluded). For 2011, it was estimated that there were 70,230 new cases of melanoma and 8,790 deaths from the disease. Please see the DICOM converted Slide Microscopy images for the TCGA-SKCM collection page to learn more about the histopathology images and to obtain any supporting metadata for this collection.","one_liner":null,"identifiers":[{"scheme":"gdc_project_id","value":"TCGA-SKCM","url":"https://portal.gdc.cancer.gov/projects/TCGA-SKCM","is_primary":true,"evidence":[{"method":"api","source_url":"https://api.gdc.cancer.gov/projects/TCGA-SKCM?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":"TCGA","url":null,"is_primary":false,"evidence":[{"method":"api","source_url":"https://api.gdc.cancer.gov/projects/TCGA-SKCM?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":"phs000178","url":"https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000178","is_primary":false,"evidence":[{"method":"api","source_url":"https://api.gdc.cancer.gov/projects/TCGA-SKCM?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":"idc_collection_id","value":"tcga_skcm","url":"https://portal.imaging.datacommons.cancer.gov/explore/?collection_id=tcga_skcm","is_primary":true,"evidence":[{"method":"api","source_url":"https://api.imaging.datacommons.cancer.gov/v3/collections/tcga_skcm","source_label":"IDC v3 API /collections","retrieved_at":"2026-09-18T02:44:36.389375Z","snippet":null,"locator":null,"confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"scheme":"tcia_collection","value":"TCGA-SKCM","url":"https://www.cancerimagingarchive.net/collections/","is_primary":false,"evidence":[{"method":"api","source_url":"https://api.imaging.datacommons.cancer.gov/v3/collections/tcga_skcm","source_label":"IDC v3 API /collections","retrieved_at":"2026-09-18T02:44:36.389375Z","snippet":null,"locator":null,"confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"scheme":"zenodo","value":"10.5281/zenodo.12690039","url":null,"is_primary":false,"evidence":[{"method":"fulltext","source_url":"https://api.imaging.datacommons.cancer.gov/v3/collections/tcga_skcm","source_label":"IDC collection description","retrieved_at":"2026-09-18T02:44:36.389375Z","snippet":"from the disease. Please see the DICOM converted Slide Microscopy images for the TCGA-SKCM collection page to learn more about the histopathology images and to obtain any supporting metadata for th","locator":"accession extracted from description prose","confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Cross-repository link recovered from prose; verify before relying on it."}]}],"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":[{"name":"NCI Imaging Data 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peritoneum","Skin","Small intestine","Spinal cord, cranial nerves, and other parts of central nervous system","Vagina","Vulva"],"subject":{"scope":"single","tissues":["SKIN"],"evidence":[{"method":"derived","source_url":null,"source_label":"cds.subjects","retrieved_at":null,"snippet":null,"locator":"cancer_types: Nevi and Melanomas; primary_sites: Adrenal gland, Anus and anal canal, Bones, joints and articular cartilage of other and unspecified sites, Brain, Breast, Bronchus and lung, Colon, Connective, subcutaneous and other soft tissues, Corpus uteri, Liver and intrahepatic bile ducts, Lymph nodes, Nasal cavity and middle ear, Other and ill-defined sites, Parotid gland, Retroperitoneum and peritoneum, Skin, Small intestine, Spinal cord, cranial nerves, and other parts of central nervous system, Vagina, Vulva","confidence":"high","reviewer":null,"reviewed_at":null,"note":"A two-thirds histology majority determined the 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This is a lower bound on availability."}]},"underexplored":{"is_underexplored":false,"basis":["Reuse is within the expected range for comparable datasets (index +1.48)."],"index_value":1.476,"percentile":82.6,"comparator_set":"132 datasets in this corpus with a citable accession and sufficient metadata","evidence":[{"method":"derived","source_url":null,"source_label":"Reuse Gap Index (rgi-huber-v2)","retrieved_at":"2026-09-21T02:11:22.976067Z","snippet":null,"locator":"Huber robust regression of log2(analyzing articles + 1) on cohort size, years available, modality breadth and access tier","confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Model, covariates and coefficients are published with the dataset export so the label can be recomputed or contested."}]},"grants":[{"core_project_num":"P30CA008748","project_num":null,"title":"Antitumor Assessment","pi_names":["Elisa de Stanchina","FRANCESCA M GANY","Scott Freeswick","Serge K Lyashchenko","Neeman Mohibullah","ALEX MACDONALD","SELWYN M VICKERS","Hongbiao Carl Lekaye","Michael Jason de la Cruz","Rui Gardner","PAUL J SABBATINI","YASUHIDE FURUTA","Thomas Michael Atkinson","MITHAT GONEN","Frances Weis-Garcia","Joachim Silber","Ouathek Ouerfelli","Ralph J. 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Resolved from RePORTER's publication index; only a repository-supplied or reviewer-supplied marker paper is used, never one this pipeline nominated itself."}]},{"core_project_num":"U24CA143867","project_num":null,"title":"Genome Characterization Center (GCC)","pi_names":["Stacey Gabriel","Matthew L. 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Resolved from RePORTER's publication index; only a repository-supplied or reviewer-supplied marker paper is used, never one this pipeline nominated itself."}]},{"core_project_num":"U24CA143866","project_num":null,"title":"Cancer transcriptome characterization using massively parallel DNA sequencing","pi_names":["Marco Antonio Marra"],"agency_ic":"CA","activity_code":"U24","fiscal_years":[2009,2010,2011,2012,2013,2014,2015],"award_amount_usd":10876224,"org_name":"BRITISH COLUMBIA CANCER AGENCY","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U24CA143866","role":"generation","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:21:14.041075Z","snippet":null,"locator":"PMID 26091043 (this dataset's marker paper) reported under U24CA143866","confidence":"high","reviewer":null,"reviewed_at":null,"note":"The award is credited on the dataset's own marker paper, so it paid to produce these data rather than to analyse them. 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Resolved from RePORTER's publication index; only a repository-supplied or reviewer-supplied marker paper is used, never one this pipeline nominated itself."}]},{"core_project_num":"U24CA143848","project_num":null,"title":"Gene Expression Patterns in Human Tumors Identified Using Transcript Sequencing","pi_names":["David N Hayes","CHARLES M PEROU"],"agency_ic":"CA","activity_code":"U24","fiscal_years":[2009,2010,2011,2012,2013,2014,2016],"award_amount_usd":20842970,"org_name":"UNIV OF NORTH CAROLINA CHAPEL HILL","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U24CA143848","role":"generation","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:21:14.041075Z","snippet":null,"locator":"PMID 26091043 (this dataset's marker paper) reported under U24CA143848","confidence":"high","reviewer":null,"reviewed_at":null,"note":"The award is credited on the dataset's own marker paper, so it paid to produce these data rather than to analyse them. 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Resolved from RePORTER's publication index; only a repository-supplied or reviewer-supplied marker paper is used, never one this pipeline nominated itself."}]},{"core_project_num":"U24CA143840","project_num":null,"title":"MSKCC Center for Translational Cancer Genomic Analysis","pi_names":["Marc Ladanyi","CHRIS SANDER"],"agency_ic":"CA","activity_code":"U24","fiscal_years":[2009,2010,2011,2012,2013,2014,2016],"award_amount_usd":11508790,"org_name":"SLOAN-KETTERING INST CAN RESEARCH","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U24CA143840","role":"generation","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:21:14.041075Z","snippet":null,"locator":"PMID 26091043 (this dataset's marker paper) reported under U24CA143840","confidence":"high","reviewer":null,"reviewed_at":null,"note":"The award is credited on the dataset's own marker paper, so it paid to produce these data rather than to analyse them. Resolved from RePORTER's publication index; only a repository-supplied or reviewer-supplied marker paper is used, never one this pipeline nominated itself."}]},{"core_project_num":"U24CA143835","project_num":null,"title":"Center for Systems Analysis of the Cancer Regulome","pi_names":["ILYA SHMULEVICH"],"agency_ic":"CA","activity_code":"U24","fiscal_years":[2009,2010,2011,2012,2013,2014,2016],"award_amount_usd":10612504,"org_name":"INSTITUTE FOR SYSTEMS BIOLOGY","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U24CA143835","role":"generation","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:21:14.041075Z","snippet":null,"locator":"PMID 26091043 (this dataset's marker paper) reported under U24CA143835","confidence":"high","reviewer":null,"reviewed_at":null,"note":"The award is credited on the dataset's own marker paper, so it paid to produce these data rather than to analyse them. Resolved from RePORTER's publication index; only a repository-supplied or reviewer-supplied marker paper is used, never one this pipeline nominated itself."}]},{"core_project_num":"U24CA143799","project_num":null,"title":"TCGA Data Analysis Center at Berkeley","pi_names":["PAUL T. 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Resolved from RePORTER's publication index; only a repository-supplied or reviewer-supplied marker paper is used, never one this pipeline nominated itself."}]},{"core_project_num":"R01CA163896","project_num":null,"title":"In vivo murine models of metastasis for therapeutic testing","pi_names":["NORMAN E SHARPLESS","Kwok Kin Wong"],"agency_ic":"NCI","activity_code":"R01","fiscal_years":[2012,2013,2014,2015,2016],"award_amount_usd":1977025,"org_name":"UNIV OF NORTH CAROLINA CHAPEL HILL","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=R01CA163896","role":"generation","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:21:14.041075Z","snippet":null,"locator":"PMID 26091043 (this dataset's marker paper) reported under R01CA163896","confidence":"high","reviewer":null,"reviewed_at":null,"note":"The award is credited on the dataset's own marker paper, so it paid to produce these data rather than to analyse them. Resolved from RePORTER's publication index; only a repository-supplied or reviewer-supplied marker paper is used, never one this pipeline nominated itself."}]}],"access_steps":[{"order":1,"action":"Open the project in the GDC Data Portal","detail":"Check the portal's current case and file counts before requesting anything; the cohort can change after this record was built.","url":"https://portal.gdc.cancer.gov/projects/TCGA-SKCM","requires":[],"est_time":"5 minutes","cli_snippet":null,"audience":"human","evidence":[{"method":"derived","source_url":"https://portal.gdc.cancer.gov/projects/TCGA-SKCM","source_label":"GDC access documentation","retrieved_at":"2026-09-21T12:30:59.429911Z","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. 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It is not a reviewer's account of this dataset."}]},{"order":3,"action":"Request controlled access through dbGaP","detail":"17,703 controlled-access files require an approved data access request. The request starts at dbGaP, not in the portal. The relevant study is phs000178.","url":"https://gdc.cancer.gov/access-data/obtaining-access-controlled-data","requires":["eRA Commons account","institutional signing official approval","dbGaP data access request for phs000178"],"est_time":"days to a few weeks after signing official approval","cli_snippet":null,"audience":"human","evidence":[{"method":"derived","source_url":"https://gdc.cancer.gov/access-data/obtaining-access-controlled-data","source_label":"GDC access documentation","retrieved_at":"2026-09-21T12:30:59.429916Z","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":"Download controlled files with your token","detail":"An approved request yields a token. The same manifest fetches nothing controlled without it.","url":"https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000178","requires":["approved dbGaP request","GDC authentication token"],"est_time":null,"cli_snippet":"gdc-client download -m gdc_manifest.txt -t gdc-user-token.txt","audience":"human","evidence":[{"method":"derived","source_url":"https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000178","source_label":"GDC access documentation","retrieved_at":"2026-09-21T12:30:59.429918Z","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. 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