{"id":"cbio-sarc-mskcc","title":"Sarcoma (MSKCC/Broad, Nat Genet 2010)","short_title":"sarc_mskcc","aliases":["sarc_mskcc"],"summary":"Sanger-sequenced 226 protein-coding genes (3,849 exons and adjacent intronic) on 207 samples (with 205 matched normals) encompassing 7 major sarcoma subtypes.","one_liner":null,"identifiers":[{"scheme":"cbioportal_study_id","value":"sarc_mskcc","url":"https://www.cbioportal.org/study/summary?id=sarc_mskcc","is_primary":true,"evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/sarc_mskcc","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=sarc_mskcc","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=sarc_mskcc","cancer_types":[{"label":"Soft Tissue","ontology":"cBioPortal","code":"soft_tissue","url":null}],"primary_sites":["tissue"],"subject":{"scope":"single","tissues":["SOFT_TISSUE"],"evidence":[{"method":"derived","source_url":null,"source_label":"cds.subjects","retrieved_at":null,"snippet":null,"locator":"cancer_types: Soft Tissue; primary_sites: tissue","confidence":"high","reviewer":null,"reviewed_at":null,"note":"OncoTree code rolled up to its pinned tissue."}]},"is_pediatric":null,"model_systems":[],"cohort":{"n_cases":207,"n_samples":207,"n_aliquots":null,"n_files":null,"total_bytes":null,"n_tumor_cases":null,"n_normal_cases":null,"has_matched_normal":null,"demographics":{"sex":{},"race":{},"ethnicity":{},"age_at_diagnosis_years":{},"vital_status":{},"country_or_region":{},"evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/sarc_mskcc","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:25:28.353767Z","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/sarc_mskcc","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":207,"n_files":null,"data_levels":["processed matrix"],"access_tier":"open","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/sarc_mskcc","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}]},{"modality":"copy_number","label":"Copy number alterations","platform":null,"n_cases":null,"n_samples":207,"n_files":null,"data_levels":["processed matrix"],"access_tier":"open","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/sarc_mskcc","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-18T02:48:40.878054Z","snippet":null,"locator":"field: cnaSampleCount","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"modality":"rna_seq","label":"Microarray expression","platform":null,"n_cases":null,"n_samples":89,"n_files":null,"data_levels":["processed matrix"],"access_tier":"open","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/sarc_mskcc","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-18T02:48:40.878054Z","snippet":null,"locator":"field: mrnaMicroarraySampleCount","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":207,"n_not_reported":0,"n_informative":207,"n_total":207,"coverage_pct":100.0,"populated_pct":100.0,"is_repeated":false,"example_values":["SARCNOS"],"unit":"samples","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/sarc_mskcc","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:25:28.110668Z","snippet":null,"locator":"POST /clinical-data-counts/fetch, attribute ONCOTREE_CODE; denominator is 207 samples","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/sarc_mskcc","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:25:28.353767Z","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/sarc_mskcc","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":"20601955","pmcid":null,"doi":null,"title":null,"journal":null,"year":null,"authors_short":"Barretina et al. Nat Genet 2010","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/20601955/","is_open_access":null,"citation_count":null,"evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/sarc_mskcc","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":599,"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":"2026-09-20T18:07:48.303867Z","no_reuse_identified":false,"evidence":[{"method":"derived","source_url":null,"source_label":"reuse index","retrieved_at":"2026-09-20T18:07:48.303867Z","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":"P50CA140146","project_num":null,"title":"Biostatistics/Bioinformatics Core","pi_names":["Li-Xuan Qin","SAMUEL SINGER","CRISTINA R ANTONESCU","Marc Ladanyi","GARY K SCHWARTZ","DAVID R SPRIGGS"],"agency_ic":"CA","activity_code":"P50","fiscal_years":[2010,2011,2012,2013,2014],"award_amount_usd":22226327,"org_name":"SLOAN-KETTERING INST CAN RESEARCH","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=P50CA140146","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 20601955 reported under P50CA140146","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":"P01CA047179","project_num":null,"title":"Laboratory & Clinical Develpmt of Cell Cycle Active Agents in the Treatmt of STS","pi_names":["GARY K SCHWARTZ","Marc Ladanyi","SAMUEL SINGER","CHRIS SANDER","CARLOS CORDON-CARDO","CRISTINA R ANTONESCU","Murray Brennan","DENIS H LEUNG","JOSEPH Rocco BERTINO","JAMES M WOODRUFF","ALAN N. HOUGHTON","EPHRAIM S CASPER","MURRAY F BRENNAN"],"agency_ic":"CA","activity_code":"P01","fiscal_years":[1989,1990,1991,1992,1993,1994,1996,1997,1998,2000,2001,2002,2003,2004,2006,2007,2008,2009,2010],"award_amount_usd":39685069,"org_name":"SLOAN-KETTERING INST CAN RESEARCH","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=P01CA047179","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 20601955 reported under P01CA047179","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":"K08CA122833","project_num":null,"title":"High-resolution genome-wide mapping of structural mutations in prostate cancer","pi_names":["RAMEEN BEROUKHIM"],"agency_ic":"NCI","activity_code":"K08","fiscal_years":[2007,2008,2009,2010,2011],"award_amount_usd":696600,"org_name":"DANA-FARBER CANCER INST","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=K08CA122833","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 20601955 reported under K08CA122833","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=sarc_mskcc","requires":[],"est_time":"5 minutes","cli_snippet":null,"audience":"human","evidence":[{"method":"derived","source_url":"https://www.cbioportal.org/study/summary?id=sarc_mskcc","source_label":"cBioPortal access documentation","retrieved_at":"2026-09-21T12:30:59.431743Z","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":"2026-09-21T12:30:59.431745Z","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/sarc_mskcc","audience":"human","evidence":[{"method":"derived","source_url":"https://github.com/cBioPortal/datahub","source_label":"cBioPortal access documentation","retrieved_at":"2026-09-21T12:30:59.431748Z","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/sarc_mskcc/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":"2026-09-21T12:30:59.431750Z","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-sarc-mskcc.json","jsonld_url":"/data/jsonld/cbio-sarc-mskcc.jsonld","croissant_url":"/data/croissant/cbio-sarc-mskcc.json","instructions_url":"/data/agent/cbio-sarc-mskcc.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}