{"id":"cbio-bladder-msk-2023","title":"Bladder Cancer (MSK, Clin Cancer Res 2023)","short_title":"bladder_msk_2023","aliases":["bladder_msk_2023"],"summary":"Targeted sequencing of 526 bladder tumors and their matched normals via MSK-IMPACT.","one_liner":null,"identifiers":[{"scheme":"cbioportal_study_id","value":"bladder_msk_2023","url":"https://www.cbioportal.org/study/summary?id=bladder_msk_2023","is_primary":true,"evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/bladder_msk_2023","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=bladder_msk_2023","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=bladder_msk_2023","cancer_types":[{"label":"Bladder/Urinary Tract","ontology":"cBioPortal","code":"bladder","url":null}],"primary_sites":["tissue"],"subject":{"scope":"single","tissues":["BLADDER"],"evidence":[{"method":"derived","source_url":null,"source_label":"cds.subjects","retrieved_at":null,"snippet":null,"locator":"cancer_types: Bladder/Urinary Tract; 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":400,"n_samples":526,"n_aliquots":null,"n_files":null,"total_bytes":null,"n_tumor_cases":null,"n_normal_cases":null,"has_matched_normal":null,"demographics":{"sex":{"Male":265,"Female":126},"race":{"Refused to Answer":3,"Unknown":17,"Caucasian":334,"African-american":12,"Hispanic":13,"Asian":11,"Other":1},"ethnicity":{},"age_at_diagnosis_years":{},"vital_status":{},"country_or_region":{},"evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/bladder_msk_2023","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:24:35.889721Z","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/bladder_msk_2023","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":526,"n_files":null,"data_levels":["processed matrix"],"access_tier":"open","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/bladder_msk_2023","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":526,"n_files":null,"data_levels":["processed matrix"],"access_tier":"open","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/bladder_msk_2023","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":"structural_variant","label":"Structural variants / fusions","platform":null,"n_cases":null,"n_samples":null,"n_files":104,"data_levels":[],"access_tier":"open","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/bladder_msk_2023","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-18T02:48:40.878054Z","snippet":null,"locator":"field: structuralVariantCount","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":526,"n_not_reported":0,"n_informative":526,"n_total":526,"coverage_pct":100.0,"populated_pct":100.0,"is_repeated":false,"example_values":["BLCA","UTUC","UCU","BLADDER"],"unit":"samples","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/bladder_msk_2023","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:24:35.633844Z","snippet":null,"locator":"POST /clinical-data-counts/fetch, attribute ONCOTREE_CODE; denominator is 526 samples","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"cbioportal:RACE","harmonized_name":"demographic.race","label":"Race","category":"demographic","n_nonmissing":391,"n_not_reported":20,"n_informative":371,"n_total":400,"coverage_pct":92.8,"populated_pct":97.8,"is_repeated":false,"example_values":["Caucasian","Unknown","Hispanic","African-american","Asian","Refused to Answer"],"unit":"patients","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/bladder_msk_2023","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:24:35.633844Z","snippet":null,"locator":"POST /clinical-data-counts/fetch, attribute RACE; denominator is 400 patients","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"cbioportal:SEX","harmonized_name":"demographic.sex_at_birth","label":"Sex","category":"demographic","n_nonmissing":391,"n_not_reported":0,"n_informative":391,"n_total":400,"coverage_pct":97.8,"populated_pct":97.8,"is_repeated":false,"example_values":["Male","Female"],"unit":"patients","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/bladder_msk_2023","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:24:35.633844Z","snippet":null,"locator":"POST /clinical-data-counts/fetch, attribute SEX; denominator is 400 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/bladder_msk_2023","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:24:35.889721Z","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/bladder_msk_2023","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":"37682528","pmcid":null,"doi":null,"title":null,"journal":null,"year":null,"authors_short":"Guercio et al. Clin Cancer Res. 2023","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/37682528/","is_open_access":null,"citation_count":null,"evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/bladder_msk_2023","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":63,"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":"2026-09-20T18:07:31.360260Z","no_reuse_identified":false,"evidence":[{"method":"derived","source_url":null,"source_label":"reuse index","retrieved_at":"2026-09-20T18:07:31.360260Z","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":"T32CA082088","project_num":null,"title":"T32 Urologic Oncology Research Training Grant","pi_names":["Brett Stewart Carver","PETER T SCARDINO"],"agency_ic":"NCI","activity_code":"T32","fiscal_years":[1999,2000,2001,2002,2003,2005,2006,2007,2008,2009,2010,2011,2012,2013,2014,2015,2016,2017,2018,2019,2020,2021,2022,2023,2024,2025],"award_amount_usd":6938101,"org_name":"SLOAN-KETTERING INST CAN RESEARCH","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=T32CA082088","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 37682528 reported under T32CA082088","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":"T32CA009207","project_num":null,"title":"Investigational Cancer Therapeutics Training Program (ICTTP)","pi_names":["Omar Abdel-Wahab","Alexander Drilon","Gopa Iyer","Dean F. Bajorin","Jedd D. Wolchok","MARK G. KRIS","GEORGE J. BOSL","JOHN MENDELSOHN","RAKESH KUMAR","BAYARD D CLARKSON"],"agency_ic":"NCI","activity_code":"T32","fiscal_years":[1985,1986,1987,1988,1989,1990,1991,1992,1993,1994,1995,1996,1997,1998,1999,2000,2001,2002,2003,2004,2005,2006,2007,2008,2009,2010,2011,2014,2015,2016,2017,2018,2019,2020,2021,2022,2023,2024,2025,2026],"award_amount_usd":20148739,"org_name":"SLOAN-KETTERING INST CAN RESEARCH","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=T32CA009207","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 37682528 reported under T32CA009207","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":"P50CA221745","project_num":null,"title":"Biospecimen Repository Core","pi_names":["Hikmat Al-Ahmadie","David B. Solit","Dean F. Bajorin","Jonathan Eric Rosenberg","Irina Ostrovnaya"],"agency_ic":"NCI","activity_code":"P50","fiscal_years":[2024],"award_amount_usd":1792550,"org_name":"SLOAN-KETTERING INST CAN RESEARCH","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=P50CA221745","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 37682528 reported under P50CA221745","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":"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. Garippa","Justin Cross","NEIL SCOTT LIPMAN","Nicholas D Socci","Charles M. Rudin","Xiuyan Wang","Mara Monetti","Murray Tipping","Gouri Nanjangud"],"agency_ic":"NCI","activity_code":"P30","fiscal_years":[2025,2026],"award_amount_usd":48363092,"org_name":"SLOAN-KETTERING INST CAN RESEARCH","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=P30CA008748","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 37682528 reported under P30CA008748","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":"P01CA221757","project_num":null,"title":"Modeling bladder cancer pathogenesis and tumor evolution","pi_names":["Cory Abate-Shen","David B. Solit","MICHAEL M. SHEN","Hikmat Al-Ahmadie"],"agency_ic":"CA","activity_code":"P01","fiscal_years":[2018,2019,2020,2021,2022],"award_amount_usd":17111082,"org_name":"COLUMBIA UNIVERSITY HEALTH SCIENCES","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=P01CA221757","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 37682528 reported under P01CA221757","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=bladder_msk_2023","requires":[],"est_time":"5 minutes","cli_snippet":null,"audience":"human","evidence":[{"method":"derived","source_url":"https://www.cbioportal.org/study/summary?id=bladder_msk_2023","source_label":"cBioPortal access documentation","retrieved_at":"2026-09-21T12:30:59.430207Z","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":"2026-09-21T12:30:59.430209Z","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/bladder_msk_2023","audience":"human","evidence":[{"method":"derived","source_url":"https://github.com/cBioPortal/datahub","source_label":"cBioPortal access documentation","retrieved_at":"2026-09-21T12:30:59.430211Z","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/bladder_msk_2023/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":"2026-09-21T12:30:59.430213Z","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-bladder-msk-2023.json","jsonld_url":"/data/jsonld/cbio-bladder-msk-2023.jsonld","croissant_url":"/data/croissant/cbio-bladder-msk-2023.json","instructions_url":"/data/agent/cbio-bladder-msk-2023.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}