{"id":"cbio-brca-mapk-hp-msk-2021","title":"MAPK on resistance to anti-HER2 therapy for breast cancer (MSK, Nat Commun. 2022)","short_title":"brca_mapk_hp_msk_2021","aliases":["brca_mapk_hp_msk_2021"],"summary":"MSK-IMPACT targeted sequencing of 145 breast tumors with matched normal samples.","one_liner":null,"identifiers":[{"scheme":"cbioportal_study_id","value":"brca_mapk_hp_msk_2021","url":"https://www.cbioportal.org/study/summary?id=brca_mapk_hp_msk_2021","is_primary":true,"evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/brca_mapk_hp_msk_2021","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=brca_mapk_hp_msk_2021","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=brca_mapk_hp_msk_2021","cancer_types":[{"label":"Invasive Breast Carcinoma","ontology":"cBioPortal","code":"brca","url":null}],"primary_sites":["breast"],"subject":{"scope":"single","tissues":["BREAST"],"evidence":[{"method":"derived","source_url":null,"source_label":"cds.subjects","retrieved_at":null,"snippet":null,"locator":"cancer_types: Invasive Breast Carcinoma; primary_sites: breast","confidence":"high","reviewer":null,"reviewed_at":null,"note":"OncoTree code rolled up to its pinned tissue."}]},"is_pediatric":null,"model_systems":[],"cohort":{"n_cases":145,"n_samples":145,"n_aliquots":null,"n_files":null,"total_bytes":null,"n_tumor_cases":null,"n_normal_cases":null,"has_matched_normal":null,"demographics":{"sex":{"Female":145},"race":{"OTHER":5,"WHITE":96,"PT REFUSED TO ANSWER":13,"ASIAN-FAR EAST/INDIAN SUBCONT":13,"BLACK OR AFRICAN AMERICAN":16,"NO VALUE ENTERED":1},"ethnicity":{"South/Central America (except Brazil)":1,"Non-Spanish; Non-Hispanic":129,"Spanish  NOS; Hispanic NOS, Latino NOS":8,"Unknown whether Spanish or not":5,"Puerto Rican":1},"age_at_diagnosis_years":{},"vital_status":{"DECEASED":59,"LIVING":85},"country_or_region":{},"evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/brca_mapk_hp_msk_2021","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:25:54.789807Z","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/brca_mapk_hp_msk_2021","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":145,"n_files":null,"data_levels":["processed matrix"],"access_tier":"open","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/brca_mapk_hp_msk_2021","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":145,"n_files":null,"data_levels":["processed matrix"],"access_tier":"open","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/brca_mapk_hp_msk_2021","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":43,"data_levels":[],"access_tier":"open","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/brca_mapk_hp_msk_2021","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}]},{"modality":"treatment","label":"Structured treatment records","platform":null,"n_cases":36,"n_samples":null,"n_files":36,"data_levels":[],"access_tier":"open","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/brca_mapk_hp_msk_2021","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-18T02:48:40.878054Z","snippet":null,"locator":"field: treatmentCount","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]}],"clinical_variables":[{"name":"cbioportal:ETHNICITY","harmonized_name":"demographic.ethnicity","label":"Ethnicity Category","category":"demographic","n_nonmissing":144,"n_not_reported":5,"n_informative":139,"n_total":145,"coverage_pct":95.9,"populated_pct":99.3,"is_repeated":false,"example_values":["Non-Spanish; Non-Hispanic","Spanish  NOS; Hispanic NOS, Latino NOS","Unknown whether Spanish or not","South/Central America (except Brazil)","Puerto Rican"],"unit":"patients","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/brca_mapk_hp_msk_2021","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:25:54.026322Z","snippet":null,"locator":"POST /clinical-data-counts/fetch, attribute ETHNICITY; denominator is 145 patients","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"cbioportal:ONCOTREE_CODE","harmonized_name":"diagnoses.primary_diagnosis","label":"Oncotree Code","category":"diagnosis","n_nonmissing":145,"n_not_reported":0,"n_informative":145,"n_total":145,"coverage_pct":100.0,"populated_pct":100.0,"is_repeated":false,"example_values":["IDC","BRCA","BRCNOS","ILC","BRCANOS","MDLC"],"unit":"samples","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/brca_mapk_hp_msk_2021","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:25:54.026322Z","snippet":null,"locator":"POST /clinical-data-counts/fetch, attribute ONCOTREE_CODE; denominator is 145 samples","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"cbioportal:OS_STATUS","harmonized_name":"demographic.vital_status","label":"Overall Survival Status","category":"outcome","n_nonmissing":144,"n_not_reported":0,"n_informative":144,"n_total":145,"coverage_pct":99.3,"populated_pct":99.3,"is_repeated":false,"example_values":["LIVING","DECEASED"],"unit":"patients","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/brca_mapk_hp_msk_2021","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:25:54.026322Z","snippet":null,"locator":"POST /clinical-data-counts/fetch, attribute OS_STATUS; denominator is 145 patients","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"cbioportal:PFS_STATUS","harmonized_name":"diagnoses.progression_or_recurrence","label":"Progression Free Status","category":"outcome","n_nonmissing":135,"n_not_reported":0,"n_informative":135,"n_total":145,"coverage_pct":93.1,"populated_pct":93.1,"is_repeated":false,"example_values":["Recurred/Progressed","DiseaseFree"],"unit":"patients","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/brca_mapk_hp_msk_2021","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:25:54.026322Z","snippet":null,"locator":"POST /clinical-data-counts/fetch, attribute PFS_STATUS; denominator is 145 patients","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":145,"n_not_reported":0,"n_informative":145,"n_total":145,"coverage_pct":100.0,"populated_pct":100.0,"is_repeated":false,"example_values":["Breast"],"unit":"samples","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/brca_mapk_hp_msk_2021","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:25:54.026322Z","snippet":null,"locator":"POST /clinical-data-counts/fetch, attribute PRIMARY_SITE; denominator is 145 samples","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"cbioportal:RACE","harmonized_name":"demographic.race","label":"Race Category","category":"demographic","n_nonmissing":144,"n_not_reported":14,"n_informative":130,"n_total":145,"coverage_pct":89.7,"populated_pct":99.3,"is_repeated":false,"example_values":["WHITE","BLACK OR AFRICAN AMERICAN","PT REFUSED TO ANSWER","ASIAN-FAR EAST/INDIAN SUBCONT","OTHER","NO VALUE ENTERED"],"unit":"patients","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/brca_mapk_hp_msk_2021","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:25:54.026322Z","snippet":null,"locator":"POST /clinical-data-counts/fetch, attribute RACE; denominator is 145 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":145,"n_not_reported":0,"n_informative":145,"n_total":145,"coverage_pct":100.0,"populated_pct":100.0,"is_repeated":false,"example_values":["Female"],"unit":"patients","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/brca_mapk_hp_msk_2021","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:25:54.026322Z","snippet":null,"locator":"POST /clinical-data-counts/fetch, attribute SEX; denominator is 145 patients","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"cbioportal:OS_MONTHS","harmonized_name":"diagnoses.days_to_last_follow_up","label":"Overall Survival (Months)","category":"followup","n_nonmissing":138,"n_not_reported":null,"n_informative":null,"n_total":145,"coverage_pct":null,"populated_pct":95.2,"is_repeated":false,"example_values":[],"unit":"months","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/brca_mapk_hp_msk_2021","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:25:54.250140Z","snippet":null,"locator":"GET /studies/brca_mapk_hp_msk_2021/clinical-data?attributeId=OS_MONTHS; 138 of 145 patients carry a value","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"cbioportal:PFS_MONTHS","harmonized_name":"diagnoses.days_to_recurrence","label":"Progress Free Survival (Months)","category":"outcome","n_nonmissing":145,"n_not_reported":null,"n_informative":null,"n_total":145,"coverage_pct":null,"populated_pct":100.0,"is_repeated":false,"example_values":[],"unit":"months","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/brca_mapk_hp_msk_2021","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:25:54.492911Z","snippet":null,"locator":"GET /studies/brca_mapk_hp_msk_2021/clinical-data?attributeId=PFS_MONTHS; 145 of 145 patients carry a value","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"cbioportal:therapeutic_agents","harmonized_name":"diagnoses.treatments.therapeutic_agents","label":"Named therapeutic agents","category":"treatment","n_nonmissing":36,"n_not_reported":null,"n_informative":null,"n_total":145,"coverage_pct":null,"populated_pct":24.8,"is_repeated":false,"example_values":["Trastuzumab-PERTUZumab","Trastuzumab-PERTUZumab-Paclitaxel","Trastuzumab","Paclitaxel-Trastuzumab-PERTUZumab","Tamoxifen","Denosumab"],"unit":null,"evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/brca_mapk_hp_msk_2021","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:25:54.789807Z","snippet":null,"locator":"POST /treatments/patient-counts/fetch; 36 of 145 patients have at least one named agent","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]}],"longitudinal":{"has_followup":true,"has_survival_endpoint":true,"survival_endpoints":["overall survival","progression-free interval"],"median_followup_months":40.9,"max_followup_months":87.1,"n_cases_with_followup":138,"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/brca_mapk_hp_msk_2021","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:25:54.789807Z","snippet":null,"locator":"derived from OS_MONTHS, PFS_MONTHS; 59 deaths recorded","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/brca_mapk_hp_msk_2021","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":"34795269","pmcid":null,"doi":null,"title":null,"journal":null,"year":null,"authors_short":"Alison E et al.  Nat Commun 2022","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/34795269/","is_open_access":null,"citation_count":null,"evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/brca_mapk_hp_msk_2021","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":74,"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":"2026-09-20T18:07:48.626123Z","no_reuse_identified":false,"evidence":[{"method":"derived","source_url":null,"source_label":"reuse index","retrieved_at":"2026-09-20T18:07:48.626123Z","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":"R01CA249666","project_num":null,"title":"HER2-mediated delivery of cytotoxic agents in solid tumors","pi_names":["Sarat Chandarlapaty","Bob T Li"],"agency_ic":"NCI","activity_code":"R01","fiscal_years":[2021,2022,2023,2024],"award_amount_usd":2298246,"org_name":"SLOAN-KETTERING INST CAN RESEARCH","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=R01CA249666","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 34795269 reported under R01CA249666","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":"R01CA245069","project_num":null,"title":"Defining the impact of mutant oncogene zygosity","pi_names":["Sarat Chandarlapaty"],"agency_ic":"NCI","activity_code":"R01","fiscal_years":[2020,2021,2022,2023,2024],"award_amount_usd":1988000,"org_name":"SLOAN-KETTERING INST CAN RESEARCH","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=R01CA245069","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 34795269 reported under R01CA245069","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":"R01CA234361","project_num":null,"title":"Defining mechanisms of resistance to hormonal therapy in breast cancer","pi_names":["Sarat Chandarlapaty","David B. Solit"],"agency_ic":"NCI","activity_code":"R01","fiscal_years":[2019,2020,2021,2022,2023],"award_amount_usd":2037741,"org_name":"SLOAN-KETTERING INST CAN RESEARCH","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=R01CA234361","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 34795269 reported under R01CA234361","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":"P50CA247749","project_num":null,"title":"MSK SPORE in Genomic Instability in Breast Cancer","pi_names":["Simon N. Powell","Sohrab P Shah","Samuel F Bakhoum","Sarat Chandarlapaty","GEORGE PLITAS","Maurizio Scaltriti"],"agency_ic":"NCI","activity_code":"P50","fiscal_years":[2023,2024,2025],"award_amount_usd":9507091,"org_name":"SLOAN-KETTERING INST CAN RESEARCH","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=P50CA247749","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 34795269 reported under P50CA247749","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 34795269 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."}]}],"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=brca_mapk_hp_msk_2021","requires":[],"est_time":"5 minutes","cli_snippet":null,"audience":"human","evidence":[{"method":"derived","source_url":"https://www.cbioportal.org/study/summary?id=brca_mapk_hp_msk_2021","source_label":"cBioPortal access documentation","retrieved_at":"2026-09-21T12:30:59.432794Z","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":"2026-09-21T12:30:59.432796Z","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/brca_mapk_hp_msk_2021","audience":"human","evidence":[{"method":"derived","source_url":"https://github.com/cBioPortal/datahub","source_label":"cBioPortal access documentation","retrieved_at":"2026-09-21T12:30:59.432798Z","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/brca_mapk_hp_msk_2021/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":"2026-09-21T12:30:59.432800Z","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-brca-mapk-hp-msk-2021.json","jsonld_url":"/data/jsonld/cbio-brca-mapk-hp-msk-2021.jsonld","croissant_url":"/data/croissant/cbio-brca-mapk-hp-msk-2021.json","instructions_url":"/data/agent/cbio-brca-mapk-hp-msk-2021.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","treatment-annotated","nci-funded"],"search_text":null}