{"id":"idc-cptac-brca","title":"CPTAC-BRCA","short_title":"cptac_brca","aliases":["cptac_brca"],"summary":"This collection contains subjects from the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium CPTAC Breast Invasive Carcinoma cohort. CPTAC is a national effort to accelerate the understanding of the molecular basis of cancer through the application of large-scale proteome and genome analysis, or proteogenomics. Radiology and pathology images from CPTAC patients are being collected and made publicly available by The Cancer Imaging Archive to enable researchers to investigate cancer phenotypes which may correlate to corresponding proteomic, genomic and clinical data. Please see the DICOM converted Slide Microscopy images for the CPTAC-BRCA collection wiki page to learn more about the histopathology images and to obtain any supporting metadata for this collection.","one_liner":null,"identifiers":[{"scheme":"idc_collection_id","value":"cptac_brca","url":"https://portal.imaging.datacommons.cancer.gov/explore/?collection_id=cptac_brca","is_primary":true,"evidence":[{"method":"api","source_url":"https://api.imaging.datacommons.cancer.gov/v3/collections/cptac_brca","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":"CPTAC-BRCA","url":"https://www.cancerimagingarchive.net/collections/","is_primary":false,"evidence":[{"method":"api","source_url":"https://api.imaging.datacommons.cancer.gov/v3/collections/cptac_brca","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.12666759","url":null,"is_primary":false,"evidence":[{"method":"fulltext","source_url":"https://api.imaging.datacommons.cancer.gov/v3/collections/cptac_brca","source_label":"IDC collection description","retrieved_at":"2026-09-18T02:44:36.389375Z","snippet":"nd clinical data. Please see the DICOM converted Slide Microscopy images for the CPTAC-BRCA collection wiki page to learn more about the histopathology images and to obtain any supporting metadata f","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 Imaging Data Commons","short_name":"IDC","url":"https://portal.imaging.datacommons.cancer.gov","is_nci_crdc_node":true,"is_nih_repository":true},"additional_repositories":[],"program_name":"NCI Imaging Data Commons / The Cancer Imaging Archive","program_url":"https://imaging.datacommons.cancer.gov/","nci_program":"IDC","generating_institutions":[],"data_generation_funding_role":"unknown","version":null,"release_date":null,"last_upstream_update":null,"retrieved_at":"2026-09-18T02:44:36.389375Z","landing_page_url":"https://portal.imaging.datacommons.cancer.gov/explore/?collection_id=cptac_brca","cancer_types":[{"label":"Breast Cancer","ontology":null,"code":null,"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: Breast Cancer; primary_sites: Breast","confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Repository disease labels or primary sites mapped to pinned tissues."}]},"is_pediatric":null,"model_systems":[],"cohort":{"n_cases":198,"n_samples":null,"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":[]},"evidence":[{"method":"api","source_url":"https://api.imaging.datacommons.cancer.gov/v3/collections/cptac_brca","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}]},"assays":[{"modality":"radiology","label":"DICOM medical imaging","platform":null,"n_cases":198,"n_samples":null,"n_files":null,"data_levels":["DICOM series"],"access_tier":"open","evidence":[{"method":"api","source_url":"https://api.imaging.datacommons.cancer.gov/v3/collections/cptac_brca","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}]},{"modality":"clinical","label":"Clinical (accompanying data, per IDC supporting_data)","platform":null,"n_cases":null,"n_samples":null,"n_files":null,"data_levels":[],"access_tier":null,"evidence":[{"method":"api","source_url":"https://api.imaging.datacommons.cancer.gov/v3/collections/cptac_brca","source_label":"IDC v3 API /collections","retrieved_at":"2026-09-18T02:44:36.389375Z","snippet":null,"locator":"field: supporting_data","confidence":"medium","reviewer":null,"reviewed_at":null,"note":null}]},{"modality":"wgs","label":"Genomics (accompanying data, per IDC supporting_data)","platform":null,"n_cases":null,"n_samples":null,"n_files":null,"data_levels":[],"access_tier":null,"evidence":[{"method":"api","source_url":"https://api.imaging.datacommons.cancer.gov/v3/collections/cptac_brca","source_label":"IDC v3 API /collections","retrieved_at":"2026-09-18T02:44:36.389375Z","snippet":null,"locator":"field: supporting_data","confidence":"medium","reviewer":null,"reviewed_at":null,"note":null}]},{"modality":"proteome","label":"Proteomics (accompanying data, per IDC supporting_data)","platform":null,"n_cases":null,"n_samples":null,"n_files":null,"data_levels":[],"access_tier":null,"evidence":[{"method":"api","source_url":"https://api.imaging.datacommons.cancer.gov/v3/collections/cptac_brca","source_label":"IDC v3 API /collections","retrieved_at":"2026-09-18T02:44:36.389375Z","snippet":null,"locator":"field: supporting_data","confidence":"medium","reviewer":null,"reviewed_at":null,"note":null}]}],"clinical_variables":[],"longitudinal":{"has_followup":null,"has_survival_endpoint":null,"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":null,"response_criteria":[],"evidence":[]},"access":{"tier":"open","open_components":[],"controlled_components":[],"mechanism":"Public DICOM download from the IDC portal, its API, or the idc-index Python package; no account required for public collections.","dua_url":null,"data_access_committee":null,"typical_turnaround":null,"embargo_until":null,"login_required":false,"citation_requirement":"Cite the collection DOI and the IDC/TCIA data-citation guidance.","license":"Per-collection license, typically CC BY 3.0/4.0 or CC BY-NC","publication_policy_url":"https://www.cancerimagingarchive.net/data-usage-policies-and-restrictions/","evidence":[{"method":"api","source_url":"https://api.imaging.datacommons.cancer.gov/v3/collections/cptac_brca","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}]},"useful_for":[],"limitations":[{"kind":"missing_data","statement":"IDC serves no clinical table for this collection, so nothing about outcome, stage, treatment or demographics can be read from the repository. Any such variable would have to come from the originating trial or publication. The collection's own supporting_data field nevertheless lists clinical data, so the two disagree.","severity":"blocking","affected_analyses":["survival","treatment response","stage-adjusted modelling","analysis by race or ethnicity"],"mitigation":null,"evidence":[{"method":"api","source_url":"https://api.imaging.datacommons.cancer.gov/v3/clinical/tables","source_label":"IDC v3 API /clinical/tables","retrieved_at":"2026-09-19T03:20:46.830869Z","snippet":null,"locator":"collection_id=cptac_brca: no clinical table is served","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]}],"inappropriate_uses":[],"primary_publications":[],"reuse":[],"reuse_metrics":{"n_candidates_screened":0,"n_by_tier":{},"n_by_tier_raw":{},"accession_precision":null,"n_citations_to_primary_publication":null,"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":"2026-09-20T18:07:48.408718Z","no_reuse_identified":false,"evidence":[{"method":"derived","source_url":null,"source_label":"reuse index","retrieved_at":"2026-09-20T18:07:48.408718Z","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":[],"access_steps":[{"order":1,"action":"Open the collection in the IDC portal","detail":"Browse the series before downloading; imaging collections can be very large.","url":"https://portal.imaging.datacommons.cancer.gov/explore/?collection_id=cptac_brca","requires":[],"est_time":"5 minutes","cli_snippet":null,"audience":"human","evidence":[{"method":"derived","source_url":"https://portal.imaging.datacommons.cancer.gov/explore/?collection_id=cptac_brca","source_label":"IDC access documentation","retrieved_at":"2026-09-21T12:30:59.431944Z","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":"Read the collection's own licence","detail":"Per-collection license, typically CC BY 3.0/4.0 or CC BY-NC. IDC licences differ by collection.","url":"https://www.cancerimagingarchive.net/data-usage-policies-and-restrictions/","requires":[],"est_time":"5 minutes","cli_snippet":null,"audience":"human","evidence":[{"method":"derived","source_url":"https://www.cancerimagingarchive.net/data-usage-policies-and-restrictions/","source_label":"IDC access documentation","retrieved_at":"2026-09-21T12:30:59.431946Z","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":"Download with idc-index","detail":"The package resolves the collection to its buckets and pulls selected data.","url":"https://github.com/ImagingDataCommons/idc-index","requires":[],"est_time":"hours for a full collection","cli_snippet":"pip install idc-index\npython - <<'PY'\nfrom idc_index import IDCClient\nIDCClient().download_from_selection(collection_id=\"cptac_brca\", downloadDir=\".\")\nPY","audience":"human","evidence":[{"method":"derived","source_url":"https://github.com/ImagingDataCommons/idc-index","source_label":"IDC access documentation","retrieved_at":"2026-09-21T12:30:59.431948Z","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":"List the series before pulling pixels","detail":"List modality and size first so an agent can choose what to fetch.","url":"https://learn.canceridc.dev/","requires":[],"est_time":null,"cli_snippet":"python - <<'PY'\nfrom idc_index import IDCClient\ni = IDCClient().index\ns = i[i[\"collection_id\"] == \"cptac_brca\"]\nprint(len(s), \"series\", s[\"PatientID\"].nunique(), \"patients\",\n      round(s[\"series_size_MB\"].sum() / 1024, 1), \"GB\")\nprint(s[\"Modality\"].value_counts().to_dict())\nPY","audience":"agent","evidence":[{"method":"derived","source_url":"https://learn.canceridc.dev/","source_label":"IDC access documentation","retrieved_at":"2026-09-21T12:30:59.431950Z","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/idc-cptac-brca.json","jsonld_url":"/data/jsonld/idc-cptac-brca.jsonld","croissant_url":"/data/croissant/idc-cptac-brca.json","instructions_url":"/data/agent/idc-cptac-brca.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":16.1,"tags":["idc","imaging","imaging-genomics","imaging-proteomics"],"search_text":null}