{"id":"gdc-wcdt-mcrpc","title":"Genomic Characterization of Metastatic Castration Resistant Prostate Cancer","short_title":"WCDT-MCRPC","aliases":["WCDT-MCRPC"],"summary":"The West Coast Dream Team cohort is one of the few public resources that sequences metastatic castration-resistant prostate cancer tissue rather than primary tumor, which is what makes it valuable: the biology that drives lethal prostate cancer is not well represented in primary-tumor cohorts. All 101 cases carry whole genome sequencing with copy number and structural variant calls, and 99 carry RNA sequencing.\nThe clinical annotation is unusual in shape. Disease state is recorded with complete consistency - every case is AJCC stage IV, every case has progression or recurrence recorded as \"yes\", and every case's last known disease status is distant metastatic recurrence or progression. But vital status is \"unknown\" for all 101 cases, and no treatment field is populated. The cohort tells you precisely where these patients were in their disease course and nothing about what happened to them next.","one_liner":"101 metastatic castration-resistant prostate cancers with whole genome and RNA sequencing from metastatic biopsies - every case stage IV with documented progression, and no usable vital status.","identifiers":[{"scheme":"gdc_project_id","value":"WCDT-MCRPC","url":"https://portal.gdc.cancer.gov/projects/WCDT-MCRPC","is_primary":true,"evidence":[{"method":"api","source_url":"https://api.gdc.cancer.gov/projects/WCDT-MCRPC?expand=summary,summary.data_categories,summary.experimental_strategies,program","source_label":"GDC API 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Not machine-generated."}]},{"question":"Which transcriptional programs mark androgen receptor pathway independence and neuroendocrine transdifferentiation in treatment-resistant disease?","rationale":"RNA sequencing on 99 metastatic biopsies is the right substrate for AR-signaling and neuroendocrine scoring, and metastatic tissue is where these phenotypes actually occur.","required_fields":[],"required_modalities":["rna_seq"],"feasibility":"needs_access","approx_n":99,"statistical_note":"Biopsy site varies across the cohort and contributes substantially to expression variance; include site as a covariate or stratify.","exemplar_pmid":null,"topics":["treatment-resistance","transcriptional-programs","prostate"],"evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908682Z","snippet":null,"locator":null,"confidence":"high","reviewer":"CD2S project curation","reviewed_at":"2026-09-18","note":"Written by a named reviewer after reading the source documentation and the measured field coverage. Not machine-generated."}]},{"question":"How do structural variants and genome rearrangement patterns differ between metastatic sites?","rationale":"Structural variant calls exist for all 101 cases from whole genome rather than exome data, which is what makes rearrangement analysis credible here.","required_fields":[],"required_modalities":["structural_variant","wgs"],"feasibility":"needs_access","approx_n":101,"statistical_note":null,"exemplar_pmid":null,"topics":["genome-structure","metastasis"],"evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908682Z","snippet":null,"locator":null,"confidence":"high","reviewer":"CD2S project curation","reviewed_at":"2026-09-18","note":"Written by a named reviewer after reading the source documentation and the measured field coverage. Not machine-generated."}]},{"question":"Can expression or genomic features predict which metastatic biopsies come from patients with the most aggressive disease trajectory?","rationale":"This is the question most people want the cohort for, and it is the one the harmonized records cannot support. It is listed here to be explicit that it requires outcome data obtained separately.","required_fields":[],"required_modalities":["rna_seq","wgs","outcome"],"feasibility":"needs_linkage","approx_n":101,"statistical_note":"Not answerable from the GDC records alone. Vital status is \"unknown\" for every case; outcomes must come from the marker publication's supplement or a dbGaP phenotype file.","exemplar_pmid":null,"topics":["prognosis","prostate"],"evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908682Z","snippet":null,"locator":null,"confidence":"high","reviewer":"CD2S project curation","reviewed_at":"2026-09-18","note":"Written by a named reviewer after reading the source documentation and the measured field coverage. Not machine-generated."}]}],"limitations":[{"kind":"missing_data","statement":"Vital status is populated for all 101 cases and informative for none - every value is \"unknown\". 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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":"R01CA125612","project_num":null,"title":"Towards Understanding Prostate Cancer Heterogeneity","pi_names":["MARK A. 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It is not a reviewer's account of this dataset."}]},{"order":5,"action":"Pass the token when the agent needs controlled files","detail":"Without a token, an API query may return only the open subset. Compare returned counts with the record before treating them as the whole cohort.","url":"https://docs.gdc.cancer.gov/API/Users_Guide/Getting_Started/","requires":["GDC authentication token"],"est_time":null,"cli_snippet":"curl -H \"X-Auth-Token: $GDC_TOKEN\" https://api.gdc.cancer.gov/data/<file_id>","audience":"agent","evidence":[{"method":"derived","source_url":"https://docs.gdc.cancer.gov/API/Users_Guide/Getting_Started/","source_label":"GDC access documentation","retrieved_at":"2026-09-21T12:30:59.434927Z","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":[{"level":"beginner","title":"Audit whether this dataset can answer your question","question":"Which classes of analysis do this cohort's clinical records actually support, and which are ruled out before I request access?","problem":"A portal can list a field even when every value is an unusable non-answer.","lesson":"Decide whether the analysis is possible before requesting data or writing a protocol.","figure":"Horizontal bars for each probed clinical field, showing the share of cases the field is populated for against the smaller share that carries an informative value, with one-to-many fields marked as not derivable per case.","featured":true,"inputs":["A GDC project identifier","Network access to api.gdc.cancer.gov"],"outputs":["Per-field coverage table separating populated from informative values","Assay coverage as a percentage of the cohort","A yes/no verdict for six common analysis classes","A chart contrasting populated with informative coverage, field by field"],"steps":["Fetch project summary and per-assay case counts","Request facet counts for the clinical fields that gate common analyses","Separate absent fields from fields populated with non-answers","Flag one-to-many fields where per-case percentages cannot be inferred","Retrieve case-level fields and test whether a survival endpoint is derivable","Print a verdict for each analysis class"],"findings":["Four of the six analysis classes pass for CGCI-HTMCP-CC; stage-adjusted modelling and progression-free endpoints are blocked.","Vital status is informative for all 212 cases with 116 deaths, so an overall-survival endpoint is derivable.","Both stage fields and the progression field are informative for 0% of cases, which no case count can fix.","Four fields hold several records per case, so their per-case share cannot be inferred from a facet count at all."],"contributor":null,"contributor_url":null,"language":"python","est_runtime":"about a minute","est_compute":null,"workbook_path":"workbooks/python/01_can_i_answer_this.py","workbook_url":null,"notebook_download_url":"/data/notebooks/01_can_i_answer_this.ipynb","notebook_preview_url":"/data/notebooks/01_can_i_answer_this.png","notebook_preview_width":1021,"notebook_preview_height":813,"colab_url":null,"binder_url":null,"receipt":{"executed":true,"executed_at":"2026-09-21T00:40:59.561676Z","runtime_seconds":6.57,"executor":"nbclient / python 3.12.13 / Darwin 25.5.0 arm64","package_versions":{"python":"3.12.13","pandas":"3.0.6","numpy":"2.5.3","matplotlib":"3.11.2","lifelines":"0.30.0","scipy":"1.18.1","requests":"2.34.2","httpx":"0.28.1"},"n_cells":7,"n_cells_executed":7,"output_hash":"dc14b4c93e7e9d6aff322ff2d0de47b8","data_retrieved_at":null,"error":null},"template_source":"01_can_i_answer_this","evidence":[{"method":"curated","source_url":null,"source_label":"CD2S workbook","retrieved_at":"2026-09-21T12:30:59.450269Z","snippet":null,"locator":"workbooks/python/01_can_i_answer_this.py","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Executed end to end against the live public APIs; the receipt records when, with which package versions and how long it took."}]}],"agent_package":{"json_url":"/data/datasets/gdc-wcdt-mcrpc.json","jsonld_url":"/data/jsonld/gdc-wcdt-mcrpc.jsonld","croissant_url":"/data/croissant/gdc-wcdt-mcrpc.json","instructions_url":"/data/agent/gdc-wcdt-mcrpc.md","bundle_url":null,"mcp_resource_uri":null},"related_dataset_ids":[],"related_underexplored_ids":[],"review":{"status":"project_curated","reviewer":"CD2S project curation","reviewer_affiliation":null,"reviewed_at":"2026-09-18","sections_reviewed":["useful_for","limitations","inappropriate_uses","access_steps","primary_publications"],"open_questions":["The PNAS marker paper reports clinical outcomes for this cohort, but vital status is \"unknown\" for all 101 cases in the GDC harmonized records. Confirm whether outcome data are obtainable from the supplementary material or only under dbGaP terms."],"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":true,"completeness_score":100.0,"tags":["cautionary","gdc","metastatic","prostate","released","treatment-resistant","wcdt"],"search_text":null}