{"id":"pdc-cptac-aml-study","title":"CPTAC AML Study","short_title":"PDC000558","aliases":["CPTAC AML Study - Acetylome","CPTAC AML Study - Glycoproteome","CPTAC AML Study - Lipidome","CPTAC AML Study - Metabolome","CPTAC AML Study - Phosphoproteome","CPTAC AML Study - Proteome"],"summary":"Lipidomics is the scarcest measurement type in the entire corpus indexed here: three studies carry it, all within CPTAC, and this is the largest. Combined with metabolomics on the same 98 patients and four proteomic layers on all 164, it supports metabolic questions in leukaemia that cannot be posed anywhere else with measured rather than inferred data.\nAML is a disease where metabolic state has clear therapeutic relevance, and where measured lipid and metabolite data on primary patient samples are close to unobtainable. The barrier to reuse here is discoverability rather than access: everything is open, and nothing about the PDC catalog entry tells a metabolism researcher that this cohort exists.","one_liner":"164 acute myeloid leukaemias with proteome, phosphoproteome, acetylome and glycoproteome, plus lipidomics and metabolomics on 98 - one of only three NCI cohorts carrying lipidomic data, openly downloadable.","identifiers":[{"scheme":"pdc_study_id","value":"PDC000558","url":"https://pdc.cancer.gov/pdc/study/PDC000558","is_primary":true,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL allPrograms","retrieved_at":"2026-09-18T02:36:15.354973Z","snippet":null,"locator":"6 fraction studies grouped by cohort 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Measured lipidomics on primary AML at this scale is essentially unavailable elsewhere.","required_fields":[],"required_modalities":["lipidome","proteome"],"feasibility":"direct","approx_n":98,"statistical_note":"98 samples supports class-level comparison and well-powered subgroup contrasts only for common subtypes; rare fusion subgroups will have single-digit counts.","exemplar_pmid":null,"topics":["metabolism","leukaemia","scarce-measurement"],"evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908928Z","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. 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Not machine-generated."}]},{"question":"Can glycoproteomic features stratify AML in ways expression cannot?","rationale":"Glycoproteome on all 164 cases; cell-surface glycosylation is directly relevant to immunotherapy target selection in myeloid disease.","required_fields":[],"required_modalities":["glycoproteome","proteome"],"feasibility":"direct","approx_n":164,"statistical_note":null,"exemplar_pmid":null,"topics":["immunotherapy-targets","subtype-discovery"],"evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908928Z","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. 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What the API does serve is vital status and follow-up time for 99% of cases, which is enough for overall survival but not for anything risk-stratified.","severity":"blocking","affected_analyses":["Risk-stratified comparison","Treatment-response analysis"],"mitigation":"Obtain cytogenetics and treatment from the GDC CPTAC records or the CPTAC data portal and join on case identifier before drawing any risk-stratified conclusion.","evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908928Z","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. 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Not machine-generated."}]},{"kind":"batch_technical","statement":"Lipidomic and metabolomic measurements are especially sensitive to sample handling and storage, and batch information is not exposed in the study metadata.","severity":"major","affected_analyses":["Quantitative cross-sample comparison"],"mitigation":"Inspect for batch structure before interpreting; treat absolute levels with caution.","evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908928Z","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."}]},{"kind":"statistical_power","statement":"98 samples limits subgroup analysis in a disease with many molecularly defined subtypes.","severity":"major","affected_analyses":["Subtype-specific metabolic profiling"],"mitigation":"Pre-specify a small number of subtype contrasts.","evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908928Z","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."}]}],"inappropriate_uses":[{"statement":"Prognostic claims that do not adjust for cytogenetic risk.","reason":"Vital status and follow-up are present for 99% of cases, so a survival model will fit - but risk group is absent, and in AML it dominates prognosis.","evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908928Z","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."}]},{"statement":"Treatment-response or resistance analysis from these data.","reason":"A treatment record of any kind exists for 2% of the cohort and no agent is named.","evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908928Z","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."}]},{"statement":"Risk-group comparisons without obtaining cytogenetics separately.","reason":"Cytogenetic risk is the primary stratifier in AML and is not present here.","evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908928Z","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."}]}],"primary_publications":[],"reuse":[],"reuse_metrics":{"n_candidates_screened":0,"n_by_tier":{"t3_analyzed":0,"t2_declared":0,"t1_accession":0,"t0_mention":0},"n_by_tier_raw":{"t3_analyzed":0,"t2_declared":0,"t1_accession":0,"t0_mention":0},"accession_precision":{"token":"PDC000558","query":"METHODS:\"PDC000558\"","strategy_id":"epmc-literal-precision-v1","needs_correction":false,"precision":1.0,"precision_low":1.0,"precision_high":1.0,"n_sampled":0,"n_checked":0,"n_literal":0,"note":"No article was found under this accession, so there is no count to correct and no sample was drawn."},"n_citations_to_primary_publication":null,"citation_to_reuse_ratio":null,"has_citable_accession":true,"n_verified_reuse":0,"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":"2026-09-20T18:07:48.560617Z","no_reuse_identified":true,"evidence":[{"method":"derived","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search","source_label":"Europe PMC section-scoped hit counts","retrieved_at":"2026-09-20T18:07:48.560617Z","snippet":null,"locator":"tokens: PDC000558, PDC000560, PDC000562; queries: METHODS:\"PDC000558\"; DATA_AVAILABILITY:\"PDC000558\"; ACCESSION_ID:\"PDC000558\"; REF:\"PDC000558\"","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Index strategy epmc-index-v3. Every dataset is measured with the same single section field per tier, so the counts are comparable; the per-tier value is the largest across the dataset's own accessions, excluding any accession shared with other datasets in the corpus. No article was found under this accession, so there is no count to correct and no sample was drawn."}]},"underexplored":{"is_underexplored":false,"basis":["Not assessed: insufficient metadata to model expected reuse."],"index_value":null,"percentile":null,"comparator_set":"rgi-huber-v2","evidence":[]},"grants":[],"access_steps":[{"order":1,"action":"Download the lipidomic and metabolomic studies from PDC","detail":"Open access, no account required.","url":"https://pdc.cancer.gov/pdc/browse","requires":[],"est_time":"1 hour","cli_snippet":null,"audience":"human","evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908928Z","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."}]},{"order":2,"action":"Retrieve matching clinical and cytogenetic data from the GDC CPTAC records","detail":null,"url":"https://portal.gdc.cancer.gov/projects/CPTAC-3","requires":[],"est_time":"2-3 hours","cli_snippet":null,"audience":"human","evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908928Z","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."}]},{"order":3,"action":"Resolve the study UUID, then fetch the file manifest","detail":"filesPerStudy keys on the study UUID, not on PDC000558: called with the pdc_study_id it returns the right number of rows with every column null. 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It is not a reviewer's account of this dataset."}]}],"analysis_examples":[{"level":"intermediate","title":"Find and use the scarcest measurements in the portfolio","question":"Where can I find ubiquitylome, lipidome or metabolome data, and which cohorts carry several scarce layers on the same tumors?","problem":"Rare proteomic layers are scattered across study records and may cover different patients.","lesson":"Find genuinely scarce measurements and bound the complete-case cohort before designing the study.","figure":"Horizontal bars of the case count for each measured layer in the target cohort, with a dashed line at the smallest layer marking the ceiling on any analysis needing every layer at once.","featured":false,"inputs":["Public PDC GraphQL API, no account required","pandas"],"outputs":["Scarcity ranking of every analytical fraction","Cohorts carrying two or more scarce layers","Layer overlap bounding a complete-case analysis","Citation counts demonstrating that PDC accessions are not quoted","A chart of per-layer coverage with the complete-case ceiling marked"],"steps":["Enumerate every PDC study through the public GraphQL endpoint","Rank analytical fractions by number of studies","Group per-fraction studies back into biological cohorts","Report the per-layer case counts that bound a complete-case analysis","Query Europe PMC for each accession to show citation tracing is blind here"],"findings":["Across 255 PDC studies the proteome appears 109 times, the ubiquitylome 5 and the lipidome 3.","CPTAC STAD carries five scarce layers on 193 cases, but a complete-case analysis across all seven is capped at 153.","Each of the six STAD accessions returns one article, so accession tracing is blind to proteomic reuse."],"contributor":null,"contributor_url":null,"language":"python","est_runtime":"about a minute","est_compute":null,"workbook_path":"workbooks/python/04_scarce_modality_cptac.py","workbook_url":null,"notebook_download_url":"/data/notebooks/04_scarce_modality_cptac.ipynb","notebook_preview_url":"/data/notebooks/04_scarce_modality_cptac.png","notebook_preview_width":1045,"notebook_preview_height":616,"colab_url":null,"binder_url":null,"receipt":{"executed":true,"executed_at":"2026-09-21T00:42:56.314549Z","runtime_seconds":107.84,"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":"016ed4e8fdca36b1dd852eabc6e6ca96","data_retrieved_at":null,"error":null},"template_source":"04_scarce_modality_cptac","evidence":[{"method":"curated","source_url":null,"source_label":"CD2S workbook","retrieved_at":"2026-09-21T12:30:59.450333Z","snippet":null,"locator":"workbooks/python/04_scarce_modality_cptac.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/pdc-cptac-aml-study.json","jsonld_url":"/data/jsonld/pdc-cptac-aml-study.jsonld","croissant_url":"/data/croissant/pdc-cptac-aml-study.json","instructions_url":"/data/agent/pdc-cptac-aml-study.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"],"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":true,"completeness_score":85.7,"tags":["acetylome","glycoproteome","leukaemia","lipidome","lipidomics","metabolome","metabolomics","open-access","pdc","proteogenomics","rare-modality","scarce-modality","underexplored-candidate"],"search_text":null}