{"id":"pdc-cptac-luad-confirmatory-study","title":"CPTAC LUAD Confirmatory Study","short_title":"PDC000491","aliases":["CPTAC LUAD Confirmatory Study - Acetylome","CPTAC LUAD Confirmatory Study - Phosphoproteome","CPTAC LUAD Confirmatory Study - Proteome","CPTAC LUAD Confirmatory Study - Ubiquitylome"],"summary":null,"one_liner":null,"identifiers":[{"scheme":"pdc_study_id","value":"PDC000491","url":"https://pdc.cancer.gov/pdc/study/PDC000491","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":"4 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"scheme":"pdc_study_id","value":"PDC000490","url":"https://pdc.cancer.gov/pdc/study/PDC000490","is_primary":false,"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":"4 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"scheme":"pdc_study_id","value":"PDC000489","url":"https://pdc.cancer.gov/pdc/study/PDC000489","is_primary":false,"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":"4 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"scheme":"pdc_study_id","value":"PDC000492","url":"https://pdc.cancer.gov/pdc/study/PDC000492","is_primary":false,"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":"4 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]}],"repository":{"name":"NCI Proteomic Data Commons","short_name":"PDC","url":"https://pdc.cancer.gov","is_nci_crdc_node":true,"is_nih_repository":true},"additional_repositories":[],"program_name":"Clinical Proteomic Tumor Analysis Consortium","program_url":"https://pdc.cancer.gov/pdc/browse","nci_program":"Clinical Proteomic Tumor Analysis Consortium","generating_institutions":[],"data_generation_funding_role":"generation","version":null,"release_date":"2025-01-01","last_upstream_update":null,"retrieved_at":"2026-09-18T02:36:15.354973Z","landing_page_url":"https://pdc.cancer.gov/pdc/study/PDC000491","cancer_types":[{"label":"Lung Adenocarcinoma","ontology":null,"code":null,"url":null}],"primary_sites":["Bronchus and lung"],"subject":{"scope":"single","tissues":["LUNG"],"evidence":[{"method":"derived","source_url":null,"source_label":"cds.subjects","retrieved_at":null,"snippet":null,"locator":"cancer_types: Lung Adenocarcinoma; primary_sites: Bronchus and lung","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":131,"n_samples":null,"n_aliquots":916,"n_files":null,"total_bytes":null,"n_tumor_cases":null,"n_normal_cases":null,"has_matched_normal":null,"demographics":{"sex":{"female":47,"not reported":11,"male":73},"race":{"other":15,"white":56,"not reported":11,"asian":44,"black or african american":5},"ethnicity":{"not reported":98,"not hispanic or latino":33},"age_at_diagnosis_years":{"n":117.0,"min":36.8,"median":64.4,"max":79.4},"vital_status":{"Alive":76,"Dead":27,"Not Reported":18},"country_or_region":{},"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:52.545628Z","snippet":null,"locator":"PDC000491: clinicalPerStudy demographic fields","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},"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":"4 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},"assays":[{"modality":"acetylproteome","label":"Acetylome mass spectrometry (TMT11 / DDA)","platform":"TMT11","n_cases":131,"n_samples":245,"n_files":null,"data_levels":["raw","peptide/protein matrix"],"access_tier":"open","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":"4 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"modality":"phosphoproteome","label":"Phosphoproteome mass spectrometry (TMT11 / DDA)","platform":"TMT11","n_cases":131,"n_samples":245,"n_files":null,"data_levels":["raw","peptide/protein matrix"],"access_tier":"open","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":"4 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"modality":"proteome","label":"Proteome mass spectrometry (TMT11 / DDA)","platform":"TMT11","n_cases":131,"n_samples":245,"n_files":null,"data_levels":["raw","peptide/protein matrix"],"access_tier":"open","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":"4 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"modality":"ubiquitylome","label":"Ubiquitylome mass spectrometry (TMT11 / DDA)","platform":"TMT11","n_cases":96,"n_samples":181,"n_files":null,"data_levels":["raw","peptide/protein matrix"],"access_tier":"open","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":"4 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]}],"clinical_variables":[{"name":"pdc:vital_status","harmonized_name":"demographic.vital_status","label":"Vital status","category":"outcome","n_nonmissing":121,"n_not_reported":18,"n_informative":103,"n_total":131,"coverage_pct":78.6,"populated_pct":92.4,"is_repeated":false,"example_values":["Alive","Dead","Not Reported"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:52.545628Z","snippet":null,"locator":"PDC000491: clinicalPerStudy, field vital_status over 131 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:cause_of_death","harmonized_name":"demographic.cause_of_death","label":"Cause of death","category":"outcome","n_nonmissing":27,"n_not_reported":13,"n_informative":14,"n_total":131,"coverage_pct":10.7,"populated_pct":20.6,"is_repeated":false,"example_values":["Unknown","Cancer Related","Cardiovascular Disorder, NOS","Not Cancer Related"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:52.545628Z","snippet":null,"locator":"PDC000491: clinicalPerStudy, field cause_of_death over 131 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:race","harmonized_name":"demographic.race","label":"Race","category":"demographic","n_nonmissing":131,"n_not_reported":11,"n_informative":120,"n_total":131,"coverage_pct":91.6,"populated_pct":100.0,"is_repeated":false,"example_values":["white","asian","other","not reported","black or african american"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:52.545628Z","snippet":null,"locator":"PDC000491: clinicalPerStudy, field race over 131 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:ethnicity","harmonized_name":"demographic.ethnicity","label":"Ethnicity","category":"demographic","n_nonmissing":131,"n_not_reported":98,"n_informative":33,"n_total":131,"coverage_pct":25.2,"populated_pct":100.0,"is_repeated":false,"example_values":["not reported","not hispanic or latino"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:52.545628Z","snippet":null,"locator":"PDC000491: clinicalPerStudy, field ethnicity over 131 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:gender","harmonized_name":"demographic.sex_at_birth","label":"Sex at birth (gender)","category":"demographic","n_nonmissing":131,"n_not_reported":11,"n_informative":120,"n_total":131,"coverage_pct":91.6,"populated_pct":100.0,"is_repeated":false,"example_values":["male","female","not reported"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:52.545628Z","snippet":null,"locator":"PDC000491: clinicalPerStudy, field gender over 131 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:morphology","harmonized_name":"diagnoses.morphology","label":"Morphology (ICD-O)","category":"pathology","n_nonmissing":131,"n_not_reported":11,"n_informative":120,"n_total":131,"coverage_pct":91.6,"populated_pct":100.0,"is_repeated":false,"example_values":["8140/3","Not Reported","8070/3"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:52.545628Z","snippet":null,"locator":"PDC000491: clinicalPerStudy, field morphology over 131 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:primary_diagnosis","harmonized_name":"diagnoses.primary_diagnosis","label":"Primary diagnosis","category":"diagnosis","n_nonmissing":131,"n_not_reported":11,"n_informative":120,"n_total":131,"coverage_pct":91.6,"populated_pct":100.0,"is_repeated":false,"example_values":["Adenocarcinoma, NOS","Not Reported","Squamous cell carcinoma, NOS"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:52.545628Z","snippet":null,"locator":"PDC000491: clinicalPerStudy, field primary_diagnosis over 131 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:tissue_or_organ_of_origin","harmonized_name":"diagnoses.tissue_or_organ_of_origin","label":"Tissue or organ of origin","category":"diagnosis","n_nonmissing":131,"n_not_reported":11,"n_informative":120,"n_total":131,"coverage_pct":91.6,"populated_pct":100.0,"is_repeated":false,"example_values":["Lung, NOS","Not Reported"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:52.545628Z","snippet":null,"locator":"PDC000491: clinicalPerStudy, field tissue_or_organ_of_origin over 131 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:tumor_grade","harmonized_name":"diagnoses.tumor_grade","label":"Tumor grade","category":"pathology","n_nonmissing":131,"n_not_reported":11,"n_informative":120,"n_total":131,"coverage_pct":91.6,"populated_pct":100.0,"is_repeated":false,"example_values":["G2","G3","G1","Not Reported","GX"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:52.545628Z","snippet":null,"locator":"PDC000491: clinicalPerStudy, field tumor_grade over 131 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:ajcc_pathologic_stage","harmonized_name":"diagnoses.ajcc_pathologic_stage","label":"AJCC pathologic stage","category":"staging","n_nonmissing":120,"n_not_reported":3,"n_informative":117,"n_total":131,"coverage_pct":89.3,"populated_pct":91.6,"is_repeated":false,"example_values":["Stage IIIA","Stage IB","Stage IA","Stage IIA","Stage IIB","Stage IA3"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:52.545628Z","snippet":null,"locator":"PDC000491: clinicalPerStudy, field ajcc_pathologic_stage over 131 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:ajcc_clinical_stage","harmonized_name":"diagnoses.ajcc_clinical_stage","label":"AJCC clinical stage","category":"staging","n_nonmissing":0,"n_not_reported":0,"n_informative":0,"n_total":131,"coverage_pct":0.0,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:52.545628Z","snippet":null,"locator":"PDC000491: clinicalPerStudy, field ajcc_clinical_stage over 131 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:tumor_stage","harmonized_name":"diagnoses.ajcc_pathologic_stage","label":"AJCC pathologic stage (tumor_stage)","category":"staging","n_nonmissing":131,"n_not_reported":131,"n_informative":0,"n_total":131,"coverage_pct":0.0,"populated_pct":100.0,"is_repeated":false,"example_values":["Not Reported"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:52.545628Z","snippet":null,"locator":"PDC000491: clinicalPerStudy, field tumor_stage over 131 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:progression_or_recurrence","harmonized_name":"diagnoses.progression_or_recurrence","label":"Progression or recurrence","category":"outcome","n_nonmissing":0,"n_not_reported":0,"n_informative":0,"n_total":131,"coverage_pct":0.0,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:52.545628Z","snippet":null,"locator":"PDC000491: clinicalPerStudy, field progression_or_recurrence over 131 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:last_known_disease_status","harmonized_name":"diagnoses.last_known_disease_status","label":"Last known disease status","category":"outcome","n_nonmissing":0,"n_not_reported":0,"n_informative":0,"n_total":131,"coverage_pct":0.0,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:52.545628Z","snippet":null,"locator":"PDC000491: clinicalPerStudy, field last_known_disease_status over 131 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:prior_treatment","harmonized_name":"diagnoses.prior_treatment","label":"Prior treatment","category":"treatment","n_nonmissing":0,"n_not_reported":0,"n_informative":0,"n_total":131,"coverage_pct":0.0,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:52.545628Z","snippet":null,"locator":"PDC000491: clinicalPerStudy, field prior_treatment over 131 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:prior_malignancy","harmonized_name":"diagnoses.prior_malignancy","label":"Prior malignancy","category":"diagnosis","n_nonmissing":0,"n_not_reported":0,"n_informative":0,"n_total":131,"coverage_pct":0.0,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:52.545628Z","snippet":null,"locator":"PDC000491: clinicalPerStudy, field prior_malignancy over 131 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:synchronous_malignancy","harmonized_name":"diagnoses.synchronous_malignancy","label":"Synchronous malignancy","category":"diagnosis","n_nonmissing":0,"n_not_reported":0,"n_informative":0,"n_total":131,"coverage_pct":0.0,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:52.545628Z","snippet":null,"locator":"PDC000491: clinicalPerStudy, field synchronous_malignancy over 131 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:classification_of_tumor","harmonized_name":"diagnoses.classification_of_tumor","label":"Classification of tumor","category":"pathology","n_nonmissing":0,"n_not_reported":0,"n_informative":0,"n_total":131,"coverage_pct":0.0,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:52.545628Z","snippet":null,"locator":"PDC000491: clinicalPerStudy, field classification_of_tumor over 131 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:age_at_diagnosis","harmonized_name":"diagnoses.age_at_diagnosis","label":"Age at diagnosis","category":"demographic","n_nonmissing":117,"n_not_reported":null,"n_informative":null,"n_total":131,"coverage_pct":null,"populated_pct":89.3,"is_repeated":false,"example_values":[],"unit":"days","evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:52.545628Z","snippet":null,"locator":"PDC000491: clinicalPerStudy, field age_at_diagnosis; a value for 117 of 131 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:days_to_death","harmonized_name":"demographic.days_to_death","label":"Days to death","category":"outcome","n_nonmissing":27,"n_not_reported":null,"n_informative":null,"n_total":131,"coverage_pct":null,"populated_pct":20.6,"is_repeated":false,"example_values":[],"unit":"days","evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:52.545628Z","snippet":null,"locator":"PDC000491: clinicalPerStudy, field days_to_death; a value for 27 of 131 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:days_to_last_follow_up","harmonized_name":"diagnoses.days_to_last_follow_up","label":"Days to last follow-up","category":"followup","n_nonmissing":103,"n_not_reported":null,"n_informative":null,"n_total":131,"coverage_pct":null,"populated_pct":78.6,"is_repeated":false,"example_values":[],"unit":"days","evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:52.545628Z","snippet":null,"locator":"PDC000491: clinicalPerStudy, field days_to_last_follow_up; a value for 103 of 131 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:days_to_recurrence","harmonized_name":"diagnoses.days_to_recurrence","label":"Days to recurrence","category":"outcome","n_nonmissing":4,"n_not_reported":null,"n_informative":null,"n_total":131,"coverage_pct":null,"populated_pct":3.1,"is_repeated":false,"example_values":[],"unit":"days","evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:52.545628Z","snippet":null,"locator":"PDC000491: clinicalPerStudy, field days_to_recurrence; a value for 4 of 131 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:treatments.treatment_type","harmonized_name":"diagnoses.treatments.treatment_type","label":"Treatment type","category":"treatment","n_nonmissing":0,"n_not_reported":null,"n_informative":null,"n_total":131,"coverage_pct":null,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T03:23:13.800863Z","snippet":null,"locator":"PDC000491: paginatedCaseTreatmentsPerStudy, field treatment_type; informative for 0 of 131 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:treatments.therapeutic_agents","harmonized_name":"diagnoses.treatments.therapeutic_agents","label":"Therapeutic agents","category":"treatment","n_nonmissing":0,"n_not_reported":null,"n_informative":null,"n_total":131,"coverage_pct":null,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T03:23:13.800863Z","snippet":null,"locator":"PDC000491: paginatedCaseTreatmentsPerStudy, field therapeutic_agents; informative for 0 of 131 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:treatments.treatment_outcome","harmonized_name":"diagnoses.treatments.treatment_outcome","label":"Treatment outcome","category":"treatment","n_nonmissing":0,"n_not_reported":null,"n_informative":null,"n_total":131,"coverage_pct":null,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T03:23:13.800863Z","snippet":null,"locator":"PDC000491: paginatedCaseTreatmentsPerStudy, field treatment_outcome; informative for 0 of 131 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:treatments.regimen_or_line_of_therapy","harmonized_name":"diagnoses.treatments.regimen_or_line_of_therapy","label":"Regimen or line of therapy","category":"treatment","n_nonmissing":0,"n_not_reported":null,"n_informative":null,"n_total":131,"coverage_pct":null,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T03:23:13.800863Z","snippet":null,"locator":"PDC000491: paginatedCaseTreatmentsPerStudy, field regimen_or_line_of_therapy; informative for 0 of 131 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:treatments.treatment_or_therapy","harmonized_name":"diagnoses.treatments.treatment_or_therapy","label":"Treatment given","category":"treatment","n_nonmissing":0,"n_not_reported":null,"n_informative":null,"n_total":131,"coverage_pct":null,"populated_pct":0.0,"is_repeated":false,"example_values":[],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T03:23:13.800863Z","snippet":null,"locator":"PDC000491: paginatedCaseTreatmentsPerStudy, field treatment_or_therapy; informative for 0 of 131 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]}],"longitudinal":{"has_followup":true,"has_survival_endpoint":true,"survival_endpoints":["overall survival"],"median_followup_months":18.7,"max_followup_months":72.0,"n_cases_with_followup":102,"has_serial_samples":null,"timepoints":[],"n_cases_with_serial":null,"has_treatment_response":false,"response_criteria":[],"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:11:52.545628Z","snippet":null,"locator":"PDC000491: computed from 131 cases: 27 deaths, 102 with a follow-up time, progression informative for 0","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},"access":{"tier":"open","open_components":["4 analytical fraction studies"],"controlled_components":[],"mechanism":"Direct download from the PDC portal or its API; no account required","dua_url":null,"data_access_committee":null,"typical_turnaround":null,"embargo_until":null,"login_required":false,"citation_requirement":"Cite the PDC study identifier and the study's primary publication; PDC asks that the consortium be acknowledged.","license":"Open access under the PDC data use terms","publication_policy_url":"https://pdc.cancer.gov/pdc/data-use-guidelines","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":"4 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},"useful_for":[],"limitations":[],"inappropriate_uses":[],"primary_publications":[],"reuse":[{"publication":{"pmid":"40749670","pmcid":"PMC12393171","doi":"10.1016/j.ccell.2025.07.011","title":"Integrative analysis of lung adenocarcinoma across diverse ethnicities and exposures.","journal":"Cancer cell","year":2025,"authors_short":"Satpathy et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/40749670/","is_open_access":false,"citation_count":14,"evidence":[]},"tier":"t3_analyzed","kind":"secondary_analysis","independent_of_generators":null,"what_they_analyzed":null,"what_they_found":null,"methods_summary":null,"modalities_used":[],"accession_snippet":null,"accession_locator":"TABLE","author_keys":["akiyama y","allen j","anand s","avanessian s","bergstrom e","carr s","chang g","chang y","charytonowicz d","chen h","chen j","chen k","chen y","chinnaiyan a","cho h","cieslik m","clark n","clauser k","clinical p","deng e","deng y","dhanasekaran s","ding l","espinoza r","fang h","fenyö d","geffen y","getz g","gillette m","gohsman s","govindan r","haines m","heiman d","hollenberg m","hosseini n","hostetter g","hsiao y","hsieh m","hsu h","hsu k","hsu y","hussey g","jaehnig e","kane m","keshishian h","kinarivala m","krek a","kumar-sinha c","lazar a","lei j","lin j","lin k","lin m","lin z","liu w","ma'ayan a","mani d","mannan r","marino g","mesri m","miller b","monovoukas a","nesvizhskii a","newton c","omenn g","paik p","parolia a","paul i","petralia f","robles a","ruggles k","satpathy s","sebra r","sheng-wen c","taiwan c","thiagarajan m","thorup j","wang p","wang y","white c","wolfe a","yang p","yeh c","zhang b","zhang h","zhang x"],"nci_funded_reuse":true,"linked_grants":["U24CA271114","U24CA271079","U24CA271076","U24CA271075","U24CA271037","U24CA271012","U24CA270823","U24CA210986","U24CA210979","U24CA210972","U01CA271412","U01CA271410","U01CA271407","U01CA271402","P30CA196521","P30CA008748"],"adjudicated_by":null,"adjudicated_at":null,"evidence":[{"method":"fulltext","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=TABLE:\"PDC000491\"","source_label":"Europe PMC section search (TABLE)","retrieved_at":"2026-09-18T03:24:47.988961Z","snippet":null,"locator":"accession \"PDC000491\" indexed in TABLE","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]},{"publication":{"pmid":"42343131","pmcid":"PMC13384240","doi":"10.1038/s41586-026-10678-2","title":"Alternate RNA decoding results in stable and abundant proteins in mammals.","journal":"Nature","year":2026,"authors_short":"Tsour et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/42343131/","is_open_access":false,"citation_count":5,"evidence":[]},"tier":"t3_analyzed","kind":"secondary_analysis","independent_of_generators":null,"what_they_analyzed":null,"what_they_found":null,"methods_summary":null,"modalities_used":[],"accession_snippet":null,"accession_locator":"DATA_AVAILABILITY, METHODS","author_keys":["guez j","karczewski k","koo e","leduc a","machné r","slavov n","tsour s","widmer s"],"nci_funded_reuse":false,"linked_grants":[],"adjudicated_by":null,"adjudicated_at":null,"evidence":[{"method":"fulltext","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DATA_AVAILABILITY:\"PDC000491\"","source_label":"Europe PMC section search (DATA_AVAILABILITY)","retrieved_at":"2026-09-18T03:24:47.988961Z","snippet":null,"locator":"accession \"PDC000491\" indexed in DATA_AVAILABILITY","confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]},{"publication":{"pmid":"41115212","pmcid":"PMC12536875","doi":"10.1093/bib/bbaf558","title":"SysML: adaptive recommendation system for heterogeneous biomedical data preprocessing and modeling workflows.","journal":"Briefings in bioinformatics","year":2025,"authors_short":"Zhao et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/41115212/","is_open_access":true,"citation_count":0,"evidence":[]},"tier":"t3_analyzed","kind":"secondary_analysis","independent_of_generators":null,"what_they_analyzed":null,"what_they_found":null,"methods_summary":null,"modalities_used":[],"accession_snippet":null,"accession_locator":"METHODS","author_keys":["zhao c","zhao j","zhao x","zhao y"],"nci_funded_reuse":false,"linked_grants":[],"adjudicated_by":null,"adjudicated_at":null,"evidence":[{"method":"fulltext","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=METHODS:\"PDC000491\"","source_label":"Europe PMC section search (METHODS)","retrieved_at":"2026-09-18T03:24:47.988961Z","snippet":null,"locator":"accession \"PDC000491\" indexed in METHODS","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]}],"reuse_metrics":{"n_candidates_screened":2,"n_by_tier":{"t3_analyzed":2,"t2_declared":1,"t1_accession":0,"t0_mention":0},"n_by_tier_raw":{"t3_analyzed":2,"t2_declared":1,"t1_accession":0,"t0_mention":0},"accession_precision":{"token":"PDC000489","query":"METHODS:\"PDC000489\"","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":"This accession is a single indexed term, so Europe PMC matches it exactly and the hit count needs no correction."},"n_citations_to_primary_publication":null,"citation_to_reuse_ratio":null,"has_citable_accession":true,"n_verified_reuse":2,"n_reuse_examined":3,"n_independent_reuse":0,"n_nci_funded_reuse":1,"first_reuse_year":2025,"latest_reuse_year":2026,"years_since_release":1.72,"expected_reuse":5.34,"reuse_gap_index":-1.08,"reuse_gap_percentile":24.2,"search_strategy_id":"epmc-index-v3","searched_at":"2026-09-20T18:07:48.635838Z","no_reuse_identified":false,"evidence":[{"method":"derived","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search","source_label":"Europe PMC section-scoped hit counts","retrieved_at":"2026-09-20T18:07:48.635838Z","snippet":null,"locator":"tokens: PDC000491, PDC000490, PDC000489; queries: METHODS:\"PDC000489\"; DATA_AVAILABILITY:\"PDC000489\"; ACCESSION_ID:\"PDC000491\"; REF:\"PDC000491\"","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. This accession is a single indexed term, so Europe PMC matches it exactly and the hit count needs no correction."},{"method":"derived","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search","source_label":"Europe PMC first-reference dating","retrieved_at":"2026-09-20T18:13:04.294656Z","snippet":null,"locator":"first referenced in 2025 (METHODS section)","confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Availability dated from the literature (epmc-first-reference-v2) rather than from repository file timestamps, which record re-harmonization. This is a lower bound on availability."}]},"underexplored":{"is_underexplored":false,"basis":["Reuse is within the expected range for comparable datasets (index -1.08)."],"index_value":-1.08,"percentile":24.2,"comparator_set":"132 datasets in this corpus with a citable accession and sufficient metadata","evidence":[{"method":"derived","source_url":null,"source_label":"Reuse Gap Index (rgi-huber-v2)","retrieved_at":"2026-09-21T02:11:22.976067Z","snippet":null,"locator":"Huber robust regression of log2(analyzing articles + 1) on cohort size, years available, modality breadth and access tier","confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Model, covariates and coefficients are published with the dataset export so the label can be recomputed or contested."}]},"grants":[{"core_project_num":"U24CA271114","project_num":null,"title":"Proteogenomic translator for cancer biomarker discovery towards precision medicine","pi_names":["Avi Ma'ayan","Pei Wang"],"agency_ic":"NCI","activity_code":"U24","fiscal_years":[2022,2023,2024,2025,2026],"award_amount_usd":5022764,"org_name":"ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U24CA271114","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:36:13.059177Z","snippet":null,"locator":"PMID 40749670 reported under U24CA271114","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":"U24CA271079","project_num":null,"title":"Proteogenomic Characterization of Tumor Tissues and Preclinical Models with High Precision","pi_names":["DANIEL Wanyui CHAN","Hui Zhang"],"agency_ic":"NCI","activity_code":"U24","fiscal_years":[2022,2023,2024,2025,2026],"award_amount_usd":6618085,"org_name":"JOHNS HOPKINS UNIVERSITY","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U24CA271079","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:36:13.059177Z","snippet":null,"locator":"PMID 40749670 reported under U24CA271079","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":"U24CA271076","project_num":null,"title":"iPGDAC, An Integrative Proteogenomic Data Analysis Center for CPTAC","pi_names":["Bing Zhang"],"agency_ic":"NCI","activity_code":"U24","fiscal_years":[2022,2023,2024,2025,2026],"award_amount_usd":4952892,"org_name":"BAYLOR COLLEGE OF MEDICINE","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U24CA271076","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:36:13.059177Z","snippet":null,"locator":"PMID 40749670 reported under U24CA271076","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":"U24CA271075","project_num":null,"title":"Center for comprehensive proteogenomic data analysis","pi_names":["GAD A GETZ","Denkanikota R Mani"],"agency_ic":"NCI","activity_code":"U24","fiscal_years":[2022,2023,2024,2025,2026],"award_amount_usd":3897520,"org_name":"BROAD INSTITUTE, INC.","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U24CA271075","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:36:13.059177Z","snippet":null,"locator":"PMID 40749670 reported under U24CA271075","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":"U24CA271037","project_num":null,"title":"Michigan Center for Translational Cancer Proteogenomics","pi_names":["Saravana Mohan Dhanasekaran","Alexey I Nesvizhskii"],"agency_ic":"NCI","activity_code":"U24","fiscal_years":[2022,2023,2024,2025,2026],"award_amount_usd":4411659,"org_name":"UNIVERSITY OF MICHIGAN AT ANN ARBOR","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U24CA271037","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:36:13.059177Z","snippet":null,"locator":"PMID 40749670 reported under U24CA271037","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":"U24CA271012","project_num":null,"title":"Center for Advanced Multi-Omic Characterization of Cancer","pi_names":["Tao Liu"],"agency_ic":"NCI","activity_code":"U24","fiscal_years":[2022,2023,2024,2025,2026],"award_amount_usd":6630183,"org_name":"BATTELLE PACIFIC NORTHWEST LABORATORIES","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U24CA271012","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:36:13.059177Z","snippet":null,"locator":"PMID 40749670 reported under U24CA271012","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":"U24CA270823","project_num":null,"title":"Center of Excellence for High Throughput Proteogenomic Characterization","pi_names":["STEVEN A CARR","MICHAEL A GILLETTE","Shankha Satpathy"],"agency_ic":"NCI","activity_code":"U24","fiscal_years":[2022,2023,2024,2025,2026],"award_amount_usd":5349895,"org_name":"BROAD INSTITUTE, INC.","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U24CA270823","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:36:13.059177Z","snippet":null,"locator":"PMID 40749670 reported under U24CA270823","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":"U24CA210986","project_num":null,"title":"Center of Excellence for High Throughput Proteogenomic Characterization","pi_names":["STEVEN A CARR","MICHAEL A GILLETTE"],"agency_ic":"NCI","activity_code":"U24","fiscal_years":[2016,2017,2018,2019,2020],"award_amount_usd":6399756,"org_name":"BROAD INSTITUTE, INC.","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U24CA210986","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:36:13.059177Z","snippet":null,"locator":"PMID 40749670 reported under U24CA210986","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":"U24CA210979","project_num":null,"title":"Integrated high throughput proteogenomic data analysis center for CPTAC","pi_names":["Chet Birger","GAD A GETZ","Denkanikota R Mani","Michael Noble"],"agency_ic":"NCI","activity_code":"U24","fiscal_years":[2016,2017,2018,2019,2020],"award_amount_usd":4417536,"org_name":"BROAD INSTITUTE, INC.","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U24CA210979","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:36:13.059177Z","snippet":null,"locator":"PMID 40749670 reported under U24CA210979","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":"U24CA210972","project_num":null,"title":"Proteogenomic Data Analysis for Cancer Systems Biology and Clinical Translation","pi_names":["Li Ding","David Fenyo","Samuel H Payne"],"agency_ic":"NCI","activity_code":"U24","fiscal_years":[2016,2017,2018,2019,2020],"award_amount_usd":3309088,"org_name":"NEW YORK UNIVERSITY SCHOOL OF MEDICINE","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U24CA210972","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:36:13.059177Z","snippet":null,"locator":"PMID 40749670 reported under U24CA210972","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":"U01CA271412","project_num":null,"title":"Proteogenomic characterization of early and late resistance mechanisms in acute myeloid leukemia","pi_names":["BRIAN J DRUKER","Paul D Piehowski","Jeffrey Wallace Tyner"],"agency_ic":"NCI","activity_code":"U01","fiscal_years":[2022,2023,2024,2025,2026],"award_amount_usd":5771926,"org_name":"OREGON HEALTH & SCIENCE UNIVERSITY","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U01CA271412","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:36:13.059177Z","snippet":null,"locator":"PMID 40749670 reported under U01CA271412","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":"U01CA271410","project_num":null,"title":"Mayo Clinic Center for Clinical Proteomics","pi_names":["Rafael Fonseca","AKHILESH PANDEY"],"agency_ic":"NCI","activity_code":"U01","fiscal_years":[2022,2023,2024,2025,2026],"award_amount_usd":5347809,"org_name":"MAYO CLINIC ROCHESTER","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U01CA271410","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:36:13.059177Z","snippet":null,"locator":"PMID 40749670 reported under U01CA271410","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":"U01CA271407","project_num":null,"title":"Proteogenomic studies to understand mechanisms and drivers of resistance to immunotherapies","pi_names":["Diwakar Davar","AMANDA G PAULOVICH"],"agency_ic":"NCI","activity_code":"U01","fiscal_years":[2022,2023,2024,2025,2026],"award_amount_usd":5551903,"org_name":"FRED HUTCHINSON CANCER CENTER","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U01CA271407","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:36:13.059177Z","snippet":null,"locator":"PMID 40749670 reported under U01CA271407","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":"U01CA271402","project_num":null,"title":"Proteogenomic Predictors of Recurrence in Non-small Cell Lung Cancer","pi_names":["STEVEN A CARR","MICHAEL A GILLETTE","Ramaswamy Govindan"],"agency_ic":"NCI","activity_code":"U01","fiscal_years":[2022,2023,2024,2025,2026],"award_amount_usd":4970159,"org_name":"WASHINGTON UNIVERSITY","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U01CA271402","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:36:13.059177Z","snippet":null,"locator":"PMID 40749670 reported under U01CA271402","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":"P30CA196521","project_num":null,"title":"The Tisch Cancer Institute - Cancer Center Support Grant","pi_names":["Ramon E Parsons","Nina Bhardwaj","Keren Osman","Siu-Hong Ho","Marcio Diniz","Dan Hasson","Robert Sebra","Sharon Mias","Samir Parekh","Emily Bernstein","JANICE L GABRILOVE","EMANUELA TAIOLI","Deanna L Benson","Melissa Mazor","Erick Herrscher","Rachel I Brody","Sacha Gnjatic","Jordi Ochando","Madhu madhu Mazumdar","Ernesto Guccione","Matthew Galsky","Therica Miller","DEBORAH DOROSHOW","Julio A. Aguirre-Ghiso","MARSHALL R POSNER","KEVIN A KELLEY","Nina A. Bickell","Cardinale B Smith","SCOTT L. FRIEDMAN","MYRON E SCHWARTZ","Paolo Boffetta","VICTOR Louis FRIEDRICH","Steven J. Burakoff"],"agency_ic":"NCI","activity_code":"P30","fiscal_years":[2015,2016,2017,2018,2019,2020,2021,2022,2023,2024,2025,2026],"award_amount_usd":63610997,"org_name":"ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=P30CA196521","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:36:13.059177Z","snippet":null,"locator":"PMID 40749670 reported under P30CA196521","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":"Cancer Center Administration","pi_names":["ALEX MACDONALD","SELWYN M VICKERS","FRANCESCA M GANY","Hongbiao Carl Lekaye","Elisa de Stanchina","Neeman Mohibullah","Serge K Lyashchenko","Scott Freeswick","Michael Jason de la Cruz","PAUL J SABBATINI","Frances Weis-Garcia","Joachim Silber","MITHAT GONEN","Rui Gardner","YASUHIDE FURUTA","Thomas Michael Atkinson","Nicholas D Socci","Justin Cross","NEIL SCOTT LIPMAN","Ralph J. Garippa","Ouathek Ouerfelli","Charles M. Rudin","Xiuyan Wang","Murray Tipping","Mara Monetti","Gouri Nanjangud","Yehuda Goldgur","Michael H. A. Roehrl","Isabelle Riviere","Ronald Charles Hendrickson","Jason S. Lewis","Raymond J Muller","katia Ognianova manova","Agnes Viale","CRAIG B THOMPSON","Marija Drobnjak","WILLIE H MARK","HAKIM DJABALLAH","Isabelle Rivieri","PETRUS J HENDRIKX","Carl LeKaye","MARGARET A LEVERSHA","RONALD HENDRICKSON","NICHOLAS SOCCI","ANDREW VICKERS","AGNES VIALE","RUI GARDNER","NANJANGUD GOURI","Colin B Begg","Andrew J Vickers","ARIELA NOY","JEANNE RUPERTO","QUATHEK QUERFELLI","Jamie S. Ostroff","MARK G KLANG","JASON Arthur KOUTCHER","MICHEL WJ SADELAIN","NIKOLA P PAVLETICH","VICTOR E REUTER","Victor Reuter","HAROLD E. VARMUS","PAUL TEMPST","ALEX E LASH","WILLIAM L GERALD","LISA K. DENZIN","NEIL LIPMAN","IRENE TSALAPATANIS","ZVI Y. FUKS","ELIZABETH H LACY","CHARLES D LUCARELLI","Felix Homberger","DAVID W GOLDE","Lee A. Niswander","Howard T. Petrie","JOAN MASSAGUE","JANKO Z. NIKOLICH","JAMES ROTHMAN","SCOTT E PERKINS","ELINOR MILLER","JOSEPH Rocco BERTINO","KENNETH J MARIANS","PAUL A MARKS","SIDNEY J WINAWER","ALAN N. HOUGHTON","STEVEN S STERNBERG","DAVID D MYERS","PAUL LANGNER","RONALD D FINN","KYOICHI A WATANABE","Raymond P Warrell","Raju S.K. Chaganti","RAYMOND NEGRYCZ","ELIZABETH LACY","PAUL J TEMPST","COLIN B BEGG"],"agency_ic":"NCI","activity_code":"P30","fiscal_years":[1985,1986,1987,1988,1989,1990,1991,1992,1993,1994,1995,1996,1997,1998,1999,2000,2001,2002,2003,2004,2005,2006,2007,2008,2009,2010,2011,2012,2013,2014,2015,2016,2017,2018,2019,2020,2021,2022,2023,2024,2025,2026],"award_amount_usd":717923764,"org_name":"SLOAN-KETTERING INST CAN RESEARCH","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=P30CA008748","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:36:13.059177Z","snippet":null,"locator":"PMID 40749670 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 the PDC portal","detail":"Proteomic data are released open; the portal's use guidelines still apply. This record spans 4 PDC studies; repeat for each.","url":"https://pdc.cancer.gov/pdc/study/PDC000491","requires":[],"est_time":"5 minutes","cli_snippet":null,"audience":"human","evidence":[{"method":"derived","source_url":"https://pdc.cancer.gov/pdc/study/PDC000491","source_label":"PDC access documentation","retrieved_at":"2026-09-21T12:30:59.433023Z","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":"Accept the data use guidelines and download","detail":"The portal asks for acknowledgement and citation, not a data access request.","url":"https://pdc.cancer.gov/pdc/data-use-guidelines","requires":[],"est_time":"minutes to hours, by study size","cli_snippet":null,"audience":"human","evidence":[{"method":"derived","source_url":"https://pdc.cancer.gov/pdc/data-use-guidelines","source_label":"PDC access documentation","retrieved_at":"2026-09-21T12:30:59.433025Z","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":"Resolve the study UUID, then fetch the file manifest","detail":"filesPerStudy keys on the study UUID, not on PDC000491: called with the pdc_study_id it returns the right number of rows with every column null. Resolve the UUID first and pass the terms acknowledgement.","url":"https://pdc.cancer.gov/data-dictionary/publicapi-documentation/","requires":[],"est_time":null,"cli_snippet":"python - <<'PY'\nimport requests\nAPI = \"https://proteomic.datacommons.cancer.gov/graphql\"\n\ndef gql(query, **variables):\n    r = requests.post(API, json={\"query\": query, \"variables\": variables}, timeout=180)\n    r.raise_for_status()\n    body = r.json()\n    if body.get(\"errors\"):\n        raise RuntimeError(body[\"errors\"][0][\"message\"])\n    return body[\"data\"]\n\nstudy = gql('query($id:String!){ study(pdc_study_id:$id acceptDUA:true){ study_id } }',\n            id=\"PDC000491\")[\"study\"][0]\nfiles = gql('query($sid:String!){ filesPerStudy(study_id:$sid acceptDUA:true)'\n            '{ file_id file_name file_size } }', sid=study[\"study_id\"])[\"filesPerStudy\"]\nprint(len(files), \"files\")\nPY","audience":"agent","evidence":[{"method":"derived","source_url":"https://pdc.cancer.gov/data-dictionary/publicapi-documentation/","source_label":"PDC access documentation","retrieved_at":"2026-09-21T12:30:59.433027Z","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/pdc-cptac-luad-confirmatory-study.json","jsonld_url":"/data/jsonld/pdc-cptac-luad-confirmatory-study.jsonld","croissant_url":"/data/croissant/pdc-cptac-luad-confirmatory-study.json","instructions_url":"/data/agent/pdc-cptac-luad-confirmatory-study.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":32.1,"tags":["pdc","proteogenomics","rare-modality","acetylome","ubiquitylome"],"search_text":null}