{"id":"pdc-sampling-techniques-for-enrichment-of-pdac","title":"Sampling techniques for enrichment of PDAC","short_title":"PDC000393","aliases":["Sampling techniques for enrichment of PDAC - Proteome"],"summary":null,"one_liner":null,"identifiers":[{"scheme":"pdc_study_id","value":"PDC000393","url":"https://pdc.cancer.gov/pdc/study/PDC000393","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":"1 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":"2023-01-01","last_upstream_update":null,"retrieved_at":"2026-09-18T02:36:15.354973Z","landing_page_url":"https://pdc.cancer.gov/pdc/study/PDC000393","cancer_types":[{"label":"Pancreatic Ductal Adenocarcinoma","ontology":null,"code":null,"url":null}],"primary_sites":["Pancreas"],"subject":{"scope":"single","tissues":["PANCREAS"],"evidence":[{"method":"derived","source_url":null,"source_label":"cds.subjects","retrieved_at":null,"snippet":null,"locator":"cancer_types: Pancreatic Ductal Adenocarcinoma; primary_sites: Pancreas","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":7,"n_samples":null,"n_aliquots":28,"n_files":null,"total_bytes":null,"n_tumor_cases":null,"n_normal_cases":null,"has_matched_normal":null,"demographics":{"sex":{"female":5,"not reported":1,"male":1},"race":{"other":4,"not reported":1,"white":2},"ethnicity":{"not reported":7},"age_at_diagnosis_years":{"n":6.0,"min":52.8,"median":64.4,"max":69.6},"vital_status":{"Dead":5,"Alive":1},"country_or_region":{},"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:12:39.657286Z","snippet":null,"locator":"PDC000393: 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":"1 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},"assays":[{"modality":"proteome","label":"Proteome mass spectrometry (TMT10 / DDA)","platform":"TMT10","n_cases":7,"n_samples":28,"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":"1 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":6,"n_not_reported":0,"n_informative":6,"n_total":7,"coverage_pct":85.7,"populated_pct":85.7,"is_repeated":false,"example_values":["Dead","Alive"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:12:39.657286Z","snippet":null,"locator":"PDC000393: clinicalPerStudy, field vital_status over 7 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":5,"n_not_reported":0,"n_informative":5,"n_total":7,"coverage_pct":71.4,"populated_pct":71.4,"is_repeated":false,"example_values":["Cancer Related","Not Cancer Related","Cardiovascular Disorder, NOS"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:12:39.657286Z","snippet":null,"locator":"PDC000393: clinicalPerStudy, field cause_of_death over 7 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:race","harmonized_name":"demographic.race","label":"Race","category":"demographic","n_nonmissing":7,"n_not_reported":1,"n_informative":6,"n_total":7,"coverage_pct":85.7,"populated_pct":100.0,"is_repeated":false,"example_values":["other","white","not reported"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:12:39.657286Z","snippet":null,"locator":"PDC000393: clinicalPerStudy, field race over 7 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"pdc:ethnicity","harmonized_name":"demographic.ethnicity","label":"Ethnicity","category":"demographic","n_nonmissing":7,"n_not_reported":7,"n_informative":0,"n_total":7,"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":"2026-09-19T04:12:39.657286Z","snippet":null,"locator":"PDC000393: clinicalPerStudy, field ethnicity over 7 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":7,"n_not_reported":1,"n_informative":6,"n_total":7,"coverage_pct":85.7,"populated_pct":100.0,"is_repeated":false,"example_values":["female","not reported","male"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:12:39.657286Z","snippet":null,"locator":"PDC000393: clinicalPerStudy, field gender over 7 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":7,"n_not_reported":1,"n_informative":6,"n_total":7,"coverage_pct":85.7,"populated_pct":100.0,"is_repeated":false,"example_values":["8500/3","Not Reported"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:12:39.657286Z","snippet":null,"locator":"PDC000393: clinicalPerStudy, field morphology over 7 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":7,"n_not_reported":1,"n_informative":6,"n_total":7,"coverage_pct":85.7,"populated_pct":100.0,"is_repeated":false,"example_values":["Infiltrating duct carcinoma, NOS","Not Reported"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:12:39.657286Z","snippet":null,"locator":"PDC000393: clinicalPerStudy, field primary_diagnosis over 7 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":7,"n_not_reported":1,"n_informative":6,"n_total":7,"coverage_pct":85.7,"populated_pct":100.0,"is_repeated":false,"example_values":["Pancreas, NOS","Not Reported"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:12:39.657286Z","snippet":null,"locator":"PDC000393: clinicalPerStudy, field tissue_or_organ_of_origin over 7 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":7,"n_not_reported":1,"n_informative":6,"n_total":7,"coverage_pct":85.7,"populated_pct":100.0,"is_repeated":false,"example_values":["G2","G3","Not Reported"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:12:39.657286Z","snippet":null,"locator":"PDC000393: clinicalPerStudy, field tumor_grade over 7 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":6,"n_not_reported":0,"n_informative":6,"n_total":7,"coverage_pct":85.7,"populated_pct":85.7,"is_repeated":false,"example_values":["Stage IIB","Stage IB","Stage IV"],"unit":null,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL clinicalPerStudy","retrieved_at":"2026-09-19T04:12:39.657286Z","snippet":null,"locator":"PDC000393: clinicalPerStudy, field ajcc_pathologic_stage over 7 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":7,"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":"2026-09-19T04:12:39.657286Z","snippet":null,"locator":"PDC000393: clinicalPerStudy, field ajcc_clinical_stage over 7 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":7,"n_not_reported":7,"n_informative":0,"n_total":7,"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":"2026-09-19T04:12:39.657286Z","snippet":null,"locator":"PDC000393: clinicalPerStudy, field tumor_stage over 7 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":7,"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":"2026-09-19T04:12:39.657286Z","snippet":null,"locator":"PDC000393: clinicalPerStudy, field progression_or_recurrence over 7 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":7,"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":"2026-09-19T04:12:39.657286Z","snippet":null,"locator":"PDC000393: clinicalPerStudy, field last_known_disease_status over 7 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":7,"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":"2026-09-19T04:12:39.657286Z","snippet":null,"locator":"PDC000393: clinicalPerStudy, field prior_treatment over 7 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":7,"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":"2026-09-19T04:12:39.657286Z","snippet":null,"locator":"PDC000393: clinicalPerStudy, field prior_malignancy over 7 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":7,"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":"2026-09-19T04:12:39.657286Z","snippet":null,"locator":"PDC000393: clinicalPerStudy, field synchronous_malignancy over 7 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":6,"n_not_reported":6,"n_informative":0,"n_total":7,"coverage_pct":0.0,"populated_pct":85.7,"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":"2026-09-19T04:12:39.657286Z","snippet":null,"locator":"PDC000393: clinicalPerStudy, field classification_of_tumor over 7 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":6,"n_not_reported":null,"n_informative":null,"n_total":7,"coverage_pct":null,"populated_pct":85.7,"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":"2026-09-19T04:12:39.657286Z","snippet":null,"locator":"PDC000393: clinicalPerStudy, field age_at_diagnosis; a value for 6 of 7 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":5,"n_not_reported":null,"n_informative":null,"n_total":7,"coverage_pct":null,"populated_pct":71.4,"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":"2026-09-19T04:12:39.657286Z","snippet":null,"locator":"PDC000393: clinicalPerStudy, field days_to_death; a value for 5 of 7 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":6,"n_not_reported":null,"n_informative":null,"n_total":7,"coverage_pct":null,"populated_pct":85.7,"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":"2026-09-19T04:12:39.657286Z","snippet":null,"locator":"PDC000393: clinicalPerStudy, field days_to_last_follow_up; a value for 6 of 7 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":1,"n_not_reported":null,"n_informative":null,"n_total":7,"coverage_pct":null,"populated_pct":14.3,"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":"2026-09-19T04:12:39.657286Z","snippet":null,"locator":"PDC000393: clinicalPerStudy, field days_to_recurrence; a value for 1 of 7 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":7,"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":"2026-09-19T03:24:43.919486Z","snippet":null,"locator":"PDC000393: paginatedCaseTreatmentsPerStudy, field treatment_type; informative for 0 of 7 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":7,"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":"2026-09-19T03:24:43.919486Z","snippet":null,"locator":"PDC000393: paginatedCaseTreatmentsPerStudy, field therapeutic_agents; informative for 0 of 7 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":7,"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":"2026-09-19T03:24:43.919486Z","snippet":null,"locator":"PDC000393: paginatedCaseTreatmentsPerStudy, field treatment_outcome; informative for 0 of 7 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":7,"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":"2026-09-19T03:24:43.919486Z","snippet":null,"locator":"PDC000393: paginatedCaseTreatmentsPerStudy, field regimen_or_line_of_therapy; informative for 0 of 7 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":7,"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":"2026-09-19T03:24:43.919486Z","snippet":null,"locator":"PDC000393: paginatedCaseTreatmentsPerStudy, field treatment_or_therapy; informative for 0 of 7 cases","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]}],"longitudinal":{"has_followup":true,"has_survival_endpoint":false,"survival_endpoints":[],"median_followup_months":10.5,"max_followup_months":59.3,"n_cases_with_followup":6,"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":"2026-09-19T04:12:39.657286Z","snippet":null,"locator":"PDC000393: computed from 7 cases: 5 deaths, 6 with a follow-up time, progression informative for 0","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},"access":{"tier":"open","open_components":["1 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":"1 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":"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:\"PDC000393\"","source_label":"Europe PMC section search (DATA_AVAILABILITY)","retrieved_at":"2026-09-18T03:39:09.624703Z","snippet":null,"locator":"accession \"PDC000393\" 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":"41053894","pmcid":"PMC12502162","doi":"10.1186/s13104-025-07464-0","title":"SQSTM1/p62 as a prognostic indicator in pancancer and nasopharyngeal carcinoma.","journal":"BMC research notes","year":2025,"authors_short":"Chen et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/41053894/","is_open_access":true,"citation_count":0,"evidence":[]},"tier":"t2_declared","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","author_keys":["chen l","zhang z"],"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:\"PDC000393\"","source_label":"Europe PMC section search (DATA_AVAILABILITY)","retrieved_at":"2026-09-18T03:39:09.624703Z","snippet":null,"locator":"accession \"PDC000393\" 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."}]}],"reuse_metrics":{"n_candidates_screened":2,"n_by_tier":{"t3_analyzed":2,"t2_declared":2,"t1_accession":0,"t0_mention":0},"n_by_tier_raw":{"t3_analyzed":2,"t2_declared":2,"t1_accession":0,"t0_mention":0},"accession_precision":{"token":"PDC000393","query":"METHODS:\"PDC000393\"","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":0,"first_reuse_year":2025,"latest_reuse_year":2026,"years_since_release":3.72,"expected_reuse":0.25,"reuse_gap_index":1.258,"reuse_gap_percentile":78.0,"search_strategy_id":"epmc-index-v3","searched_at":"2026-09-20T18:07:49.717931Z","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":"2026-09-20T18:07:49.717931Z","snippet":null,"locator":"tokens: PDC000393; queries: METHODS:\"PDC000393\"; DATA_AVAILABILITY:\"PDC000393\"; ACCESSION_ID:\"PDC000393\"; REF:\"PDC000393\"","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":"2026-09-20T18:18:47.773009Z","snippet":null,"locator":"first referenced in 2023 (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."},{"method":"derived","source_url":null,"source_label":"Marker-paper inference withdrawn","retrieved_at":"2026-09-20T18:18:47.942883Z","snippet":null,"locator":"PMID 37517589 was nominated for 2 datasets","confidence":"high","reviewer":null,"reviewed_at":null,"note":"A marker paper describes one cohort. This article was inferred as the marker paper for several datasets at once, which means the inference is wrong for all but one of them and we cannot tell which, so no marker paper is claimed for this record."}]},"underexplored":{"is_underexplored":false,"basis":["Reuse is within the expected range for comparable datasets (index +1.26)."],"index_value":1.258,"percentile":78.0,"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":[],"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.","url":"https://pdc.cancer.gov/pdc/study/PDC000393","requires":[],"est_time":"5 minutes","cli_snippet":null,"audience":"human","evidence":[{"method":"derived","source_url":"https://pdc.cancer.gov/pdc/study/PDC000393","source_label":"PDC access documentation","retrieved_at":"2026-09-21T12:30:59.440460Z","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":"2026-09-21T12:30:59.440463Z","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 PDC000393: 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=\"PDC000393\")[\"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":"2026-09-21T12:30:59.440465Z","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-sampling-techniques-for-enrichment-of-pdac.json","jsonld_url":"/data/jsonld/pdc-sampling-techniques-for-enrichment-of-pdac.jsonld","croissant_url":"/data/croissant/pdc-sampling-techniques-for-enrichment-of-pdac.json","instructions_url":"/data/agent/pdc-sampling-techniques-for-enrichment-of-pdac.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":25.0,"tags":["pdc","proteogenomics"],"search_text":null}