{"id":"cbio-aml-ohsu-2018","title":"Acute Myeloid Leukemia (OHSU, Nature 2018)","short_title":"aml_ohsu_2018","aliases":["aml_ohsu_2018"],"summary":"Whole-exome sequencing of 672 acute myeloid leukemia samples (with 454 matched normals) from the Beat AML program.","one_liner":null,"identifiers":[{"scheme":"cbioportal_study_id","value":"aml_ohsu_2018","url":"https://www.cbioportal.org/study/summary?id=aml_ohsu_2018","is_primary":true,"evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/aml_ohsu_2018","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-18T02:48:40.878054Z","snippet":null,"locator":null,"confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]}],"repository":{"name":"cBioPortal for Cancer Genomics","short_name":"cBioPortal","url":"https://www.cbioportal.org","is_nci_crdc_node":false,"is_nih_repository":false},"additional_repositories":[],"program_name":"Investigator-initiated cohort (harmonized in cBioPortal)","program_url":"https://www.cbioportal.org/study/summary?id=aml_ohsu_2018","nci_program":null,"generating_institutions":[],"data_generation_funding_role":"generation","version":null,"release_date":null,"last_upstream_update":null,"retrieved_at":"2026-09-18T02:48:40.878054Z","landing_page_url":"https://www.cbioportal.org/study/summary?id=aml_ohsu_2018","cancer_types":[{"label":"Acute Myeloid Leukemia","ontology":"cBioPortal","code":"aml","url":null}],"primary_sites":["mnm"],"subject":{"scope":"single","tissues":["MYELOID"],"evidence":[{"method":"derived","source_url":null,"source_label":"cds.subjects","retrieved_at":null,"snippet":null,"locator":"cancer_types: Acute Myeloid Leukemia; primary_sites: mnm","confidence":"high","reviewer":null,"reviewed_at":null,"note":"OncoTree code rolled up to its pinned tissue."}]},"is_pediatric":null,"model_systems":[],"cohort":{"n_cases":562,"n_samples":672,"n_aliquots":null,"n_files":null,"total_bytes":null,"n_tumor_cases":null,"n_normal_cases":null,"has_matched_normal":null,"demographics":{"sex":{"Male":311,"Female":251},"race":{},"ethnicity":{"White":469,"HispNative":52,"AdmixedBlack":3,"AdmixedAsian":1,"AdmixedWhite":1,"Black":22,"Asian":14},"age_at_diagnosis_years":{},"vital_status":{"DECEASED":290,"LIVING":215},"country_or_region":{},"evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/aml_ohsu_2018","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:24:30.759673Z","snippet":null,"locator":"POST /clinical-data-counts/fetch","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},"evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/aml_ohsu_2018","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-18T02:48:40.878054Z","snippet":null,"locator":"field: allSampleCount","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},"assays":[{"modality":"targeted_dna","label":"Mutation calls (panel, exome or genome)","platform":null,"n_cases":null,"n_samples":622,"n_files":null,"data_levels":["processed matrix"],"access_tier":"open","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/aml_ohsu_2018","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-18T02:48:40.878054Z","snippet":null,"locator":"field: sequencedSampleCount","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"modality":"rna_seq","label":"RNA sequencing expression","platform":null,"n_cases":null,"n_samples":451,"n_files":null,"data_levels":["processed matrix"],"access_tier":"open","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/aml_ohsu_2018","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-18T02:48:40.878054Z","snippet":null,"locator":"field: mrnaRnaSeqSampleCount","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"modality":"structural_variant","label":"Structural variants / fusions","platform":null,"n_cases":null,"n_samples":null,"n_files":16,"data_levels":[],"access_tier":"open","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/aml_ohsu_2018","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-18T02:48:40.878054Z","snippet":null,"locator":"field: structuralVariantCount","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]}],"clinical_variables":[{"name":"cbioportal:ETHNICITY","harmonized_name":"demographic.ethnicity","label":"Ethnicity Category","category":"demographic","n_nonmissing":562,"n_not_reported":0,"n_informative":562,"n_total":562,"coverage_pct":100.0,"populated_pct":100.0,"is_repeated":false,"example_values":["White","HispNative","Black","Asian","AdmixedBlack","AdmixedAsian"],"unit":"patients","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/aml_ohsu_2018","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:24:30.326502Z","snippet":null,"locator":"POST /clinical-data-counts/fetch, attribute ETHNICITY; denominator is 562 patients","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"cbioportal:ONCOTREE_CODE","harmonized_name":"diagnoses.primary_diagnosis","label":"Oncotree Code","category":"diagnosis","n_nonmissing":672,"n_not_reported":0,"n_informative":672,"n_total":672,"coverage_pct":100.0,"populated_pct":100.0,"is_repeated":false,"example_values":["AMLNPM1","AMLMRC","AMLNOS","TMN","AMLCEBPA","AMLCBFBMYH11"],"unit":"samples","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/aml_ohsu_2018","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:24:30.326502Z","snippet":null,"locator":"POST /clinical-data-counts/fetch, attribute ONCOTREE_CODE; denominator is 672 samples","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"cbioportal:OS_STATUS","harmonized_name":"demographic.vital_status","label":"Overall Survival Status","category":"outcome","n_nonmissing":505,"n_not_reported":0,"n_informative":505,"n_total":562,"coverage_pct":89.9,"populated_pct":89.9,"is_repeated":false,"example_values":["DECEASED","LIVING"],"unit":"patients","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/aml_ohsu_2018","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:24:30.326502Z","snippet":null,"locator":"POST /clinical-data-counts/fetch, attribute OS_STATUS; denominator is 562 patients","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"cbioportal:SEX","harmonized_name":"demographic.sex_at_birth","label":"Sex","category":"demographic","n_nonmissing":562,"n_not_reported":0,"n_informative":562,"n_total":562,"coverage_pct":100.0,"populated_pct":100.0,"is_repeated":false,"example_values":["Male","Female"],"unit":"patients","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/aml_ohsu_2018","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:24:30.326502Z","snippet":null,"locator":"POST /clinical-data-counts/fetch, attribute SEX; denominator is 562 patients","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"cbioportal:OS_MONTHS","harmonized_name":"diagnoses.days_to_last_follow_up","label":"Overall Survival (Months)","category":"followup","n_nonmissing":497,"n_not_reported":null,"n_informative":null,"n_total":562,"coverage_pct":null,"populated_pct":88.4,"is_repeated":false,"example_values":[],"unit":"months","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/aml_ohsu_2018","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:24:30.536722Z","snippet":null,"locator":"GET /studies/aml_ohsu_2018/clinical-data?attributeId=OS_MONTHS; 497 of 562 patients carry a value","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]}],"longitudinal":{"has_followup":true,"has_survival_endpoint":true,"survival_endpoints":["overall survival"],"median_followup_months":10.2,"max_followup_months":174.5,"n_cases_with_followup":497,"has_serial_samples":null,"timepoints":[],"n_cases_with_serial":null,"has_treatment_response":false,"response_criteria":[],"evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/aml_ohsu_2018","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:24:30.759673Z","snippet":null,"locator":"derived from OS_MONTHS; 290 deaths recorded","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},"access":{"tier":"open","open_components":["harmonized mutation, copy-number, expression and clinical files"],"controlled_components":[],"mechanism":"Processed data download from the cBioPortal study page or its public REST API; no account required. Primary raw data remain wherever the original investigators deposited them.","dua_url":null,"data_access_committee":null,"typical_turnaround":null,"embargo_until":null,"login_required":false,"citation_requirement":"Cite the original publication, and cite cBioPortal if the portal's harmonized files were used.","license":"Per-study terms; cBioPortal asks that the original study be cited","publication_policy_url":"https://www.cbioportal.org/faq","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/aml_ohsu_2018","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-18T02:48:40.878054Z","snippet":null,"locator":null,"confidence":"medium","reviewer":null,"reviewed_at":null,"note":null}]},"useful_for":[],"limitations":[],"inappropriate_uses":[],"primary_publications":[{"pmid":"30333627","pmcid":null,"doi":null,"title":null,"journal":null,"year":null,"authors_short":"Tyner et al. Nature 2018","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/30333627/","is_open_access":null,"citation_count":null,"evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/aml_ohsu_2018","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-18T02:48:40.878054Z","snippet":null,"locator":"field: pmid","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]}],"reuse":[],"reuse_metrics":{"n_candidates_screened":0,"n_by_tier":{},"n_by_tier_raw":{},"accession_precision":null,"n_citations_to_primary_publication":1161,"citation_to_reuse_ratio":null,"has_citable_accession":false,"n_verified_reuse":null,"n_reuse_examined":0,"n_independent_reuse":0,"n_nci_funded_reuse":0,"first_reuse_year":null,"latest_reuse_year":null,"years_since_release":null,"expected_reuse":null,"reuse_gap_index":null,"reuse_gap_percentile":null,"search_strategy_id":"epmc-index-v3","searched_at":"2026-09-20T18:07:31.076641Z","no_reuse_identified":false,"evidence":[{"method":"derived","source_url":null,"source_label":"reuse index","retrieved_at":"2026-09-20T18:07:31.076641Z","snippet":null,"locator":null,"confidence":"low","reviewer":null,"reviewed_at":null,"note":"This dataset has no accession specific enough to search for in the literature, so citation-based reuse cannot be measured. Absence of a count here is not evidence of absence of reuse."}]},"underexplored":{"is_underexplored":false,"basis":["Not assessed: this dataset has no accession specific enough for citation-based reuse tracing, so a shortfall cannot be measured."],"index_value":null,"percentile":null,"comparator_set":"rgi-huber-v2","evidence":[]},"grants":[{"core_project_num":"U54CA224019","project_num":null,"title":"Architecture and Trajectory of Acquired Resistance to Therapy in AML","pi_names":["BRIAN J DRUKER","Shannon K. McWeeney","Jeffrey Wallace Tyner","Anupriya Agarwal","Tothu Q Vu"],"agency_ic":"NCI","activity_code":"U54","fiscal_years":[2017,2019,2020,2021,2022,2023,2024,2025,2026],"award_amount_usd":24957380,"org_name":"OREGON HEALTH & SCIENCE UNIVERSITY","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U54CA224019","role":"generation","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-18T02:48:44.992046Z","snippet":null,"locator":"PMID 30333627 reported under U54CA224019","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":"U01CA217862","project_num":null,"title":"Functional Genomic Discovery of Pathway Targeted and Immune Modulatory Therapeutic Combinations in Hematologic Malignancies","pi_names":["BRIAN J DRUKER","Jeffrey Wallace Tyner","Adam Arne Margolin"],"agency_ic":"NCI","activity_code":"U01","fiscal_years":[2017,2018,2019,2020,2021],"award_amount_usd":5255746,"org_name":"OREGON HEALTH & SCIENCE UNIVERSITY","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U01CA217862","role":"generation","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-18T02:48:44.992046Z","snippet":null,"locator":"PMID 30333627 reported under U01CA217862","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":"R01CA214428","project_num":null,"title":"An Academic-Industry Partnership to Advance Functional Genomics for Personalized Oncology.","pi_names":["CHRISTOPHER J KEMP"],"agency_ic":"NCI","activity_code":"R01","fiscal_years":[2018,2019,2020,2021,2022],"award_amount_usd":3022338,"org_name":"FRED HUTCHINSON CANCER RESEARCH CENTER","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=R01CA214428","role":"generation","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-18T02:48:44.992046Z","snippet":null,"locator":"PMID 30333627 reported under R01CA214428","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":"R01CA183974","project_num":null,"title":"Pathogenetic Mechanism and Clinical Targeting of CSF3R-Driven Cancer","pi_names":["Jeffrey Wallace Tyner"],"agency_ic":"NCI","activity_code":"R01","fiscal_years":[2014,2015,2016,2017,2018],"award_amount_usd":1597750,"org_name":"OREGON HEALTH & SCIENCE UNIVERSITY","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=R01CA183974","role":"generation","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-18T02:48:44.992046Z","snippet":null,"locator":"PMID 30333627 reported under R01CA183974","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":"R00CA237630","project_num":null,"title":"Characterizing the pathogenesis and targeted therapeutics of Wilms' Tumor 1 (WT1) mutations in AML","pi_names":["Haijiao Zhang"],"agency_ic":"NCI","activity_code":"R00","fiscal_years":[2023],"award_amount_usd":249000,"org_name":"OREGON HEALTH & SCIENCE UNIVERSITY","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=R00CA237630","role":"generation","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-18T02:48:44.992046Z","snippet":null,"locator":"PMID 30333627 reported under R00CA237630","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":"P30CA069533","project_num":null,"title":"Translational Oncology Research Program","pi_names":["Jeffrey Wallace Tyner","Mindy Roberts","SUSAN A. FLOCKE","Eneida R Nemecek","Shivaani Kummar","Luiz Eduardo Bertassoni","Grace B Gill","Laura Madeline Heiser","JACKILEN SHANNON","Michael Tworoger","LISA M COUSSENS"],"agency_ic":"NCI","activity_code":"P30","fiscal_years":[2025,2026],"award_amount_usd":8830605,"org_name":"OREGON HEALTH & SCIENCE UNIVERSITY","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=P30CA069533","role":"generation","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-18T02:48:44.992046Z","snippet":null,"locator":"PMID 30333627 reported under P30CA069533","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":"K99CA237630","project_num":null,"title":"Characterizing the pathogenesis and targeted therapeutics of Wilms' Tumor 1 (WT1) mutations in AML","pi_names":["Haijiao Zhang"],"agency_ic":"CA","activity_code":"K99","fiscal_years":[2019,2020],"award_amount_usd":204284,"org_name":"OREGON HEALTH & SCIENCE UNIVERSITY","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=K99CA237630","role":"generation","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-18T02:48:44.992046Z","snippet":null,"locator":"PMID 30333627 reported under K99CA237630","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 cBioPortal","detail":"Harmonized molecular and clinical files are open. Cite the original publication, and cite cBioPortal if the portal's harmonized files were used.","url":"https://www.cbioportal.org/study/summary?id=aml_ohsu_2018","requires":[],"est_time":"5 minutes","cli_snippet":null,"audience":"human","evidence":[{"method":"derived","source_url":"https://www.cbioportal.org/study/summary?id=aml_ohsu_2018","source_label":"cBioPortal access documentation","retrieved_at":"2026-09-21T12:30:59.429524Z","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":"Download the whole study as a zip","detail":"The datasets page carries the staging files used by the portal.","url":"https://www.cbioportal.org/datasets","requires":[],"est_time":"minutes","cli_snippet":null,"audience":"human","evidence":[{"method":"derived","source_url":"https://www.cbioportal.org/datasets","source_label":"cBioPortal access documentation","retrieved_at":"2026-09-21T12:30:59.429526Z","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":"Or pull the staging files with git-lfs","detail":"Study folders are named by study id under public/.","url":"https://github.com/cBioPortal/datahub","requires":[],"est_time":null,"cli_snippet":"git clone https://github.com/cBioPortal/datahub.git && cd datahub\ngit -c lfs.fetchexclude=\"\" lfs pull -I public/aml_ohsu_2018","audience":"human","evidence":[{"method":"derived","source_url":"https://github.com/cBioPortal/datahub","source_label":"cBioPortal access documentation","retrieved_at":"2026-09-21T12:30:59.429528Z","snippet":null,"locator":null,"confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Generated by applying the repository's documented access policy to this dataset's identifiers. It is not a reviewer's account of this dataset."}]},{"order":4,"action":"Read the study straight from the REST API","detail":"No key is required; pace requests when sweeping many studies.","url":"https://docs.cbioportal.org/web-api-and-clients/","requires":[],"est_time":null,"cli_snippet":"curl -s 'https://www.cbioportal.org/api/studies/aml_ohsu_2018/clinical-data?clinicalDataType=PATIENT&projection=SUMMARY'","audience":"agent","evidence":[{"method":"derived","source_url":"https://docs.cbioportal.org/web-api-and-clients/","source_label":"cBioPortal access documentation","retrieved_at":"2026-09-21T12:30:59.429529Z","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/cbio-aml-ohsu-2018.json","jsonld_url":"/data/jsonld/cbio-aml-ohsu-2018.jsonld","croissant_url":"/data/croissant/cbio-aml-ohsu-2018.json","instructions_url":"/data/agent/cbio-aml-ohsu-2018.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":35.7,"tags":["cbioportal","investigator-cohort","harmonized-for-reuse","nci-funded"],"search_text":null}