{"id":"cbio-lgg-ucsf-2014","title":"Low-Grade Gliomas (UCSF, Science 2014)","short_title":"lgg_ucsf_2014","aliases":["lgg_ucsf_2014"],"summary":"Whole exome sequencing of 23 grade II glioma tumor/normal pairs.","one_liner":null,"identifiers":[{"scheme":"cbioportal_study_id","value":"lgg_ucsf_2014","url":"https://www.cbioportal.org/study/summary?id=lgg_ucsf_2014","is_primary":true,"evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/lgg_ucsf_2014","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=lgg_ucsf_2014","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=lgg_ucsf_2014","cancer_types":[{"label":"Diffuse Glioma","ontology":"cBioPortal","code":"difg","url":null}],"primary_sites":["brain"],"subject":{"scope":"single","tissues":["BRAIN"],"evidence":[{"method":"derived","source_url":null,"source_label":"cds.subjects","retrieved_at":null,"snippet":null,"locator":"cancer_types: Diffuse Glioma; primary_sites: brain","confidence":"high","reviewer":null,"reviewed_at":null,"note":"OncoTree code rolled up to its pinned tissue."}]},"is_pediatric":null,"model_systems":[],"cohort":{"n_cases":23,"n_samples":61,"n_aliquots":null,"n_files":null,"total_bytes":null,"n_tumor_cases":null,"n_normal_cases":null,"has_matched_normal":null,"demographics":{"sex":{"Male":16,"Female":7},"race":{},"ethnicity":{},"age_at_diagnosis_years":{},"vital_status":{"DECEASED":14,"LIVING":8},"country_or_region":{},"evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/lgg_ucsf_2014","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:27:41.145433Z","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/lgg_ucsf_2014","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":61,"n_files":null,"data_levels":["processed matrix"],"access_tier":"open","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/lgg_ucsf_2014","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":"treatment","label":"Structured treatment records","platform":null,"n_cases":10,"n_samples":null,"n_files":12,"data_levels":[],"access_tier":"open","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/lgg_ucsf_2014","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-18T02:48:40.878054Z","snippet":null,"locator":"field: treatmentCount","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]}],"clinical_variables":[{"name":"cbioportal:GRADE","harmonized_name":"diagnoses.tumor_grade","label":"Neoplasm Histologic Grade","category":"pathology","n_nonmissing":61,"n_not_reported":0,"n_informative":61,"n_total":61,"coverage_pct":100.0,"populated_pct":100.0,"is_repeated":false,"example_values":["II","IV","III"],"unit":"samples","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/lgg_ucsf_2014","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:27:40.685716Z","snippet":null,"locator":"POST /clinical-data-counts/fetch, attribute GRADE; denominator is 61 samples","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":61,"n_not_reported":0,"n_informative":61,"n_total":61,"coverage_pct":100.0,"populated_pct":100.0,"is_repeated":false,"example_values":["ASTR","OAST","GB","AASTR","ODG"],"unit":"samples","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/lgg_ucsf_2014","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:27:40.685716Z","snippet":null,"locator":"POST /clinical-data-counts/fetch, attribute ONCOTREE_CODE; denominator is 61 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":22,"n_not_reported":0,"n_informative":22,"n_total":23,"coverage_pct":95.7,"populated_pct":95.7,"is_repeated":false,"example_values":["DECEASED","LIVING"],"unit":"patients","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/lgg_ucsf_2014","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:27:40.685716Z","snippet":null,"locator":"POST /clinical-data-counts/fetch, attribute OS_STATUS; denominator is 23 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":23,"n_not_reported":0,"n_informative":23,"n_total":23,"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/lgg_ucsf_2014","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:27:40.685716Z","snippet":null,"locator":"POST /clinical-data-counts/fetch, attribute SEX; denominator is 23 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":23,"n_not_reported":null,"n_informative":null,"n_total":23,"coverage_pct":null,"populated_pct":100.0,"is_repeated":false,"example_values":[],"unit":"months","evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/lgg_ucsf_2014","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:27:40.950697Z","snippet":null,"locator":"GET /studies/lgg_ucsf_2014/clinical-data?attributeId=OS_MONTHS; 23 of 23 patients carry a value","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"name":"cbioportal:therapeutic_agents","harmonized_name":"diagnoses.treatments.therapeutic_agents","label":"Named therapeutic agents","category":"treatment","n_nonmissing":10,"n_not_reported":null,"n_informative":null,"n_total":23,"coverage_pct":null,"populated_pct":43.5,"is_repeated":false,"example_values":["TMZ","TMZ + accutane","CCNU + thalidomide","TMZ + thalidomide"],"unit":null,"evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/lgg_ucsf_2014","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:27:41.145433Z","snippet":null,"locator":"POST /treatments/patient-counts/fetch; 10 of 23 patients have at least one named agent","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]}],"longitudinal":{"has_followup":true,"has_survival_endpoint":true,"survival_endpoints":["overall survival"],"median_followup_months":74.0,"max_followup_months":186.0,"n_cases_with_followup":23,"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/lgg_ucsf_2014","source_label":"cBioPortal API /studies","retrieved_at":"2026-09-19T03:27:41.145433Z","snippet":null,"locator":"derived from OS_MONTHS; 14 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/lgg_ucsf_2014","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":"24336570","pmcid":null,"doi":null,"title":null,"journal":null,"year":null,"authors_short":"Johnson et al. Science 2014","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/24336570/","is_open_access":null,"citation_count":null,"evidence":[{"method":"api","source_url":"https://www.cbioportal.org/api/studies/lgg_ucsf_2014","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":1113,"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":"2026-09-20T18:07:49.652327Z","no_reuse_identified":false,"evidence":[{"method":"derived","source_url":null,"source_label":"reuse index","retrieved_at":"2026-09-20T18:07:49.652327Z","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":"T32CA128583","project_num":null,"title":"Research Training in Childhood Cancer","pi_names":["Eric Alejandro Sweet-Cordero","KEVIN M. SHANNON"],"agency_ic":"NCI","activity_code":"T32","fiscal_years":[2007,2008,2009,2010,2011,2012,2013,2014,2015,2016,2017,2018,2019,2020,2021,2022,2023,2024,2025,2026],"award_amount_usd":6027869,"org_name":"UNIVERSITY OF CALIFORNIA, SAN FRANCISCO","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=T32CA128583","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 24336570 reported under T32CA128583","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":"R01CA169316","project_num":null,"title":"Imaging Guided Genomics of Malignant Transformation","pi_names":["Joseph F Costello"],"agency_ic":"NCI","activity_code":"R01","fiscal_years":[2013,2014,2015,2016,2017],"award_amount_usd":3046428,"org_name":"UNIVERSITY OF CALIFORNIA, SAN FRANCISCO","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=R01CA169316","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 24336570 reported under R01CA169316","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":"R01CA163336","project_num":null,"title":"Predicting Transcriptional and Epigenetic Networks in Cancer from Sequencing Data","pi_names":["Jun S Song"],"agency_ic":"NCI","activity_code":"R01","fiscal_years":[2012,2013,2014,2015,2016,2018,2019,2020,2021,2022,2024,2025,2026],"award_amount_usd":4383675,"org_name":"UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=R01CA163336","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 24336570 reported under R01CA163336","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":"P50CA097257","project_num":null,"title":"Administrative Core","pi_names":["MITCHEL S. BERGER","Susan M Chang","ANNETTE M MOLINARO","Joseph F Costello","Joanna Phillips","Hideho Okada"],"agency_ic":"NCI","activity_code":"P50","fiscal_years":[2025,2026],"award_amount_usd":8391087,"org_name":"UNIVERSITY OF CALIFORNIA, SAN FRANCISCO","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=P50CA097257","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 24336570 reported under P50CA097257","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":"P30CA082103","project_num":null,"title":"Leadership, Planning and Evaluation","pi_names":["Alan Ashworth","Charles Scott Craik","BENJAMIN BRAUN","Jennifer Leigh Clarke","Tung T. Nguyen","Eric Alejandro Sweet-Cordero","Susan M Chang","Nynikka Palmer","ERIC J SMALL","ANDREI GOGA","Tom Martin","EMILY K BERGSLAND","Pamela May Ling","Kate Taylor Shumate","Nicholas Butowski"],"agency_ic":"NCI","activity_code":"P30","fiscal_years":[2025,2026],"award_amount_usd":24675200,"org_name":"UNIVERSITY OF CALIFORNIA, SAN FRANCISCO","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=P30CA082103","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 24336570 reported under P30CA082103","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":"P01CA081403","project_num":null,"title":"PATHOLOGY","pi_names":["HIROYUKI SHIMADA","ROBERT Charles SEEGER","Michael A Sheard","Susan G. Groshen","KATHERINE Kurshan MATTHAY","WILLIAM A WEISS","Yves DeClerck","Nino Keshelava","PATRICK J REYNOLDS","Yves A DeClerck","CHARLES Patrick REYNOLDS"],"agency_ic":"CA","activity_code":"P01","fiscal_years":[2000,2001,2002,2003,2004,2005,2006,2007,2008,2009,2010,2011,2012,2013,2014],"award_amount_usd":45847776,"org_name":"CHILDREN'S HOSPITAL OF LOS ANGELES","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=P01CA081403","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 24336570 reported under P01CA081403","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=lgg_ucsf_2014","requires":[],"est_time":"5 minutes","cli_snippet":null,"audience":"human","evidence":[{"method":"derived","source_url":"https://www.cbioportal.org/study/summary?id=lgg_ucsf_2014","source_label":"cBioPortal access documentation","retrieved_at":"2026-09-21T12:30:59.439658Z","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":"2026-09-21T12:30:59.439661Z","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/lgg_ucsf_2014","audience":"human","evidence":[{"method":"derived","source_url":"https://github.com/cBioPortal/datahub","source_label":"cBioPortal access documentation","retrieved_at":"2026-09-21T12:30:59.439663Z","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/lgg_ucsf_2014/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":"2026-09-21T12:30:59.439665Z","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-lgg-ucsf-2014.json","jsonld_url":"/data/jsonld/cbio-lgg-ucsf-2014.jsonld","croissant_url":"/data/croissant/cbio-lgg-ucsf-2014.json","instructions_url":"/data/agent/cbio-lgg-ucsf-2014.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","treatment-annotated","nci-funded"],"search_text":null}