{"id":"https://openalex.org/W3007416007","doi":"https://doi.org/10.1177/1176935120907399","title":"A Pan-Cancer and Polygenic Bayesian Hierarchical Model for the Effect of Somatic Mutations on Survival","display_name":"A Pan-Cancer and Polygenic Bayesian Hierarchical Model for the Effect of Somatic Mutations on Survival","publication_year":2020,"publication_date":"2020-01-01","ids":{"openalex":"https://openalex.org/W3007416007","doi":"https://doi.org/10.1177/1176935120907399","mag":"3007416007","pmid":"https://pubmed.ncbi.nlm.nih.gov/32116467","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/7029540"},"language":"en","primary_location":{"id":"doi:10.1177/1176935120907399","doi":"https://doi.org/10.1177/1176935120907399","is_oa":true,"landing_page_url":"https://doi.org/10.1177/1176935120907399","pdf_url":null,"source":{"id":"https://openalex.org/S55012689","display_name":"Cancer Informatics","issn_l":"1176-9351","issn":["1176-9351"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","norway-1","poland-40","russia-white-list-3"],"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Cancer Informatics","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["arxiv","crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1177/1176935120907399","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022527874","display_name":"Sarah Samorodnitsky","orcid":"https://orcid.org/0000-0001-7909-0245","observed_orcids":["https://orcid.org/0000-0001-7909-0245"]},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sarah Samorodnitsky","raw_affiliation_strings":["Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002773659","display_name":"Katherine A. Hoadley","orcid":"https://orcid.org/0000-0002-1216-477X","observed_orcids":["https://orcid.org/0000-0002-1216-477X"]},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]},{"id":"https://openalex.org/I4390039329","display_name":"UNC Lineberger Comprehensive Cancer Center","ror":"https://ror.org/043ehm030","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I114027177","https://openalex.org/I4390039329"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Katherine A Hoadley","raw_affiliation_strings":["Department of Genetics, Computational Medicine Program, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, Computational Medicine Program, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I114027177","https://openalex.org/I4390039329"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055014782","display_name":"Eric F. Lock","orcid":"https://orcid.org/0000-0003-4663-2356","observed_orcids":["https://orcid.org/0000-0003-4663-2356"]},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Eric F Lock","raw_affiliation_strings":["Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA"],"raw_orcid":"https://orcid.org/0000-0003-4663-2356","affiliations":[{"raw_affiliation_string":"Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA","institution_ids":["https://openalex.org/I130238516"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5055014782"],"corresponding_institution_ids":["https://openalex.org/I130238516"],"apc_list":{"value":1848,"currency":"USD","value_usd":1848},"apc_paid":{"value":1848,"currency":"USD","value_usd":1848},"fwci":0.1671,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.32924586,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":96},"biblio":{"volume":"19","issue":null,"first_page":"1176935120907399","last_page":"1176935120907399"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.8281000256538391,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.8281000256538391,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.06679999828338623,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10136","display_name":"Statistical Methods and Inference","score":0.010099999606609344,"subfield":{"id":"https://openalex.org/subfields/2613","display_name":"Statistics and Probability"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/somatic-mutations","display_name":"somatic mutations","score":0.9290000200271606},{"id":"https://openalex.org/keywords/patient-survival","display_name":"patient survival","score":0.6890000104904175},{"id":"https://openalex.org/keywords/bayesian-hierarchical-model","display_name":"Bayesian hierarchical model","score":0.7620000243186951},{"id":"https://openalex.org/keywords/pan-cancer-analysis","display_name":"pan-cancer analysis","score":0.9110000133514404},{"id":"https://openalex.org/keywords/polygenic-risk","display_name":"polygenic risk","score":0.593999981880188},{"id":"https://openalex.org/keywords/survival-prediction","display_name":"survival prediction","score":0.5519999861717224},{"id":"https://openalex.org/keywords/tp53","display_name":"TP53","score":0.6909999847412109},{"id":"https://openalex.org/keywords/fat4","display_name":"FAT4","score":0.9980000257492065},{"id":"https://openalex.org/keywords/parametric-survival-models","display_name":"parametric survival models","score":0.8370000123977661},{"id":"https://openalex.org/keywords/cross-validation","display_name":"cross-validation","score":0.75},{"id":"https://openalex.org/keywords/forward-selection","display_name":"forward selection","score":0.5820000171661377}],"concepts":[{"id":"https://openalex.org/C10515644","wikidata":"https://www.wikidata.org/wiki/Q543310","display_name":"Survival analysis","level":2,"score":0.5772705674171448},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.5639017224311829},{"id":"https://openalex.org/C168136583","wikidata":"https://www.wikidata.org/wiki/Q1988242","display_name":"Bayesian information criterion","level":2,"score":0.4717501103878021},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.4663025438785553},{"id":"https://openalex.org/C98638677","wikidata":"https://www.wikidata.org/wiki/Q2067051","display_name":"Mutation rate","level":3,"score":0.4655402898788452},{"id":"https://openalex.org/C50382708","wikidata":"https://www.wikidata.org/wiki/Q223218","display_name":"Proportional hazards model","level":2,"score":0.46187615394592285},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.44557806849479675},{"id":"https://openalex.org/C93959086","wikidata":"https://www.wikidata.org/wiki/Q6888345","display_name":"Model selection","level":2,"score":0.4445207417011261},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.42640814185142517},{"id":"https://openalex.org/C33114746","wikidata":"https://www.wikidata.org/wiki/Q4672282","display_name":"Accelerated failure time model","level":3,"score":0.426127552986145},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.42495840787887573},{"id":"https://openalex.org/C117251300","wikidata":"https://www.wikidata.org/wiki/Q1849855","display_name":"Parametric statistics","level":2,"score":0.42089128494262695},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3888856768608093},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.3771935701370239},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3652072548866272},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3528482913970947},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.338878333568573},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.20636451244354248},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.14479324221611023}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1177/1176935120907399","doi":"https://doi.org/10.1177/1176935120907399","is_oa":true,"landing_page_url":"https://doi.org/10.1177/1176935120907399","pdf_url":null,"source":{"id":"https://openalex.org/S55012689","display_name":"Cancer Informatics","issn_l":"1176-9351","issn":["1176-9351"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","norway-1","poland-40","russia-white-list-3"],"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Cancer Informatics","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7029540","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7029540","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Cancer Inform","raw_type":"Text"},{"id":"pmid:32116467","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32116467","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Cancer informatics","raw_type":"Journal Article"},{"id":"pmh:oai:arXiv.org:1910.03447","doi":null,"is_oa":true,"landing_page_url":"http://arxiv.org/abs/1910.03447","pdf_url":"https://arxiv.org/pdf/1910.03447","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:oai:doaj.org/article:33f9892188bd431f9c20693a8c0f0878","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/33f9892188bd431f9c20693a8c0f0878","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Cancer Informatics, Vol 19 (2020)","raw_type":"article"},{"id":"doi:10.48550/arxiv.1910.03447","doi":"https://doi.org/10.48550/arxiv.1910.03447","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.1910.03447","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"doi:10.1177/1176935120907399","doi":"https://doi.org/10.1177/1176935120907399","is_oa":true,"landing_page_url":"https://doi.org/10.1177/1176935120907399","pdf_url":null,"source":{"id":"https://openalex.org/S55012689","display_name":"Cancer Informatics","issn_l":"1176-9351","issn":["1176-9351"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","norway-1","poland-40","russia-white-list-3"],"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Cancer Informatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.8999999761581421}],"study_designs":[],"awards":[{"id":"https://openalex.org/G3712162557","display_name":"Bidimensional integration for pan-omics pan-cancer analysis","funder_award_id":"R21CA231214","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3007416007.pdf","grobid_xml":"https://content.openalex.org/works/W3007416007.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W128740895","https://openalex.org/W1967220865","https://openalex.org/W1986241711","https://openalex.org/W2010522003","https://openalex.org/W2016219233","https://openalex.org/W2016661249","https://openalex.org/W2022495797","https://openalex.org/W2044702943","https://openalex.org/W2129769331","https://openalex.org/W2130448611","https://openalex.org/W2158485828","https://openalex.org/W2161289668","https://openalex.org/W2180481128","https://openalex.org/W2182055431","https://openalex.org/W2204695746","https://openalex.org/W2245213139","https://openalex.org/W2560367415","https://openalex.org/W2795686629","https://openalex.org/W2795989238","https://openalex.org/W2796153844","https://openalex.org/W2796408191","https://openalex.org/W2942596637","https://openalex.org/W2967978211","https://openalex.org/W4301159569","https://openalex.org/W4376143856"],"related_works":["https://openalex.org/W4379378700","https://openalex.org/W4386257980","https://openalex.org/W6958409232","https://openalex.org/W7070337274","https://openalex.org/W3100329089","https://openalex.org/W2167278498","https://openalex.org/W2952051154","https://openalex.org/W3152072428","https://openalex.org/W2027654939","https://openalex.org/W4384664196"],"abstract_inverted_index":{"We":[0,171],"built":[1],"a":[2,65,108,148],"novel":[3],"Bayesian":[4],"hierarchical":[5],"survival":[6,53,95,146],"model":[7,29,116,131,174],"based":[8],"on":[9,52,117,126,145],"the":[10,28,38,78,122,133,139,164,173,202],"somatic":[11],"mutation":[12,42,66],"profile":[13],"of":[14,57,64,81,142],"patients":[15],"across":[16,33,54,86],"50":[17],"genes":[18],"and":[19,100,102,120,136,160,201],"27":[20],"cancer":[21,34,75],"types.":[22,61],"The":[23,62,129,189],"pan-cancer":[24],"quality":[25],"allows":[26],"for":[27,167,182,192],"to":[30,72,177],"\u201cborrow\u201d":[31],"information":[32],"types,":[35],"motivated":[36],"by":[37,74],"assumption":[39],"that":[40,156,179],"similar":[41,46],"profiles":[43],"may":[44],"have":[45],"(but":[47],"not":[48],"necessarily":[49],"identical)":[50],"effects":[51],"different":[55],"tissues":[56],"origin":[58],"or":[59],"tumor":[60],"effect":[63,80,141],"at":[67,158,198,206],"each":[68,82,115,143],"gene":[69,83,144],"was":[70,84],"allowed":[71],"vary":[73],"type,":[76],"whereas":[77],"mean":[79],"shared":[85],"cancers.":[87],"Within":[88],"this":[89,153,193],"framework,":[90],"we":[91,103,113,137,154],"considered":[92],"4":[93],"parametric":[94],"models":[96],"(normal,":[97],"log-normal,":[98],"exponential,":[99],"Weibull),":[101],"compared":[104],"their":[105],"performance":[106],"via":[107,147,175],"cross-validation":[109],"approach":[110],"in":[111],"which":[112],"fit":[114],"training":[118],"data":[119],"estimate":[121],"log-posterior":[123],"predictive":[124],"likelihood":[125],"test":[127],"data.":[128],"log-normal":[130],"gave":[132,185],"best":[134],"fit,":[135],"investigated":[138],"partial":[140],"forward":[149],"selection":[150],"procedure.":[151],"Through":[152],"determined":[155],"mutations":[157],"TP53":[159],"FAT4":[161],"were":[162],"together":[163],"most":[165],"useful":[166],"predicting":[168],"patient":[169],"survival.":[170],"validated":[172],"simulation":[176],"ensure":[178],"our":[180],"algorithm":[181],"posterior":[183],"computation":[184],"nominal":[186],"coverage":[187],"rates.":[188],"code":[190],"used":[191],"analysis":[194],"can":[195],"be":[196],"found":[197],"https://github.com/sarahsamorodnitsky/Pan-Cancer-Survival-Modeling.git":[199],",":[200],"results":[203],"are":[204],"summarized":[205],"http://ericfrazerlock.com/surv_figs/SurvivalDisplay.html":[207],".":[208]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2020-03-06T00:00:00"}
