{"id":"https://openalex.org/W2131039280","doi":"https://doi.org/10.1093/bioinformatics/btt750","title":"Subclonal variant calling with multiple samples and prior knowledge","display_name":"Subclonal variant calling with multiple samples and prior knowledge","publication_year":2014,"publication_date":"2014-01-16","ids":{"openalex":"https://openalex.org/W2131039280","doi":"https://doi.org/10.1093/bioinformatics/btt750","mag":"2131039280","pmid":"https://pubmed.ncbi.nlm.nih.gov/24443148"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt750","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt750","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1093/bioinformatics/btt750","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005354262","display_name":"Moritz Gerstung","orcid":"https://orcid.org/0000-0001-6709-963X"},"institutions":[{"id":"https://openalex.org/I4210156194","display_name":"Addenbrooke's Hospital","ror":"https://ror.org/055vbxf86","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2802466933","https://openalex.org/I4210156194"]},{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Moritz Gerstung","raw_affiliation_strings":["1 Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK, 2Department of Haematology, Addenbrooke\u2019s Hospital, Cambridge CB2 0QQ, UK and 3Department of Haematology, University of Cambridge, Cambridge CB22XY, UK"],"affiliations":[{"raw_affiliation_string":"1 Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK, 2Department of Haematology, Addenbrooke\u2019s Hospital, Cambridge CB2 0QQ, UK and 3Department of Haematology, University of Cambridge, Cambridge CB22XY, UK","institution_ids":["https://openalex.org/I2802476451","https://openalex.org/I4210156194","https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077331342","display_name":"Elli Papaemmanuil","orcid":"https://orcid.org/0000-0003-1709-8983"},"institutions":[{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]},{"id":"https://openalex.org/I4210156194","display_name":"Addenbrooke's Hospital","ror":"https://ror.org/055vbxf86","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2802466933","https://openalex.org/I4210156194"]},{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Elli Papaemmanuil","raw_affiliation_strings":["1 Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK, 2Department of Haematology, Addenbrooke\u2019s Hospital, Cambridge CB2 0QQ, UK and 3Department of Haematology, University of Cambridge, Cambridge CB22XY, UK"],"affiliations":[{"raw_affiliation_string":"1 Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK, 2Department of Haematology, Addenbrooke\u2019s Hospital, Cambridge CB2 0QQ, UK and 3Department of Haematology, University of Cambridge, Cambridge CB22XY, UK","institution_ids":["https://openalex.org/I2802476451","https://openalex.org/I4210156194","https://openalex.org/I241749"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026738636","display_name":"Peter J. Campbell","orcid":"https://orcid.org/0000-0002-3921-0510"},"institutions":[{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]},{"id":"https://openalex.org/I4210156194","display_name":"Addenbrooke's Hospital","ror":"https://ror.org/055vbxf86","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2802466933","https://openalex.org/I4210156194"]},{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Peter J. Campbell","raw_affiliation_strings":["1 Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK, 2Department of Haematology, Addenbrooke\u2019s Hospital, Cambridge CB2 0QQ, UK and 3Department of Haematology, University of Cambridge, Cambridge CB22XY, UK"],"affiliations":[{"raw_affiliation_string":"1 Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK, 2Department of Haematology, Addenbrooke\u2019s Hospital, Cambridge CB2 0QQ, UK and 3Department of Haematology, University of Cambridge, Cambridge CB22XY, UK","institution_ids":["https://openalex.org/I2802476451","https://openalex.org/I4210156194","https://openalex.org/I241749"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5005354262"],"corresponding_institution_ids":["https://openalex.org/I241749","https://openalex.org/I2802476451","https://openalex.org/I4210156194"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.7789,"has_fulltext":false,"cited_by_count":161,"citation_normalized_percentile":{"value":0.90396242,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"30","issue":"9","first_page":"1198","last_page":"1204"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9998999834060669,"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":0.9998999834060669,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.9962000250816345,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9915000200271606,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5609320402145386},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5266485214233398},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5037943720817566},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.48699718713760376},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4707282781600952},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.4379521608352661},{"id":"https://openalex.org/keywords/point-mutation","display_name":"Point mutation","score":0.4190223813056946},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.4149111211299896},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.28831231594085693},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.20169848203659058}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5609320402145386},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5266485214233398},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5037943720817566},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.48699718713760376},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4707282781600952},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.4379521608352661},{"id":"https://openalex.org/C176944494","wikidata":"https://www.wikidata.org/wiki/Q1415380","display_name":"Point mutation","level":4,"score":0.4190223813056946},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.4149111211299896},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.28831231594085693},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.20169848203659058}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001699","descriptor_name":"Biometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001699","descriptor_name":"Biometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001699","descriptor_name":"Biometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011379","descriptor_name":"Prognosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011379","descriptor_name":"Prognosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011379","descriptor_name":"Prognosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012985","descriptor_name":"Software Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012985","descriptor_name":"Software Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012985","descriptor_name":"Software Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btt750","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt750","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:24443148","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24443148","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,"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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:2975772","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3998123","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt750","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt750","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2132831713","display_name":null,"funder_award_id":"077012/Z/05/Z","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G7554413032","display_name":null,"funder_award_id":"WT088340MA","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"}],"funders":[{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320320104","display_name":"Kay Kendall Leukaemia Fund","ror":"https://ror.org/03j2wfg84"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W1967997373","https://openalex.org/W1979946545","https://openalex.org/W1989773675","https://openalex.org/W1993236149","https://openalex.org/W2015049472","https://openalex.org/W2033666853","https://openalex.org/W2062375641","https://openalex.org/W2080660780","https://openalex.org/W2088580309","https://openalex.org/W2103441770","https://openalex.org/W2109991075","https://openalex.org/W2129925362","https://openalex.org/W2138601221","https://openalex.org/W2140419897","https://openalex.org/W2143197030","https://openalex.org/W2144892629","https://openalex.org/W2151794156","https://openalex.org/W2161724277","https://openalex.org/W2582743722","https://openalex.org/W4247053599"],"related_works":["https://openalex.org/W2160983714","https://openalex.org/W2943623134","https://openalex.org/W2550943714","https://openalex.org/W3212350425","https://openalex.org/W2388007221","https://openalex.org/W2511508046","https://openalex.org/W2363458739","https://openalex.org/W2028961943","https://openalex.org/W2375287167","https://openalex.org/W1994083192"],"abstract_inverted_index":{"Here":[0],"we":[1],"present":[2],"a":[3,49,58],"novel":[4],"statistical":[5],"approach":[6],"for":[7,21],"calling":[8,62],"mutations":[9,30,64],"from":[10],"large":[11],"cohorts":[12],"of":[13,44,48,61],"deeply":[14],"resequenced":[15],"cancer":[16,63],"genes.":[17],"These":[18],"data":[19],"allow":[20],"precisely":[22],"estimating":[23],"local":[24],"error":[25],"profiles":[26],"and":[27,34,65,71],"enable":[28],"detecting":[29],"with":[31],"high":[32,59],"sensitivity":[33],"specificity.":[35],"Our":[36],"probabilistic":[37],"method":[38],"incorporates":[39],"knowledge":[40],"about":[41],"the":[42,68],"distribution":[43],"variants":[45,73],"in":[46],"terms":[47],"prior":[50],"probability.":[51],"We":[52],"show":[53],"that":[54,67],"our":[55],"algorithm":[56],"has":[57],"accuracy":[60],"demonstrate":[66],"detected":[69],"clonal":[70],"subclonal":[72],"have":[74],"important":[75],"prognostic":[76],"consequences.":[77]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":15},{"year":2023,"cited_by_count":19},{"year":2022,"cited_by_count":26},{"year":2021,"cited_by_count":23},{"year":2020,"cited_by_count":15},{"year":2019,"cited_by_count":10},{"year":2018,"cited_by_count":17},{"year":2017,"cited_by_count":13},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":5}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}