{"id":"https://openalex.org/W3005774532","doi":"https://doi.org/10.1371/journal.pcbi.1007603","title":"SuperFreq: Integrated mutation detection and clonal tracking in cancer","display_name":"SuperFreq: Integrated mutation detection and clonal tracking in cancer","publication_year":2020,"publication_date":"2020-02-13","ids":{"openalex":"https://openalex.org/W3005774532","doi":"https://doi.org/10.1371/journal.pcbi.1007603","mag":"3005774532","pmid":"https://pubmed.ncbi.nlm.nih.gov/32053599"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1007603","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007603","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007603&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007603&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5015244755","display_name":"Christoffer Flensburg","orcid":"https://orcid.org/0000-0002-3280-8966"},"institutions":[{"id":"https://openalex.org/I196021976","display_name":"Walter and Eliza Hall Institute of Medical Research","ror":"https://ror.org/01b6kha49","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I196021976"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Christoffer Flensburg","raw_affiliation_strings":["Division of Cancer and Haematology, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia"],"raw_orcid":"https://orcid.org/0000-0002-3280-8966","affiliations":[{"raw_affiliation_string":"Division of Cancer and Haematology, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia","institution_ids":["https://openalex.org/I196021976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037664752","display_name":"Tobias Sargeant","orcid":"https://orcid.org/0000-0002-0909-7182"},"institutions":[{"id":"https://openalex.org/I196021976","display_name":"Walter and Eliza Hall Institute of Medical Research","ror":"https://ror.org/01b6kha49","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I196021976"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Tobias Sargeant","raw_affiliation_strings":["Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia","institution_ids":["https://openalex.org/I196021976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066632434","display_name":"Alicia Oshlack","orcid":"https://orcid.org/0000-0001-9788-5690"},"institutions":[{"id":"https://openalex.org/I1321649718","display_name":"Royal Children's Hospital","ror":"https://ror.org/02rktxt32","country_code":"AU","type":"healthcare","lineage":["https://openalex.org/I1321649718"]},{"id":"https://openalex.org/I2800555584","display_name":"Peter MacCallum Cancer Centre","ror":"https://ror.org/02a8bt934","country_code":"AU","type":"healthcare","lineage":["https://openalex.org/I2800555584"]},{"id":"https://openalex.org/I4210150290","display_name":"Murdoch Children's Research Institute","ror":"https://ror.org/048fyec77","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I4210150290"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Alicia Oshlack","raw_affiliation_strings":["Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Australia","Peter MacCallum Cancer Centre, Melbourne, Australia"],"raw_orcid":"https://orcid.org/0000-0001-9788-5690","affiliations":[{"raw_affiliation_string":"Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Australia","institution_ids":["https://openalex.org/I1321649718","https://openalex.org/I4210150290"]},{"raw_affiliation_string":"Peter MacCallum Cancer Centre, Melbourne, Australia","institution_ids":["https://openalex.org/I2800555584"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5002572034","display_name":"Ian J. Majewski","orcid":"https://orcid.org/0000-0002-6087-635X"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I196021976","display_name":"Walter and Eliza Hall Institute of Medical Research","ror":"https://ror.org/01b6kha49","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I196021976"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Ian J. Majewski","raw_affiliation_strings":["Division of Cancer and Haematology, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia","Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia"],"raw_orcid":"https://orcid.org/0000-0002-6087-635X","affiliations":[{"raw_affiliation_string":"Division of Cancer and Haematology, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia","institution_ids":["https://openalex.org/I196021976"]},{"raw_affiliation_string":"Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia","institution_ids":["https://openalex.org/I165779595"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5002572034","https://openalex.org/A5015244755"],"corresponding_institution_ids":["https://openalex.org/I165779595","https://openalex.org/I196021976"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":3.6725,"has_fulltext":true,"cited_by_count":56,"citation_normalized_percentile":{"value":0.95105228,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"16","issue":"2","first_page":"e1007603","last_page":"e1007603"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9983999729156494,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9955999851226807,"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/exome-sequencing","display_name":"Exome sequencing","score":0.668157696723938},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6125043630599976},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5857529640197754},{"id":"https://openalex.org/keywords/exome","display_name":"Exome","score":0.5691224336624146},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.514837920665741},{"id":"https://openalex.org/keywords/somatic-cell","display_name":"Somatic cell","score":0.4535653293132782},{"id":"https://openalex.org/keywords/germline","display_name":"Germline","score":0.43378424644470215},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.41684696078300476},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.410925954580307},{"id":"https://openalex.org/keywords/germline-mutation","display_name":"Germline mutation","score":0.41046178340911865},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.3387499451637268},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2571435868740082}],"concepts":[{"id":"https://openalex.org/C16671776","wikidata":"https://www.wikidata.org/wiki/Q5420592","display_name":"Exome sequencing","level":4,"score":0.668157696723938},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6125043630599976},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5857529640197754},{"id":"https://openalex.org/C10590036","wikidata":"https://www.wikidata.org/wiki/Q417664","display_name":"Exome","level":5,"score":0.5691224336624146},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.514837920665741},{"id":"https://openalex.org/C134305767","wikidata":"https://www.wikidata.org/wiki/Q725508","display_name":"Somatic cell","level":3,"score":0.4535653293132782},{"id":"https://openalex.org/C109825262","wikidata":"https://www.wikidata.org/wiki/Q1139164","display_name":"Germline","level":3,"score":0.43378424644470215},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.41684696078300476},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.410925954580307},{"id":"https://openalex.org/C13514818","wikidata":"https://www.wikidata.org/wiki/Q5552256","display_name":"Germline mutation","level":4,"score":0.41046178340911865},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.3387499451637268},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2571435868740082}],"mesh":[{"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":"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":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060965","descriptor_name":"Clonal Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060965","descriptor_name":"Clonal Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060965","descriptor_name":"Clonal Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1007603","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007603","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007603&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:32053599","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32053599","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:jupiter.its.unimelb.edu.au:11343/245619","is_oa":true,"landing_page_url":"http://hdl.handle.net/11343/245619","pdf_url":"http://hdl.handle.net/11343/245619","source":{"id":"https://openalex.org/S4377196259","display_name":"Minerva Access (University of Melbourne)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I165779595","host_organization_name":"The University of Melbourne","host_organization_lineage":["https://openalex.org/I165779595"],"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":"","raw_type":"Journal Article"},{"id":"pmh:oai:doaj.org/article:d340fd5794ea4940b93de0376ed72bed","is_oa":true,"landing_page_url":"https://doaj.org/article/d340fd5794ea4940b93de0376ed72bed","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 16, Iss 2, p e1007603 (2020)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/11851839","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/SuperFreq_Integrated_mutation_detection_and_clonal_tracking_in_cancer/11851839","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Dataset"},{"id":"pmh:oai:pubmedcentral.nih.gov:7043783","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7043783","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,"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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1007603","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007603","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007603&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5832491806","display_name":null,"funder_award_id":"1145912","funder_id":"https://openalex.org/F4320334705","funder_display_name":"National Health and Medical Research Council"}],"funders":[{"id":"https://openalex.org/F4320325591","display_name":"Instituto Carlos Slim de la Salud","ror":null},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320334705","display_name":"National Health and Medical Research Council","ror":"https://ror.org/011kf5r70"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3005774532.pdf","grobid_xml":"https://content.openalex.org/works/W3005774532.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W1979115864","https://openalex.org/W2015182193","https://openalex.org/W2025000087","https://openalex.org/W2048968984","https://openalex.org/W2081098333","https://openalex.org/W2093144236","https://openalex.org/W2111874706","https://openalex.org/W2118151336","https://openalex.org/W2122732537","https://openalex.org/W2137526110","https://openalex.org/W2138207763","https://openalex.org/W2138601221","https://openalex.org/W2139838486","https://openalex.org/W2146290346","https://openalex.org/W2150575159","https://openalex.org/W2151794156","https://openalex.org/W2155943701","https://openalex.org/W2170490448","https://openalex.org/W2171892226","https://openalex.org/W2256016639","https://openalex.org/W2417483443","https://openalex.org/W2426586472","https://openalex.org/W2513185582","https://openalex.org/W2565436052","https://openalex.org/W2566331076","https://openalex.org/W2611387862","https://openalex.org/W2625174343","https://openalex.org/W2756224533","https://openalex.org/W2765315748","https://openalex.org/W2783702177","https://openalex.org/W2896450660","https://openalex.org/W2947588609","https://openalex.org/W2952265064","https://openalex.org/W2952615074","https://openalex.org/W4253347679"],"related_works":["https://openalex.org/W2000783020","https://openalex.org/W2606201227","https://openalex.org/W2086399984","https://openalex.org/W1491598325","https://openalex.org/W2310082378","https://openalex.org/W3026290368","https://openalex.org/W3134821389","https://openalex.org/W4296060409","https://openalex.org/W2041452721","https://openalex.org/W3024875366"],"abstract_inverted_index":{"Analysing":[0],"multiple":[1,53,120],"cancer":[2,81,161,188],"samples":[3,121,158,191],"from":[4,44,122,140],"an":[5,269],"individual":[6],"patient":[7],"can":[8,250],"provide":[9],"insight":[10],"into":[11],"the":[12,14,18,28,32,49,73,171,174,216,237,259],"way":[13],"disease":[15,33],"evolves.":[16],"Monitoring":[17],"expansion":[19],"and":[20,34,95,100,112,143,169,176,189,211,222,249,263,278],"contraction":[21],"of":[22,75,89,173,187,201,207,231,236,261,271],"distinct":[23],"clones":[24,202],"helps":[25,136],"to":[26,51,131,137,144,215,273],"reveal":[27],"mutations":[29,212],"that":[30,36,55,86,197],"initiate":[31],"those":[35],"drive":[37],"progression.":[38],"Existing":[39],"approaches":[40],"for":[41,59,103,233,258],"clonal":[42,101,133,181],"tracking":[43,102],"sequencing":[45,83],"data":[46],"typically":[47],"require":[48,65,108],"user":[50],"combine":[52],"tools":[54],"are":[56],"not":[57,107],"purpose-built":[58],"this":[60],"task.":[61],"Furthermore,":[62],"most":[63,234],"methods":[64],"a":[66,80,109,123,204,228,242],"matched":[67,110,243],"normal":[68,111,190],"(non-tumour)":[69],"sample,":[70],"which":[71,135],"limits":[72],"scope":[74],"application.":[76],"We":[77,179,195,267],"developed":[78],"SuperFreq,":[79],"exome":[82,157],"analysis":[84,238,260],"pipeline":[85],"integrates":[87],"identification":[88],"somatic":[90,139],"single":[91,124],"nucleotide":[92],"variants":[93],"(SNVs)":[94],"copy":[96],"number":[97],"alterations":[98],"(CNAs)":[99],"both.":[104],"SuperFreq":[105,126,198,226,245,272],"does":[106],"instead":[113],"relies":[114],"on":[115],"unrelated":[116],"controls.":[117],"When":[118],"analysing":[119],"patient,":[125],"cross":[127],"checks":[128],"variant":[129],"calls":[130],"improve":[132],"tracking,":[134],"separate":[138],"germline":[141],"variants,":[142],"resolve":[145],"overlapping":[146],"CNA":[147,177],"calls.":[148,178],"To":[149],"demonstrate":[150,268],"our":[151],"software":[152],"we":[153],"analysed":[154],"304":[155],"cancer-normal":[156],"across":[159],"33":[160],"types":[162],"in":[163,184,192,253],"The":[164],"Cancer":[165],"Genome":[166],"Atlas":[167],"(TCGA)":[168],"evaluated":[170],"quality":[172],"SNV":[175],"simulated":[180],"evolution":[182],"through":[183],"silico":[185],"mixing":[186],"known":[193],"proportion.":[194],"found":[196],"identified":[199],"93%":[200],"with":[203,219,276],"cellular":[205],"fraction":[206],"at":[208],"least":[209],"50%":[210],"were":[213],"assigned":[214],"correct":[217],"clone":[218],"high":[220],"recall":[221],"precision.":[223],"In":[224],"addition,":[225],"maintained":[227],"similar":[229],"level":[230],"performance":[232],"aspects":[235],"when":[239],"run":[240],"without":[241],"normal.":[244],"is":[246],"highly":[247],"versatile":[248],"be":[251],"applied":[252],"many":[254],"different":[255],"experimental":[256],"settings":[257],"exomes":[262],"other":[264],"capture":[265],"libraries.":[266],"application":[270],"leukaemia":[274],"patients":[275],"diagnosis":[277],"relapse":[279],"samples.":[280]},"counts_by_year":[{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":21},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":2},{"year":2017,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}