{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T16:14:15Z","timestamp":1761581655679,"version":"3.37.3"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2018,1,27]],"date-time":"2018-01-27T00:00:00Z","timestamp":1517011200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"China Thousand-Talent"},{"name":"Chinese Academy of Sciences Hundred-Talent","award":["Y6G7011018"],"award-info":[{"award-number":["Y6G7011018"]}]},{"name":"Personalized Medicines"},{"name":"Molecular Signature-based Drug Discovery and Development"},{"name":"Strategic Priority Research Program of the Chinese Academy of Sciences","award":["XDA12050202"],"award-info":[{"award-number":["XDA12050202"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Tumor purity and ploidy have a substantial impact on next-gen sequence analyses of tumor samples and may alter the biological and clinical interpretation of results. Despite the existence of several computational methods that are dedicated to estimate tumor purity and\/or ploidy from The Cancer Genome Atlas (TCGA) tumor-normal whole-genome-sequencing (WGS) data, an accurate, fast and fully-automated method that works in a wide range of sequencing coverage, level of tumor purity and level of intra-tumor heterogeneity, is still missing.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We describe a computational method called Accurity that infers tumor purity, tumor cell ploidy and absolute allelic copy numbers for somatic copy number alterations (SCNAs) from tumor-normal WGS data by jointly modelling SCNAs and heterozygous germline single-nucleotide-variants (HGSNVs). Results from both in silico and real sequencing data demonstrated that Accurity is highly accurate and robust, even in low-purity, high-ploidy and low-coverage settings in which several existing methods perform poorly. Accounting for tumor purity and ploidy, Accurity significantly increased signal\/noise gaps between different copy numbers. We are hopeful that Accurity is of clinical use for identifying cancer diagnostic biomarkers.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Accurity is implemented in C++\/Rust, available at http:\/\/www.yfish.org\/software\/.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty043","type":"journal-article","created":{"date-parts":[[2018,1,26]],"date-time":"2018-01-26T20:10:38Z","timestamp":1516997438000},"page":"2004-2011","source":"Crossref","is-referenced-by-count":21,"title":["Accurity: accurate tumor purity and ploidy inference from tumor-normal WGS data by jointly modelling somatic copy number alterations and heterozygous germline single-nucleotide-variants"],"prefix":"10.1093","volume":"34","author":[{"given":"Zhihui","family":"Luo","sequence":"first","affiliation":[{"name":"State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China"}]},{"given":"Xinping","family":"Fan","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China"},{"name":"University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, China"}]},{"given":"Yao","family":"Su","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5967-4948","authenticated-orcid":false,"given":"Yu S","family":"Huang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China"},{"name":"University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, China"}]}],"member":"286","published-online":{"date-parts":[[2018,1,27]]},"reference":[{"key":"2023012713392421500_bty043-B1","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1093\/bib\/bbu004","article-title":"Comparative analysis of methods for identifying somatic copy number alterations from deep sequencing data","volume":"16","author":"Alkodsi","year":"2015","journal-title":"Brief. Bioinf"},{"key":"2023012713392421500_bty043-B2","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1093\/bioinformatics\/btt622","article-title":"EXPANDS: expanding ploidy and allele frequency on nested subpopulations","volume":"30","author":"Andor","year":"2014","journal-title":"Bioinformatics"},{"key":"2023012713392421500_bty043-B3","doi-asserted-by":"crossref","first-page":"8971","DOI":"10.1038\/ncomms9971","article-title":"Systematic pan-cancer analysis of tumour purity","volume":"6","author":"Aran","year":"2015","journal-title":"Nat. Commun"},{"key":"2023012713392421500_bty043-B4","doi-asserted-by":"crossref","first-page":"e72.","DOI":"10.1093\/nar\/gks001","article-title":"Summarizing and correcting the GC content bias in high-throughput sequencing","volume":"40","author":"Benjamini","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2023012713392421500_bty043-B5","doi-asserted-by":"crossref","first-page":"899","DOI":"10.1038\/nature08822","article-title":"The landscape of somatic copy-number alteration across human cancers","volume":"463","author":"Beroukhim","year":"2010","journal-title":"Nature"},{"key":"2023012713392421500_bty043-B6","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1038\/nrc1976","article-title":"Linking oncogenic pathways with therapeutic opportunities","volume":"6","author":"Bild","year":"2006","journal-title":"Nat. Rev. Cancer"},{"key":"2023012713392421500_bty043-B7","doi-asserted-by":"crossref","first-page":"3443","DOI":"10.1093\/bioinformatics\/btu436","article-title":"Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data","volume":"30","author":"Boeva","year":"2014","journal-title":"Bioinformatics"},{"key":"2023012713392421500_bty043-B8","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1038\/nbt.2203","article-title":"Absolute quantification of somatic DNA alterations in human cancer","volume":"30","author":"Carter","year":"2012","journal-title":"Nat. Biotechnol"},{"key":"2023012713392421500_bty043-B9","doi-asserted-by":"crossref","first-page":"293","DOI":"10.2217\/bmm.11.37","article-title":"Comprehensive next-generation cancer genome sequencing in the era of targeted therapy and personalized oncology","volume":"5","author":"Cronin","year":"2011","journal-title":"Biomark. Med"},{"key":"2023012713392421500_bty043-B10","doi-asserted-by":"crossref","first-page":"3207","DOI":"10.1093\/bioinformatics\/btp579","article-title":"Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data","volume":"25","author":"Degner","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012713392421500_bty043-B11","doi-asserted-by":"crossref","first-page":"54.","DOI":"10.1186\/1755-8794-4-54","article-title":"Systematic bias in genomic classification due to contaminating non-neoplastic tissue in breast tumor samples","volume":"4","author":"Elloumi","year":"2011","journal-title":"BMC Med. Genomics"},{"key":"2023012713392421500_bty043-B12","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1093\/annonc\/mdu479","article-title":"Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data","volume":"26","author":"Favero","year":"2015","journal-title":"Ann. Oncol. Off. J. Eur. Soc. Med. Oncol"},{"key":"2023012713392421500_bty043-B13","doi-asserted-by":"crossref","first-page":"79.","DOI":"10.1186\/s13073-016-0333-9","article-title":"The impact of tumor profiling approaches and genomic data strategies for cancer precision medicine","volume":"8","author":"Garofalo","year":"2016","journal-title":"Genome Med"},{"key":"2023012713392421500_bty043-B14","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1093\/bioinformatics\/btr593","article-title":"Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data","volume":"28","author":"Gusnanto","year":"2012","journal-title":"Bioinformatics"},{"key":"2023012713392421500_bty043-B15","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1016\/j.cell.2011.02.013","article-title":"Hallmarks of cancer: the next generation","volume":"144","author":"Hanahan","year":"2011","journal-title":"Cell"},{"key":"2023012713392421500_bty043-B16","doi-asserted-by":"crossref","first-page":"568","DOI":"10.1101\/gr.129684.111","article-title":"VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing","volume":"22","author":"Koboldt","year":"2012","journal-title":"Genome Res"},{"key":"2023012713392421500_bty043-B17","doi-asserted-by":"crossref","first-page":"1888","DOI":"10.1093\/bioinformatics\/btt293","article-title":"PurBayes: estimating tumor cellularity and subclonality in next-generation sequencing data","volume":"29","author":"Larson","year":"2013","journal-title":"Bioinformatics"},{"key":"2023012713392421500_bty043-B18","doi-asserted-by":"crossref","first-page":"2121","DOI":"10.1093\/bioinformatics\/btu174","article-title":"Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity","volume":"30","author":"Li","year":"2014","journal-title":"Bioinformatics"},{"key":"2023012713392421500_bty043-B19","doi-asserted-by":"crossref","first-page":"1868","DOI":"10.18632\/oncotarget.1537","article-title":"Computational methods for detecting copy number variations in cancer genome using next generation sequencing: principles and challenges","volume":"4","author":"Liu","year":"2013","journal-title":"Oncotarget"},{"key":"2023012713392421500_bty043-B20","doi-asserted-by":"crossref","first-page":"R24.","DOI":"10.1186\/gb-2013-14-3-r24","article-title":"Patchwork: allele-specific copy number analysis of whole-genome sequenced tumor tissue","volume":"14","author":"Mayrhofer","year":"2013","journal-title":"Genome Biol"},{"key":"2023012713392421500_bty043-B21","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1038\/nrg3445","article-title":"Cancer genome-sequencing study design","volume":"14","author":"Mwenifumbo","year":"2013","journal-title":"Nat. Rev. Genet"},{"key":"2023012713392421500_bty043-B22","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1038\/nature09807","article-title":"Tumour evolution inferred by single-cell sequencing","volume":"472","author":"Navin","year":"2011","journal-title":"Nature"},{"key":"2023012713392421500_bty043-B23","doi-asserted-by":"crossref","first-page":"R80.","DOI":"10.1186\/gb-2013-14-7-r80","article-title":"THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data","volume":"14","author":"Oesper","year":"2013","journal-title":"Genome Biol"},{"key":"2023012713392421500_bty043-B24","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1056\/NEJMoa060467","article-title":"A genomic strategy to refine prognosis in early-stage non-small-cell lung cancer","volume":"355","author":"Potti","year":"2006","journal-title":"N. Engl. J. Med"},{"key":"2023012713392421500_bty043-B25","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1309\/AJCPR1SVT1VHUGXW","article-title":"Whole cancer genome sequencing by next-generation methods","volume":"136","author":"Ross","year":"2011","journal-title":"Am. J. Clin. Pathol"},{"key":"2023012713392421500_bty043-B26","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1146\/annurev-genom-090413-025552","article-title":"Translating genomics for precision cancer medicine","volume":"15","author":"Roychowdhury","year":"2014","journal-title":"Annu. Rev. Genomics Hum. Genet"},{"key":"2023012713392421500_bty043-B27","first-page":"123","article-title":"Molecular signature and therapeutic perspective of the epithelial-to-mesenchymal transitions in epithelial cancers","volume":"11","author":"Sabbah","year":"2008","journal-title":"Drug Resistance Updates Rev. Comment. Antimicrob. Anticancer Chemother"},{"key":"2023012713392421500_bty043-B28","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1038\/nature10933","article-title":"The clonal and mutational evolution spectrum of primary triple-negative breast cancers","volume":"486","author":"Shah","year":"2012","journal-title":"Nature"},{"key":"2023012713392421500_bty043-B29","doi-asserted-by":"crossref","first-page":"2265","DOI":"10.1093\/bioinformatics\/bts365","article-title":"PurityEst: estimating purity of human tumor samples using next-generation sequencing data","volume":"28","author":"Su","year":"2012","journal-title":"Bioinformatics"},{"key":"2023012713392421500_bty043-B30","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1038\/nature13600","article-title":"Clonal evolution in breast cancer revealed by single nucleus genome sequencing","volume":"512","author":"Wang","year":"2014","journal-title":"Nature"},{"key":"2023012713392421500_bty043-B31","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1093\/bib\/bbu002","article-title":"An assessment of computational methods for estimating purity and clonality using genomic data derived from heterogeneous tumor tissue samples","volume":"16","author":"Yadav","year":"2015","journal-title":"Brief. Bioinf"},{"key":"2023012713392421500_bty043-B32","doi-asserted-by":"crossref","first-page":"2612.","DOI":"10.1038\/ncomms3612","article-title":"Inferring tumour purity and stromal and immune cell admixture from expression data","volume":"4","author":"Yoshihara","year":"2013","journal-title":"Nat. Commun"},{"key":"2023012713392421500_bty043-B33","doi-asserted-by":"crossref","first-page":"2576","DOI":"10.1093\/bioinformatics\/btu346","article-title":"CLImAT: accurate detection of copy number alteration and loss of heterozygosity in impure and aneuploid tumor samples using whole-genome sequencing data","volume":"30","author":"Yu","year":"2014","journal-title":"Bioinformatics"},{"key":"2023012713392421500_bty043-B34","doi-asserted-by":"crossref","first-page":"1134","DOI":"10.1038\/ng.2760","article-title":"Pan-cancer patterns of somatic copy number alteration","volume":"45","author":"Zack","year":"2013","journal-title":"Nat. Genet"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/12\/2004\/48935847\/bioinformatics_34_12_2004.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/12\/2004\/48935847\/bioinformatics_34_12_2004.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T14:19:45Z","timestamp":1674829185000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/12\/2004\/4827681"}},"subtitle":[],"editor":[{"given":"Inanc","family":"Birol","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,1,27]]},"references-count":34,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2018,6,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty043","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2018,6,15]]},"published":{"date-parts":[[2018,1,27]]}}}