{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:39:07Z","timestamp":1740184747855,"version":"3.37.3"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2019,3,29]],"date-time":"2019-03-29T00:00:00Z","timestamp":1553817600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Grant-in-Aid for JSPS Research Fellow","award":["17J08884"],"award-info":[{"award-number":["17J08884"]}]},{"DOI":"10.13039\/501100001700","name":"MEXT","doi-asserted-by":"publisher","award":["15H05912","hp180198","hp170227"],"award-info":[{"award-number":["15H05912","hp180198","hp170227"]}],"id":[{"id":"10.13039\/501100001700","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Detection of somatic mutations from tumor and matched normal sequencing data has become among the most important analysis methods in cancer research. Some existing mutation callers have focused on additional information, e.g. heterozygous single-nucleotide polymorphisms (SNPs) nearby mutation candidates or overlapping paired-end read information. However, existing methods cannot take multiple information sources into account simultaneously. Existing Bayesian hierarchical model-based methods construct two generative models, the tumor model and error model, and limited information sources have been modeled.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We proposed a Bayesian model integration framework named as partitioning-based model integration. In this framework, through introducing partitions for paired-end reads based on given information sources, we integrate existing generative models and utilize multiple information sources. Based on that, we constructed a novel Bayesian hierarchical model-based method named as OHVarfinDer. In both the tumor model and error model, we introduced partitions for a set of paired-end reads that cover a mutation candidate position, and applied a different generative model for each category of paired-end reads. We demonstrated that our method can utilize both heterozygous SNP information and overlapping paired-end read information effectively in simulation datasets and real datasets.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/takumorizo\/OHVarfinDer.<\/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\/btz233","type":"journal-article","created":{"date-parts":[[2019,3,28]],"date-time":"2019-03-28T12:54:42Z","timestamp":1553777682000},"page":"4247-4254","source":"Crossref","is-referenced-by-count":5,"title":["A Bayesian model integration for mutation calling through data partitioning"],"prefix":"10.1093","volume":"35","author":[{"given":"Takuya","family":"Moriyama","sequence":"first","affiliation":[{"name":"Human Genome Center, The Institute of Medical Science, The University of Tokyo , Tokyo, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Seiya","family":"Imoto","sequence":"additional","affiliation":[{"name":"Health Intelligence Center, The Institute of Medical Science, The University of Tokyo , Tokyo, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1623-0738","authenticated-orcid":false,"given":"Shuto","family":"Hayashi","sequence":"additional","affiliation":[{"name":"Human Genome Center, The Institute of Medical Science, The University of Tokyo , Tokyo, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuichi","family":"Shiraishi","sequence":"additional","affiliation":[{"name":"Center for Cancer Genomics and Advanced Therapeutics, National Cancer Center , Tokyo, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Satoru","family":"Miyano","sequence":"additional","affiliation":[{"name":"Human Genome Center, The Institute of Medical Science, The University of Tokyo , Tokyo, Japan"},{"name":"Health Intelligence Center, The Institute of Medical Science, The University of Tokyo , Tokyo, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rui","family":"Yamaguchi","sequence":"additional","affiliation":[{"name":"Human Genome Center, The Institute of Medical Science, The University of Tokyo , Tokyo, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,3,29]]},"reference":[{"key":"2023062712461925400_btz233-B1","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1101\/gr.112326.110","article-title":"Dindel: accurate indel calls from short-read data","volume":"21","author":"Albers","year":"2011","journal-title":"Genome Res"},{"year":"2003","author":"Beal","key":"2023062712461925400_btz233-B2"},{"key":"2023062712461925400_btz233-B3","doi-asserted-by":"crossref","first-page":"1145","DOI":"10.1016\/S0031-3203(96)00142-2","article-title":"The use of the area under the ROC curve in the evaluation of machine learning algorithms","volume":"30","author":"Bradley","year":"1997","journal-title":"Pattern Recognit"},{"key":"2023062712461925400_btz233-B4","doi-asserted-by":"crossref","first-page":"96.","DOI":"10.1186\/1471-2164-14-96","article-title":"Ultra-deep mutant spectrum profiling: improving sequencing accuracy using overlapping read pairs","volume":"14","author":"Chen-Harris","year":"2013","journal-title":"BMC Genomics"},{"key":"2023062712461925400_btz233-B5","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1038\/nbt.2514","article-title":"Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples","volume":"31","author":"Cibulskis","year":"2013","journal-title":"Nat. Biotechnol"},{"volume-title":"Statistical Methods for Research Workers","year":"1925","author":"Fisher","key":"2023062712461925400_btz233-B6"},{"key":"2023062712461925400_btz233-B7","first-page":"382","article-title":"Bayesian model averaging: a tutorial","volume":"14","author":"Hoeting","year":"1999","journal-title":"Statist. Sci"},{"key":"2023062712461925400_btz233-B8","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1007\/BF02418571","article-title":"Sur les fonctions convexes et les in\u00e9galit\u00e9s entre les valeurs moyennes","volume":"30","author":"Jensen","year":"1906","journal-title":"Acta Math"},{"key":"2023062712461925400_btz233-B9","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1080\/01621459.1995.10476572","article-title":"Bayes Factors","volume":"90","author":"Kass","year":"1995","journal-title":"J. Am. Stat. Assoc"},{"key":"2023062712461925400_btz233-B10","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":"2023062712461925400_btz233-B11","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1038\/nrg2841","article-title":"Advances in understanding cancer genomes through second-generation sequencing","volume":"11","author":"Meyerson","year":"2010","journal-title":"Nat. Rev. Genet"},{"key":"2023062712461925400_btz233-B12","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1109\/TNB.2017.2670601","article-title":"OVarCall: Bayesian mutation calling method utilizing overlapping paired-end reads","volume":"16","author":"Moriyama","year":"2017","journal-title":"IEEE Trans. Nanobioscience"},{"key":"2023062712461925400_btz233-B13","first-page":"907","article-title":"JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal\/tumour paired next-generation sequencing data","volume":"28","author":"Roth","year":"2012","journal-title":"Bioinformatics (Oxford, England)"},{"key":"2023062712461925400_btz233-B14","doi-asserted-by":"crossref","first-page":"e89.","DOI":"10.1093\/nar\/gkt126","article-title":"An empirical Bayesian framework for somatic mutation detection from cancer genome sequencing data","volume":"41","author":"Shiraishi","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023062712461925400_btz233-B15","first-page":"3302","article-title":"HapMuC: somatic mutation calling using heterozygous germ line variants near candidate mutations","volume":"30","author":"Usuyama","year":"2014","journal-title":"Bioinformatics (Oxford, England)"},{"key":"2023062712461925400_btz233-B16","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1038\/nature10496","article-title":"Frequent pathway mutations of splicing machinery in myelodysplasia","volume":"478","author":"Yoshida","year":"2011","journal-title":"Nature"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz233\/28492260\/btz233.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/21\/4247\/50722047\/bioinformatics_35_21_4247.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/21\/4247\/50722047\/bioinformatics_35_21_4247.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,27]],"date-time":"2023-06-27T12:47:21Z","timestamp":1687870041000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/21\/4247\/5423180"}},"subtitle":[],"editor":[{"given":"Inanc","family":"Birol","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2019,3,29]]},"references-count":16,"journal-issue":{"issue":"21","published-print":{"date-parts":[[2019,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz233","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2019,11,1]]},"published":{"date-parts":[[2019,3,29]]}}}