{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:47Z","timestamp":1772138087268,"version":"3.50.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2018,2,5]],"date-time":"2018-02-05T00:00:00Z","timestamp":1517788800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["P01 CA142538"],"award-info":[{"award-number":["P01 CA142538"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R01 HG006137"],"award-info":[{"award-number":["R01 HG006137"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"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>Summary<\/jats:title>\n                    <jats:p>Copy number variation is an important and abundant source of variation in the human genome, which has been associated with a number of diseases, especially cancer. Massively parallel next-generation sequencing allows copy number profiling with fine resolution. Such efforts, however, have met with mixed successes, with setbacks arising partly from the lack of reliable analytical methods to meet the diverse and unique challenges arising from the myriad experimental designs and study goals in genetic studies. In cancer genomics, detection of somatic copy number changes and profiling of allele-specific copy number (ASCN) are complicated by experimental biases and artifacts as well as normal cell contamination and cancer subclone admixture. Furthermore, careful statistical modeling is warranted to reconstruct tumor phylogeny by both somatic ASCN changes and single nucleotide variants. Here we describe a flexible computational pipeline, MARATHON, which integrates multiple related statistical software for copy number profiling and downstream analyses in disease genetic studies.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>MARATHON is publicly available at https:\/\/github.com\/yuchaojiang\/MARATHON.<\/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\/bty057","type":"journal-article","created":{"date-parts":[[2018,2,2]],"date-time":"2018-02-02T15:12:29Z","timestamp":1517584349000},"page":"2126-2128","source":"Crossref","is-referenced-by-count":26,"title":["Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny"],"prefix":"10.1093","volume":"34","author":[{"given":"Eugene","family":"Urrutia","sequence":"first","affiliation":[{"name":"Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA"}]},{"given":"Hao","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Statistics, University of California, Davis, Davis, CA, USA"}]},{"given":"Zilu","family":"Zhou","sequence":"additional","affiliation":[{"name":"Genomics and Computational Biology Graduate Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA"}]},{"given":"Nancy R","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6905-6377","authenticated-orcid":false,"given":"Yuchao","family":"Jiang","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA"},{"name":"Department of Genetics, University of North Carolina, Chapel Hill, NC, USA"}]}],"member":"286","published-online":{"date-parts":[[2018,2,5]]},"reference":[{"key":"2023012713393727400_bty057-B1","doi-asserted-by":"crossref","first-page":"e23","DOI":"10.1093\/nar\/gku1252","article-title":"Allele-specific copy number profiling by next-generation DNA sequencing","volume":"43","author":"Chen","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023012713393727400_bty057-B2","doi-asserted-by":"crossref","first-page":"1169","DOI":"10.1214\/17-AOAS1043","article-title":"Allele-specific copy number estimation by whole exome sequencing","volume":"11","author":"Chen","year":"2017","journal-title":"Ann. Appl. Stat"},{"key":"2023012713393727400_bty057-B3","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1038\/ng.806","article-title":"A framework for variation discovery and genotyping using next-generation DNA sequencing data","volume":"43","author":"DePristo","year":"2011","journal-title":"Nat. Genet"},{"key":"2023012713393727400_bty057-B4","doi-asserted-by":"crossref","first-page":"864","DOI":"10.1038\/ng.3333","article-title":"Relapsed neuroblastomas show frequent RAS-MAPK pathway mutations","volume":"47","author":"Eleveld","year":"2015","journal-title":"Nat. Genet"},{"key":"2023012713393727400_bty057-B5","doi-asserted-by":"crossref","first-page":"1936","DOI":"10.1016\/j.celrep.2017.10.052","article-title":"Genetic and genomic characterization of 462 melanoma patient-derived xenografts, tumor biopsies, and cell lines","volume":"21","author":"Garman","year":"2017","journal-title":"Cell. Rep"},{"key":"2023012713393727400_bty057-B6","first-page":"211698","article-title":"CODEX2: full-spectrum copy number variation detection by high-throughput DNA sequencing","author":"Jiang","year":"2017","journal-title":"bioRxiv"},{"key":"2023012713393727400_bty057-B7","doi-asserted-by":"crossref","first-page":"e39","DOI":"10.1093\/nar\/gku1363","article-title":"CODEX: a normalization and copy number variation detection method for whole exome sequencing","volume":"43","author":"Jiang","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023012713393727400_bty057-B8","doi-asserted-by":"crossref","first-page":"E5528","DOI":"10.1073\/pnas.1522203113","article-title":"Assessing intratumor heterogeneity and tracking longitudinal and spatial clonal evolutionary history by next-generation sequencing","volume":"113","author":"Jiang","year":"2016","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023012713393727400_bty057-B9","first-page":"127","article-title":"Advances in understanding tumour evolution through single-cell sequencing","volume":"1867","author":"Kuipers","year":"2017","journal-title":"Biochim. Biophys. Acta"},{"key":"2023012713393727400_bty057-B10","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1038\/s41467-017-00388-9","article-title":"BRCA locus-specific loss of heterozygosity in germline BRCA1 and BRCA2 carriers","volume":"8","author":"Maxwell","year":"2017","journal-title":"Nat. Commun"},{"key":"2023012713393727400_bty057-B11","first-page":"172700","article-title":"Integrative DNA copy number detection and genotyping from sequencing and array-based platforms","author":"Zhou","year":"2017","journal-title":"bioRxiv"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/12\/2126\/48936003\/bioinformatics_34_12_2126.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/12\/2126\/48936003\/bioinformatics_34_12_2126.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T09:20:11Z","timestamp":1674811211000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/12\/2126\/4838234"}},"subtitle":[],"editor":[{"given":"Bonnie","family":"Berger","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,2,5]]},"references-count":11,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2018,6,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty057","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/195230","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,6,15]]},"published":{"date-parts":[[2018,2,5]]}}}