{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,5]],"date-time":"2026-01-05T22:19:42Z","timestamp":1767651582969,"version":"3.37.3"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2019,3,12]],"date-time":"2019-03-12T00:00:00Z","timestamp":1552348800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100004917","name":"Cancer Prevention and Research Institute of Texas","doi-asserted-by":"publisher","award":["RP150596"],"award-info":[{"award-number":["RP150596"]}],"id":[{"id":"10.13039\/100004917","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["P50CA196516"],"award-info":[{"award-number":["P50CA196516"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Detection of somatic copy number alterations (SCNAs) using high-throughput sequencing has become popular because of rapid developments in sequencing technology. Existing methods do not perform well in calling SCNAs for the unstable tumor genomes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed a new method, DEFOR, to detect SCNAs in tumor samples from exome-sequencing data. The evaluation showed that DEFOR has a higher accuracy for SCNA detection from exome sequencing compared with the five existing tools. This advantage is especially apparent in unstable tumor genomes with a large proportion of SCNAs.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>DEFOR is available at https:\/\/github.com\/drzh\/defor.<\/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\/btz170","type":"journal-article","created":{"date-parts":[[2019,3,11]],"date-time":"2019-03-11T20:13:00Z","timestamp":1552335180000},"page":"3824-3825","source":"Crossref","is-referenced-by-count":6,"title":["DEFOR: depth- and frequency-based somatic copy number alteration detector"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9198-6503","authenticated-orcid":false,"given":"He","family":"Zhang","sequence":"first","affiliation":[{"name":"Department of Clinical Sciences, University of Texas Southwestern Medical Center , Dallas, TX, USA"}]},{"given":"Xiaowei","family":"Zhan","sequence":"additional","affiliation":[{"name":"Department of Clinical Sciences, University of Texas Southwestern Medical Center , Dallas, TX, USA"}]},{"given":"James","family":"Brugarolas","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine and Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center , Dallas, TX, USA"}]},{"given":"Yang","family":"Xie","sequence":"additional","affiliation":[{"name":"Department of Clinical Sciences, University of Texas Southwestern Medical Center , Dallas, TX, USA"},{"name":"Department of Internal Medicine and Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center , Dallas, TX, USA"}]}],"member":"286","published-online":{"date-parts":[[2019,3,12]]},"reference":[{"key":"2023013108184927100_btz170-B1","doi-asserted-by":"crossref","first-page":"974","DOI":"10.1101\/gr.114876.110","article-title":"CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing","volume":"21","author":"Abyzov","year":"2011","journal-title":"Genome Res"},{"key":"2023013108184927100_btz170-B2","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. 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