{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T02:48:20Z","timestamp":1774493300864,"version":"3.50.1"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2016,10,26]],"date-time":"2016-10-26T00:00:00Z","timestamp":1477440000000},"content-version":"vor","delay-in-days":122,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Sequencing of matched tumor and normal samples is the standard study design for reliable detection of somatic alterations. However, even very low levels of cross-sample contamination significantly impact calling of somatic mutations, because contaminant germline variants can be incorrectly interpreted as somatic. There are currently no sequence-only based methods that reliably estimate contamination levels in tumor samples, which frequently display copy number changes. As a solution, we developed Conpair, a tool for detection of sample swaps and cross-individual contamination in whole-genome and whole-exome tumor\u2013normal sequencing experiments.<\/jats:p>\n               <jats:p>Results: On a ladder of in silico contaminated samples, we demonstrated that Conpair reliably measures contamination levels as low as 0.1%, even in presence of copy number changes. We also estimated contamination levels in glioblastoma WGS and WXS tumor\u2013normal datasets from TCGA and showed that they strongly correlate with tumor\u2013normal concordance, as well as with the number of germline variants called as somatic by several widely-used somatic callers.<\/jats:p>\n               <jats:p>Availability and Implementation: The method is available at: https:\/\/github.com\/nygenome\/conpair.<\/jats:p>\n               <jats:p>Contact: \u00a0egrabowska@gmail.com or mczody@nygenome.org<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw389","type":"journal-article","created":{"date-parts":[[2016,6,29]],"date-time":"2016-06-29T14:57:42Z","timestamp":1467212262000},"page":"3196-3198","source":"Crossref","is-referenced-by-count":98,"title":["Conpair: concordance and contamination estimator for matched tumor\u2013normal pairs"],"prefix":"10.1093","volume":"32","author":[{"given":"Ewa A.","family":"Bergmann","sequence":"first","affiliation":[{"name":"New York Genome Center, New York, NY 10013, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bo-Juen","family":"Chen","sequence":"additional","affiliation":[{"name":"New York Genome Center, New York, NY 10013, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kanika","family":"Arora","sequence":"additional","affiliation":[{"name":"New York Genome Center, New York, NY 10013, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vladimir","family":"Vacic","sequence":"additional","affiliation":[{"name":"New York Genome Center, New York, NY 10013, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael C.","family":"Zody","sequence":"additional","affiliation":[{"name":"New York Genome Center, New York, NY 10013, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,6,26]]},"reference":[{"key":"2023020113441829700_btw389-B1","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1016\/j.cell.2013.09.034","article-title":"The somatic genomic landscape of glioblastoma","volume":"155","author":"Brennan","year":"2013","journal-title":"Cell"},{"key":"2023020113441829700_btw389-B2","first-page":"2601","article-title":"ContEst: estimating cross-contamination of human samples in next-generation sequencing data","volume":"27","author":"Cibulskis","year":"2011","journal-title":"Bioinf. Oxf. Engl"},{"key":"2023020113441829700_btw389-B3","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"},{"key":"2023020113441829700_btw389-B4","doi-asserted-by":"crossref","first-page":"839","DOI":"10.1016\/j.ajhg.2012.09.004","article-title":"Detecting and estimating contamination of human DNA samples in sequencing and array-based genotype data","volume":"91","author":"Jun","year":"2012","journal-title":"Am. J. Hum. 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Engl"},{"key":"2023020113441829700_btw389-B8","doi-asserted-by":"crossref","first-page":"11189","DOI":"10.1093\/nar\/gks918","article-title":"LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets","volume":"40","author":"Wilm","year":"2012","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/20\/3196\/49020952\/bioinformatics_32_20_3196.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/20\/3196\/49020952\/bioinformatics_32_20_3196.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T23:49:53Z","timestamp":1675295393000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/20\/3196\/2196627"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,6,26]]},"references-count":7,"journal-issue":{"issue":"20","published-print":{"date-parts":[[2016,10,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw389","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2016,10,15]]},"published":{"date-parts":[[2016,6,26]]}}}