{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,21]],"date-time":"2026-02-21T07:47:57Z","timestamp":1771660077331,"version":"3.50.1"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"18","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Here, we present ContEst, a tool for estimating the level of cross-individual contamination in next-generation sequencing data. We demonstrate the accuracy of ContEst across a range of contamination levels, sources and read depths using sequencing data mixed in silico at known concentrations. We applied our tool to published cancer sequencing datasets and report their estimated contamination levels.<\/jats:p>\n               <jats:p>Availability and Implementation: ContEst is a GATK module, and distributed under a BSD style license at http:\/\/www.broadinstitute.org\/cancer\/cga\/contest<\/jats:p>\n               <jats:p>Contact: \u00a0kcibul@broadinstitute.org; gadgetz@broadinstitute.org<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data is available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr446","type":"journal-article","created":{"date-parts":[[2011,7,30]],"date-time":"2011-07-30T02:55:41Z","timestamp":1311994541000},"page":"2601-2602","source":"Crossref","is-referenced-by-count":240,"title":["ContEst: estimating cross-contamination of human samples in next-generation sequencing data"],"prefix":"10.1093","volume":"27","author":[{"given":"Kristian","family":"Cibulskis","sequence":"first","affiliation":[{"name":"Genome Sequencing Analysis Program and Platform, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA"}]},{"given":"Aaron","family":"McKenna","sequence":"additional","affiliation":[{"name":"Genome Sequencing Analysis Program and Platform, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA"}]},{"given":"Tim","family":"Fennell","sequence":"additional","affiliation":[{"name":"Genome Sequencing Analysis Program and Platform, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA"}]},{"given":"Eric","family":"Banks","sequence":"additional","affiliation":[{"name":"Genome Sequencing Analysis Program and Platform, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA"}]},{"given":"Mark","family":"DePristo","sequence":"additional","affiliation":[{"name":"Genome Sequencing Analysis Program and Platform, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA"}]},{"given":"Gad","family":"Getz","sequence":"additional","affiliation":[{"name":"Genome Sequencing Analysis Program and Platform, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA"}]}],"member":"286","published-online":{"date-parts":[[2011,7,29]]},"reference":[{"key":"2023012512002760300_B1","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1038\/nature09744","article-title":"The genomic complexity of primary human prostate cancer","volume":"470","author":"Berger","year":"2011","journal-title":"Nature"},{"key":"2023012512002760300_B2","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1038\/nature09837","article-title":"Initial genome sequencing and analysis of multiple myeloma","volume":"471","author":"Chapman","year":"2011","journal-title":"Nature"},{"key":"2023012512002760300_B3","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1038\/nbt.1523","article-title":"Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing","volume":"27","author":"Gnirke","year":"2009","journal-title":"Nat. Biotechnol."},{"key":"2023012512002760300_B4","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012512002760300_B5","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome Res."},{"key":"2023012512002760300_B6","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1038\/nature10166","article-title":"Integrated genomic analyses of ovarian carcinoma","volume":"474","author":"TCGA Research Network","year":"2011","journal-title":"Nature"},{"key":"2023012512002760300_B7","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1038\/nbt0509-455","article-title":"How to map billions of short reads onto genomes","volume":"27","author":"Trapnell","year":"2009","journal-title":"Nat. Biotechnol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/18\/2601\/48864972\/bioinformatics_27_18_2601.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/18\/2601\/48864972\/bioinformatics_27_18_2601.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T13:49:00Z","timestamp":1674654540000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/18\/2601\/182242"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,7,29]]},"references-count":7,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2011,9,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr446","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,9,15]]},"published":{"date-parts":[[2011,7,29]]}}}