{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T02:35:39Z","timestamp":1778812539683,"version":"3.51.4"},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The use of high-density SNP arrays for investigating copy number alterations in clinical tumor samples, with intra tumor heterogeneity and varying degrees of normal cell contamination, imposes several problems for commonly used segmentation algorithms. This calls for flexibility when setting thresholds for calling gains and losses. In addition, sample normalization can induce artifacts in the copy-number ratios for the non-changed genomic elements in the tumor samples.<\/jats:p>\n               <jats:p>Results: We present an open source R package, Rseg, which allows the user to define sample-specific thresholds to call gains and losses. It also allows the user to correct for normalization artifacts.<\/jats:p>\n               <jats:p>Availability: The R package, Rseg, is available at: http:\/\/www.cs.au.dk\/~plamy\/Rseg\/ and runs on Linux and MS-Windows.<\/jats:p>\n               <jats:p>Contact: \u00a0plamy@cs.au.dk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq668","type":"journal-article","created":{"date-parts":[[2010,12,7]],"date-time":"2010-12-07T04:48:21Z","timestamp":1291697301000},"page":"419-420","source":"Crossref","is-referenced-by-count":5,"title":["Rseg\u2014an R package to optimize segmentation of SNP array data"],"prefix":"10.1093","volume":"27","author":[{"given":"Philippe","family":"Lamy","sequence":"first","affiliation":[{"name":"1 Department of Molecular Medicine, Aarhus University Hospital Skejby, Aarhus N and 2Bioinformatics Research Center, Aarhus University, Aarhus, Denmark"},{"name":"1 Department of Molecular Medicine, Aarhus University Hospital Skejby, Aarhus N and 2Bioinformatics Research Center, Aarhus University, Aarhus, Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carsten","family":"Wiuf","sequence":"additional","affiliation":[{"name":"1 Department of Molecular Medicine, Aarhus University Hospital Skejby, Aarhus N and 2Bioinformatics Research Center, Aarhus University, Aarhus, Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Torben F.","family":"\u00d8rntoft","sequence":"additional","affiliation":[{"name":"1 Department of Molecular Medicine, Aarhus University Hospital Skejby, Aarhus N and 2Bioinformatics Research Center, Aarhus University, Aarhus, Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Claus L.","family":"Andersen","sequence":"additional","affiliation":[{"name":"1 Department of Molecular Medicine, Aarhus University Hospital Skejby, Aarhus N and 2Bioinformatics Research Center, Aarhus University, Aarhus, Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2010,12,5]]},"reference":[{"key":"2023012511534369400_B1","doi-asserted-by":"crossref","first-page":"2149","DOI":"10.1093\/bioinformatics\/btp371","article-title":"A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6","volume":"25","author":"Bengtsson","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012511534369400_B2","doi-asserted-by":"crossref","first-page":"899","DOI":"10.1038\/nature08822","article-title":"The landscape of somatic copy-number alteration across human cancers","volume":"463","author":"Beroukhim","year":"2010","journal-title":"Nature"},{"key":"2023012511534369400_B3"},{"key":"2023012511534369400_B4","doi-asserted-by":"crossref","first-page":"1078","DOI":"10.1093\/bioinformatics\/btp091","article-title":"Ultrasome: efficient aberration caller for copy number studies of ultra-high resolution","volume":"25","author":"Nilsson","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012511534369400_B5","doi-asserted-by":"crossref","first-page":"657","DOI":"10.1093\/bioinformatics\/btl646","article-title":"A faster circular binary segmentation algorithm for the analysis of array CGH data","volume":"23","author":"Venkatraman","year":"2007","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/3\/419\/48862565\/bioinformatics_27_3_419.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/3\/419\/48862565\/bioinformatics_27_3_419.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T11:54:02Z","timestamp":1674647642000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/3\/419\/321268"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,12,5]]},"references-count":5,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2011,2,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq668","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,2,1]]},"published":{"date-parts":[[2010,12,5]]}}}