{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,13]],"date-time":"2025-11-13T01:29:15Z","timestamp":1762997355949},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2016,10,28]],"date-time":"2016-10-28T00:00:00Z","timestamp":1477612800000},"content-version":"vor","delay-in-days":354,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The Illumina Infinium HumanMethylation450 BeadChip (450k) is widely used for the evaluation of DNA methylation levels in large-scale datasets, particularly in cancer. The 450k design allows copy number variant (CNV) calling using existing bioinformatics tools. However, in cancer samples, numerous large-scale aberrations cause shifting in the probe intensities and thereby may result in erroneous CNV calling. Therefore, a baseline correction process is needed. We suggest the maximum peak of probe segment density to correct the shift in the intensities in cancer samples.<\/jats:p>\n               <jats:p>Availability and implementation: CopyNumber450kCancer is implemented as an R package. The package with examples can be downloaded at http:\/\/cran.r-project.org.<\/jats:p>\n               <jats:p>Contact: \u00a0nour.marzouka@medsci.uu.se<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv652","type":"journal-article","created":{"date-parts":[[2015,11,10]],"date-time":"2015-11-10T02:23:21Z","timestamp":1447122201000},"page":"1080-1082","source":"Crossref","is-referenced-by-count":23,"title":["CopyNumber450kCancer: baseline correction for accurate copy number calling from the 450k methylation array"],"prefix":"10.1093","volume":"32","author":[{"given":"Nour-al-dain","family":"Marzouka","sequence":"first","affiliation":[{"name":"1 Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jessica","family":"Nordlund","sequence":"additional","affiliation":[{"name":"1 Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christofer L.","family":"B\u00e4cklin","sequence":"additional","affiliation":[{"name":"2 Department of Medical Sciences, Cancer Pharmacology and Computational Medicine and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gudmar","family":"L\u00f6nnerholm","sequence":"additional","affiliation":[{"name":"3 Department of Women's and Children's Health, Pediatric Oncology, Uppsala University, Uppsala, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ann-Christine","family":"Syv\u00e4nen","sequence":"additional","affiliation":[{"name":"1 Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jonas","family":"Carlsson Alml\u00f6f","sequence":"additional","affiliation":[{"name":"1 Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory,"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,11,9]]},"reference":[{"key":"2023020111590406500_btv652-B1","doi-asserted-by":"crossref","first-page":"R30","DOI":"10.1186\/gb-2014-15-2-r30","article-title":"Using high-density DNA methylation arrays to profile copy number alterations","volume":"15","author":"Feber","year":"2014","journal-title":"Genome Biol."},{"key":"2023020111590406500_btv652-B2","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1186\/s13059-014-0503-2","article-title":"Functional normalization of 450k methylation array data improves replication in large cancer studies","volume":"15","author":"Fortin","year":"2014","journal-title":"Genome Biol."},{"key":"2023020111590406500_btv652-B3","author":"Lipson","year":"2007"},{"key":"2023020111590406500_btv652-B4","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1093\/bioinformatics\/btt684","article-title":"ChAMP: 450k chip analysis methylation pipeline","volume":"30","author":"Morris","year":"2014","journal-title":"Bioinformatics"},{"key":"2023020111590406500_btv652-B5","doi-asserted-by":"crossref","first-page":"r105","DOI":"10.1186\/gb-2013-14-9-r105","article-title":"Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia","volume":"14","author":"Nordlund","year":"2013","journal-title":"Genome Biol."},{"key":"2023020111590406500_btv652-B6","doi-asserted-by":"crossref","first-page":"692","DOI":"10.4161\/epi.6.6.16196","article-title":"Validation of a DNA methylation microarray for 450,000\u2009CpG sites in the human genome","volume":"6","author":"Sandoval","year":"2011","journal-title":"Epigenetics Off. J. DNA Methylation Soc."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/7\/1080\/49018302\/bioinformatics_32_7_1080.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/7\/1080\/49018302\/bioinformatics_32_7_1080.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T22:26:22Z","timestamp":1675290382000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/7\/1080\/1743576"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,11,9]]},"references-count":6,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2016,4,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv652","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2016,4,1]]},"published":{"date-parts":[[2015,11,9]]}}}