{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T19:42:44Z","timestamp":1760730164351},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2280,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Copy number variation (CNV), a major contributor to human genetic variation, comprises \u2265 1 kb genomic deletions and insertions. Yet, the identification of CNVs from microarray data is still hampered by high false negative and positive prediction rates due to the noisy nature of the raw data. Here, we present CNVineta, an R package for rapid data mining and visualization of CNVs in large case\u2013control datasets genotyped with single nucleotide polymorphism oligonucleotide arrays. CNVineta is compatible with various established CNV prediction algorithms, can be used for genome-wide association analysis of rare and common CNVs and enables rapid and serial display of log2 of raw data ratios as well as B-allele frequencies for visual quality inspection. In summary, CNVineta aides in the interpretation of large-scale CNV datasets and prioritization of target regions for follow-up experiments.<\/jats:p>\n               <jats:p>Availability and Implementation: CNVineta is available as an R package and can be downloaded from http:\/\/www.ikmb.uni-kiel.de\/CNVineta\/; the package contains a tutorial outlining a typical workflow. The CNVineta compatible HapMap dataset can also be downloaded from the link above.<\/jats:p>\n               <jats:p>Contact: \u00a0m.wittig@mucosa.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq356","type":"journal-article","created":{"date-parts":[[2010,7,7]],"date-time":"2010-07-07T01:15:32Z","timestamp":1278465332000},"page":"2208-2209","source":"Crossref","is-referenced-by-count":5,"title":["CNVineta: a data mining tool for large case\u2013control copy number variation datasets"],"prefix":"10.1093","volume":"26","author":[{"given":"Michael","family":"Wittig","sequence":"first","affiliation":[{"name":"1 Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Schittenhelmstrasse 12, 24105 Kiel and 2Department of Neuropediatrics, University Clinic Schleswig-Holstein, Campus Kiel, Arnold-Heller-Strasse 3, Building 9, 24105 Kiel, Germany"}]},{"given":"Ingo","family":"Helbig","sequence":"additional","affiliation":[{"name":"1 Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Schittenhelmstrasse 12, 24105 Kiel and 2Department of Neuropediatrics, University Clinic Schleswig-Holstein, Campus Kiel, Arnold-Heller-Strasse 3, Building 9, 24105 Kiel, Germany"}]},{"given":"Stefan","family":"Schreiber","sequence":"additional","affiliation":[{"name":"1 Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Schittenhelmstrasse 12, 24105 Kiel and 2Department of Neuropediatrics, University Clinic Schleswig-Holstein, Campus Kiel, Arnold-Heller-Strasse 3, Building 9, 24105 Kiel, Germany"}]},{"given":"Andre","family":"Franke","sequence":"additional","affiliation":[{"name":"1 Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Schittenhelmstrasse 12, 24105 Kiel and 2Department of Neuropediatrics, University Clinic Schleswig-Holstein, Campus Kiel, Arnold-Heller-Strasse 3, Building 9, 24105 Kiel, Germany"}]}],"member":"286","published-online":{"date-parts":[[2010,7,6]]},"reference":[{"key":"2023012508014125100_B1","doi-asserted-by":"crossref","first-page":"1245","DOI":"10.1038\/ng.206","article-title":"A robust statistical method for case-control association testing with copy number variation","volume":"40","author":"Barnes","year":"2008","journal-title":"Nat. Genet."},{"key":"2023012508014125100_B2","doi-asserted-by":"crossref","first-page":"2013","DOI":"10.1093\/nar\/gkm076","article-title":"QuantiSNP: an objective Bayes hidden-Markov model to detect and accurately map copy number variation using SNP genotyping data","volume":"35","author":"Colella","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023012508014125100_B3","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1038\/nature02168","article-title":"The International HapMap Project","volume":"426","author":"International HapMap Consortium","year":"2003","journal-title":"Nature"},{"key":"2023012508014125100_B4","doi-asserted-by":"crossref","DOI":"10.1002\/0471250953.bi0104s28","article-title":"The UCSC Genome Browser","author":"Karolchik","year":"2009","journal-title":"Curr. Protoc. 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Genet."},{"key":"2023012508014125100_B8","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1093\/bfgp\/elp017","article-title":"Comparing CNV detection methods for SNP arrays","volume":"8","author":"Winchester","year":"2009","journal-title":"Brief. Funct. Genomic Proteomic"},{"key":"2023012508014125100_B9","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1038\/nature05911","article-title":"Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls","volume":"447","author":"WTCCC","year":"2007","journal-title":"Nature"},{"key":"2023012508014125100_B10","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1146\/annurev.genom.9.081307.164217","article-title":"Copy number variation in human health, disease, and evolution","volume":"10","author":"Zhang","year":"2009","journal-title":"Annu. Rev. Genomics Hum. Genet."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/17\/2208\/48854828\/bioinformatics_26_17_2208.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/17\/2208\/48854828\/bioinformatics_26_17_2208.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T08:02:02Z","timestamp":1674633722000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/17\/2208\/199351"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,7,6]]},"references-count":10,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2010,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq356","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,9,1]]},"published":{"date-parts":[[2010,7,6]]}}}