{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,28]],"date-time":"2025-10-28T14:51:13Z","timestamp":1761663073541},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1490,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Despite the prevalence of copy number variation (CNV) in the human genome, only a handful of confirmed associations have been reported between common CNVs and complex disease. This may be partially attributed to the difficulty in accurately genotyping CNVs in large cohorts using array-based technologies. Exome sequencing is now widely being applied to case\u2013control cohorts and presents an exciting opportunity to look for common CNVs associated with disease.<\/jats:p>\n               <jats:p>Results: We developed ExoCNVTest: an exome sequencing analysis pipeline to identify disease-associated CNVs and to generate absolute copy number genotypes at putatively associated loci. Our method re-discovered the LCE3B_LCE3C CNV association with psoriasis (P-value = 5 \u00d7 10e\u22126) while controlling inflation of test statistics (\u03bb &amp;lt; 1). ExoCNVTest-derived absolute CNV genotypes were 97.4% concordant with PCR-derived genotypes at this locus.<\/jats:p>\n               <jats:p>Availability and implementation: ExoCNVTest has been implemented in Java and R and is freely available from www1.imperial.ac.uk\/medicine\/people\/l.coin\/.<\/jats:p>\n               <jats:p>Contact: \u00a0wangj@genomics.org.cn or Lachlan.J.M.Coin@genomics.org.cn<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts379","type":"journal-article","created":{"date-parts":[[2012,9,7]],"date-time":"2012-09-07T20:35:22Z","timestamp":1347050122000},"page":"i370-i374","source":"Crossref","is-referenced-by-count":22,"title":["An exome sequencing pipeline for identifying and genotyping common CNVs associated with disease with application to psoriasis"],"prefix":"10.1093","volume":"28","author":[{"given":"Lachlan J.M.","family":"Coin","sequence":"first","affiliation":[{"name":"1 BGI-Shenzhen, Shenzhen, 518083, China"},{"name":"2 Department of Genomics of Common Disease, Imperial College London, London W12 0NN, UK"}]},{"given":"Dandan","family":"Cao","sequence":"additional","affiliation":[{"name":"1 BGI-Shenzhen, Shenzhen, 518083, China"}]},{"given":"Jingjing","family":"Ren","sequence":"additional","affiliation":[{"name":"1 BGI-Shenzhen, Shenzhen, 518083, China"}]},{"given":"Xianbo","family":"Zuo","sequence":"additional","affiliation":[{"name":"3 Institute of Dermatology and Department of Dermatology, No.1 Hospital, Anhui Medical University, Hefei, Anhui, 230032, China"},{"name":"4 State Key Laboratory Incubation Base of Dermatology, Ministry of National Science and Technology, Hefei, Anhui, China"}]},{"given":"Liangdan","family":"Sun","sequence":"additional","affiliation":[{"name":"3 Institute of Dermatology and Department of Dermatology, No.1 Hospital, Anhui Medical University, Hefei, Anhui, 230032, China"},{"name":"4 State Key Laboratory Incubation Base of Dermatology, Ministry of National Science and Technology, Hefei, Anhui, China"}]},{"given":"Sen","family":"Yang","sequence":"additional","affiliation":[{"name":"3 Institute of Dermatology and Department of Dermatology, No.1 Hospital, Anhui Medical University, Hefei, Anhui, 230032, China"},{"name":"4 State Key Laboratory Incubation Base of Dermatology, Ministry of National Science and Technology, Hefei, Anhui, China"}]},{"given":"Xuejun","family":"Zhang","sequence":"additional","affiliation":[{"name":"3 Institute of Dermatology and Department of Dermatology, No.1 Hospital, Anhui Medical University, Hefei, Anhui, 230032, China"},{"name":"4 State Key Laboratory Incubation Base of Dermatology, Ministry of National Science and Technology, Hefei, Anhui, China"}]},{"given":"Yong","family":"Cui","sequence":"additional","affiliation":[{"name":"3 Institute of Dermatology and Department of Dermatology, No.1 Hospital, Anhui Medical University, Hefei, Anhui, 230032, China"},{"name":"4 State Key Laboratory Incubation Base of Dermatology, Ministry of National Science and Technology, Hefei, Anhui, China"}]},{"given":"Yingrui","family":"Li","sequence":"additional","affiliation":[{"name":"1 BGI-Shenzhen, Shenzhen, 518083, China"}]},{"given":"Xin","family":"Jin","sequence":"additional","affiliation":[{"name":"1 BGI-Shenzhen, Shenzhen, 518083, China"},{"name":"5 School of Bioscience and Biotechnology, South China University of Technology, Guangzhou 510641, China"}]},{"given":"Jun","family":"Wang","sequence":"additional","affiliation":[{"name":"1 BGI-Shenzhen, Shenzhen, 518083, China"}]}],"member":"286","published-online":{"date-parts":[[2012,9,3]]},"reference":[{"key":"2023012513024283400_B1","doi-asserted-by":"crossref","first-page":"851","DOI":"10.1038\/nature04489","article-title":"Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans","volume":"439","author":"Aitman","year":"2006","journal-title":"Nature"},{"key":"2023012513024283400_B2","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1038\/ng.1053","article-title":"Rare MTNR1B variants impairing melatonin receptor 1B function contribute to type 2 diabetes","volume":"44","author":"Bonnefond","year":"2012","journal-title":"Nat. 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