title: An exome sequencing pipeline for identifying and genotyping common CNVs associated with disease with application to psoriasis.
abstract: BACKGROUND
  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-control cohorts and presents an exciting opportunity to look for common CNVs associated with disease.
  
  
  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 × 10e-6) while controlling inflation of test statistics (λ < 1). ExoCNVTest-derived absolute CNV genotypes were 97.4% concordant with PCR-derived genotypes at this locus.
  
  
  METHODS
  ExoCNVTest has been implemented in Java and R and is freely available from www1.imperial.ac.uk/medicine/people/l.coin/.
  
  
  BACKGROUND
  wangj@genomics.org.cn or Lachlan.J.M.Coin@genomics.org.cn.
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China. Lachlan.J.M.Coin@genomics.org.cn
authors.forename: Lachlan J M
authors.initials: LJ
authors.lastname: Coin
authors.forename: Dandan
authors.initials: D
authors.lastname: Cao
authors.forename: Jingjing
authors.initials: J
authors.lastname: Ren
authors.forename: Xianbo
authors.initials: X
authors.lastname: Zuo
authors.forename: Liangdan
authors.initials: L
authors.lastname: Sun
authors.forename: Sen
authors.initials: S
authors.lastname: Yang
authors.forename: Xuejun
authors.initials: X
authors.lastname: Zhang
authors.forename: Yong
authors.initials: Y
authors.lastname: Cui
authors.forename: Yingrui
authors.initials: Y
authors.lastname: Li
authors.forename: Xin
authors.initials: X
authors.lastname: Jin
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
mesh_terms: D000465:Algorithms; D056915:DNA Copy Number Variations; D059472:Exome; D015894:Genome, Human; D005838:Genotype; D006801:Humans; D011565:Psoriasis / Q000235:genetics*; D017422:Sequence Analysis, DNA