Paper Info
Title
An exome sequencing pipeline for identifying and genotyping common CNVs associated with disease with application to psoriasis
Abstract
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–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. Availability and implementation: ExoCNVTest has been implemented in Java and R and is freely available from www1.imperial.ac.uk/medicine/people/l.coin/. Contact:wangj@genomics.org.cn or Lachlan.J.M.Coin@genomics.org.cn
Year
DOI
Venue
2012
10.1093/bioinformatics/bts379
Bioinformatics
Field
DocType
Volume
Genotype,Disease,Genotyping,Biology,Copy-number variation,Exome,Bioinformatics,Human genome,Genetics,Locus (genetics),Exome sequencing
Journal
28
Issue
ISSN
Citations 
18
1367-4803
6
PageRank 
References 
Authors
0.60
3
11
Name
Order
Citations
PageRank
Lachlan J.M. Coin1606.08
Dandan Cao260.60
Jingjing Ren3192.10
Xianbo Zuo460.60
Liangdan Sun560.60
Yang Sen660.60
Xuejun Zhang760.94
Yong Cui861.27
Yingrui Li955472.28
Xin Jin1060.94
Jun Wang119228736.82