New quality measure for SNP array based CNV detection

• DOI: 10.1093/bioinformatics/btw477
• Publication Date: 2016-07-12T07:21:31Z
• Authors: A. Macé; M.A. Tuke; J.S. Beckmann; L. Lin; S. Jacquemont; M.N. Weedon; A. Reymond; Z. Kutalik
• Keywords: SNP; Trait; Genome-wide Association Study

Abstract Motivation: Only a few large systematic studies have evaluated the impact of copy number variants (CNVs) on common diseases. Several million individuals been genotyped single nucleotide variation arrays, which could be used for genome-wide CNVs association studies. However, CNV calls remain prone to false positives and only empirical filtering strategies exist in literature. To overcome this issue, we defined new quality score (QS) estimating probability called by PennCNV confirmed other software. Results: Out-of-sample comparison showed that correlation between consensus status QS is twice as high it any previously proposed filters. ROC curves displayed an AUC higher than 0.8 simulations increase up 20% statistical power when using strategies. Superior performance was also alternative definition through improving known CNV-trait associations. Availability Implementation: http://goo.gl/T6yuFM Contact: [e-mail] or aurelien@[e-mail] Supplementary information: data are available at Bioinformatics online.