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- Title
cnvHap: an integrative population and haplotype-based multiplatform model of SNPs and CNVs.
- Authors
Coin, Lachlan J M; Asher, Julian E; Walters, Robin G; Moustafa, Julia S El-Sayed; de Smith, Adam J; Sladek, Rob; Balding, David J; Froguel, Philippe; Blakemore, Alexandra I F
- Abstract
Although genome-wide association studies have uncovered single-nucleotide polymorphisms (SNPs) associated with complex disease, these variants account for a small portion of heritability. Some contribution to this 'missing heritability' may come from copy-number variants (CNVs), in particular rare CNVs; but assessment of this contribution remains challenging because of the difficulty in accurately genotyping CNVs, particularly small variants. We report a population-based approach for the identification of CNVs that integrates data from multiple samples and platforms. Our algorithm, cnvHap, jointly learns a chromosome-wide haplotype model of CNVs and cluster-based models of allele intensity at each probe. Using data for 50 French individuals assayed on four separate platforms, we found that cnvHap correctly detected at least 14% more deleted and 50% more amplified genotypes than PennCNV or QuantiSNP, with an 82% and 115% improvement for aberrations containing <10 probes. Combining data from multiple platforms additionally improved sensitivity.
- Publication
Nature methods, 2010, Vol 7, Issue 7, p541
- ISSN
1548-7105
- Publication type
Journal Article
- DOI
10.1038/nmeth.1466