cnvHap: an integrative population and haplotype-based multiplatform model of SNPs and CNVs

被引：0
|
作者：
Coin, Lachlan J. M. [1 ]
Asher, Julian E. [2 ]
Walters, Robin G. [2 ]
Moustafa, Julia S. El-Sayed [2 ]
de Smith, Adam J. [2 ]
Sladek, Rob [3 ,4 ,5 ]
Balding, David J. [6 ]
Froguel, Philippe [2 ,7 ]
Blakemore, Alexandra I. F. [2 ]
机构：
[1] Univ London Imperial Coll Sci Technol & Med, Dept Epidemiol & Biostat, Sch Publ Hlth, St Marys Hosp, London, England
[2] Univ London Imperial Coll Sci Technol & Med, Dept Epidemiol & Biostat, Sch Publ Hlth, St Marys Hosp, London, England
[3] McGill Univ, Dept Med, Montreal, PQ H3A 2T5, Canada
[4] McGill Univ, Dept Human Genet, Montreal, PQ H3A 2T5, Canada
[5] Genome Quebec Innovat Ctr, Montreal, PQ, Canada
[6] UCL, Inst Genet, London, England
[7] Inst Pasteur, Ctr Natl Rech Sci 8090, Inst Biol, F-59019 Lille, France
来源：
NATURE METHODS | 2010年 / 7卷 / 07期
基金：
英国医学研究理事会;
关键词：
COPY NUMBER VARIATION; GENOME-WIDE ASSOCIATION; HIDDEN-MARKOV MODEL; MISSING GENOTYPES; GENE-EXPRESSION; RISK LOCI; DISEASE; POLYMORPHISM; DELETIONS; VARIANTS;
D O I：
10.1038/NMETH.1466
中图分类号：
Q5 [生物化学];
学科分类号：
071010 ; 081704 ;
摘要：
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.
引用
收藏
页码：541 / U85
页数：8
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