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Systematic assessment of copy number variant detection via genome-wide SNP genotyping.

Abstract：

:SNP genotyping has emerged as a technology to incorporate copy number variants (CNVs) into genetic analyses of human traits. However, the extent to which SNP platforms accurately capture CNVs remains unclear. Using independent, sequence-based CNV maps, we find that commonly used SNP platforms have limited or no probe coverage for a large fraction of CNVs. Despite this, in 9 samples we inferred 368 CNVs using Illumina SNP genotyping data and experimentally validated over two-thirds of these. We also developed a method (SNP-Conditional Mixture Modeling, SCIMM) to robustly genotype deletions using as few as two SNP probes. We find that HapMap SNPs are strongly correlated with 82% of common deletions, but the newest SNP platforms effectively tag about 50%. We conclude that currently available genome-wide SNP assays can capture CNVs accurately, but improvements in array designs, particularly in duplicated sequences, are necessary to facilitate more comprehensive analyses of genomic variation.

journal_name

Nat Genet

journal_title

Nature genetics

authors

Cooper GM,Zerr T,Kidd JM,Eichler EE,Nickerson DA

doi

10.1038/ng.236

subject

Has Abstract

pub_date

2008-10-01 00:00:00

pages

1199-203

issue

10

eissn

1061-4036

issn

1546-1718

pii

ng.236

journal_volume

40

pub_type

杂志文章

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