Journal
NATURE GENETICS
Volume 40, Issue 10, Pages 1199-1203Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/ng.236
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Funding
- Merck, Jane Coffin Childs Memorial Fund Postdoctoral Fellowship
- National Human Genome Research Institute (NHGRI) [T32 HG00035]
- National Science Foundation
- National Heart, Lung, and Blood Institute Programs [HL066682]
- NHGRI [HG004120]
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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.
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