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. 2008 Oct;40(10):1166-74.
doi: 10.1038/ng.238. Epub 2008 Sep 7.

Integrated detection and population-genetic analysis of SNPs and copy number variation

Steven A McCarroll  1 , Finny G Kuruvilla, Joshua M Korn, Simon Cawley, James Nemesh, Alec Wysoker, Michael H Shapero, Paul I W de Bakker, Julian B Maller, Andrew Kirby, Amanda L Elliott, Melissa Parkin, Earl Hubbell, Teresa Webster, Rui Mei, James Veitch, Patrick J Collins, Robert Handsaker, Steve Lincoln, Marcia Nizzari, John Blume, Keith W Jones, Rich Rava, Mark J Daly, Stacey B Gabriel, David Altshuler
Affiliations

Integrated detection and population-genetic analysis of SNPs and copy number variation

Steven A McCarroll et al. Nat Genet. 2008 Oct.

Abstract

Dissecting the genetic basis of disease risk requires measuring all forms of genetic variation, including SNPs and copy number variants (CNVs), and is enabled by accurate maps of their locations, frequencies and population-genetic properties. We designed a hybrid genotyping array (Affymetrix SNP 6.0) to simultaneously measure 906,600 SNPs and copy number at 1.8 million genomic locations. By characterizing 270 HapMap samples, we developed a map of human CNV (at 2-kb breakpoint resolution) informed by integer genotypes for 1,320 copy number polymorphisms (CNPs) that segregate at an allele frequency >1%. More than 80% of the sequence in previously reported CNV regions fell outside our estimated CNV boundaries, indicating that large (>100 kb) CNVs affect much less of the genome than initially reported. Approximately 80% of observed copy number differences between pairs of individuals were due to common CNPs with an allele frequency >5%, and more than 99% derived from inheritance rather than new mutation. Most common, diallelic CNPs were in strong linkage disequilibrium with SNPs, and most low-frequency CNVs segregated on specific SNP haplotypes.

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