To what extent do scans of non-synonymous SNPs complement denser genome-wide association studies?

David M Evans, Jeffrey C Barrett, Lon R Cardon

Research output: Contribution to journalArticle (Academic Journal)peer-review

20 Citations (Scopus)

Abstract

Several studies involving genome-wide scans of non-synonymous SNPs (nsSNPs) have successfully identified loci contributing to common complex diseases. We were interested in the extent to which these small scans involving a few thousand non-synonymous markers might complement the results from denser genome-wide association studies. We assessed the degree to which three commercially available genome-wide marker panels tagged nsSNPs on the Illumina HumanNS-12 BeadChip, a product specifically designed to capture non-synonymous variation. We demonstrate that commercially available genome-wide panels already tag the majority of common non-synonymous variants on the NS-12 BeadChip, indicating that with respect to capturing common non-synonymous variation, information from the NS-12 BeadChip is largely redundant. In contrast, genome-wide panels fail to capture most of the rare SNPs present on the NS-12 BeadChip. Power calculations reveal that non-synonymous scans involving sample sizes typical of the current wave of genome-wide association studies are unlikely to identify rare variants of small effect, but could conceivably identify rare variants of intermediate penetrance. We conclude that non-synonymous scans may facilitate the identification of rare variants of intermediate penetrance that would not otherwise be detectable using dense genome-wide panels, but are unlikely to uniquely identify common variants contributing to complex disease variation.
Original languageEnglish
Pages (from-to)718-23
Number of pages6
JournalEuropean Journal of Human Genetics
Volume16
Issue number6
DOIs
Publication statusPublished - 2008

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