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- Title
To what extent do scans of non-synonymous SNPs complement denser genome-wide association studies?
- Authors
Evans, David M.; Barrett, Jeffrey C.; Cardon, Lon R.
- 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.European Journal of Human Genetics (2008) 16, 718–723; doi:10.1038/sj.ejhg.5202011; published online 16 January 2008
- Subjects
HUMAN genetics; GENE mapping; THERAPEUTICS; GENETIC polymorphisms; PUBLIC health; GENETIC research
- Publication
European Journal of Human Genetics, 2008, Vol 16, Issue 6, p718
- ISSN
1018-4813
- Publication type
Article
- DOI
10.1038/sj.ejhg.5202011