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

Evans, David M., Barrett, Jeffrey C. and Cardon, Lon R. (2008) To what extent do scans of non-synonymous SNPs complement denser genome-wide association studies?. European Journal of Human Genetics, 16 6: 718-723. doi:10.1038/sj.ejhg.5202011


Author Evans, David M.
Barrett, Jeffrey C.
Cardon, Lon R.
Title To what extent do scans of non-synonymous SNPs complement denser genome-wide association studies?
Journal name European Journal of Human Genetics   Check publisher's open access policy
ISSN 1018-4813
1476-5438
Publication date 2008
Sub-type Article (original research)
DOI 10.1038/sj.ejhg.5202011
Open Access Status
Volume 16
Issue 6
Start page 718
End page 723
Total pages 6
Place of publication London, United Kingdom
Publisher Nature Publishing
Language eng
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.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: UQ Diamantina Institute Publications
 
Versions
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 17 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 17 times in Scopus Article | Citations
Google Scholar Search Google Scholar
Created: Thu, 13 Mar 2014, 10:13:49 EST by System User on behalf of UQ Diamantina Institute