Ottawa Heart Genomic Study: Discovery Of Novel Genes For Coronary Artery Disease By Genome-Wide Association Utilizing The 500k Snp Array

Purpose: To identify genes predisposing to Coronary Artery Disease (CAD). Methods: We selected the unbiased approach of using the genome wide scan association case control method. Using the Affymetrix 500K SNP array that that average a marker every 6,000 base pairs, we estimated that to detect a Minor Allele Frequency (MAF) of ≥ 10%, an odds ratio for risk of > 1.3 with 90% power would require 14,000 subjects (9,000 cases and 5,000 controls). Phase I consists of genotyping of 1,000 cases of early onset CAD and 1,000 asymptomatic older controls. Phase II will determine whether SNPs showing an association in Phase 1 are replicated in 8,000 cases and 4,000 controls. The phenotype is confirmed or excluded by coronary arteriograms obtained by catheterization or multi-slice CT. Cases with diabetes mellitus are excluded. Results: Initiated in 2005, over one billion genotypes have been performed and analyzed for 1,054 controls and 997 cases completing Phase I. Starting with data on 500,668 SNPs, control genotypes that were monoallelelic (21,668 SNPs) or not in Hardy Weinberg equilibrium were excluded using a false discovery rate (FDR) Q value <0.001 (1,473 SNPs). Individual SNPs with call rates <95% (30,826 SNPs) in cases and controls were excluded, leaving 446,701 SNPs. Fisher’s exact test was used to compare genotypes between cases and controls (FDR Q value <0.05), identifying 2,819 significant SNPs. SNPs with a MAF < 0.01 in both cases and controls (598 SNPs) were removed leaving 2,221 significant SNPs. 14 SNPs in exons were non-synonymous, i.e. cause amino acid substitutions. 53 clusters of SNPs (defined as ≥3 SNPs) within genes and 45 between genes were identified, including one at 9p21.3 that was replicated in multiple independent populations (McPherson et al., Science Express 2007 - in press). In addition, 13 SNPs were identified on the X chromosome. There was no evidence of stratification in our population. SNPs showing significant association with CAD are being assessed in an independent population during Phase II. Conclusions: This is the first genome wide scan for CAD genes utilizing 500,668 markers. Phase I has identified many genes not previously known to be associated with CAD.