Chunk #25 — Results — Integrating Genetic and Network Data across Species to Inform GWA Discoveries — Identifying candidate susceptibility genes for coronary artery disease and LDL cholesterol levels.
Another GWAS involving the WTCCC resulted in the identification of seven loci associated with coronary artery disease (CAD) [16]. The seven top-hitting SNPs associated with CAD at each of the seven loci in this study were represented on the Affymetrix 500K array. Therefore, we examined the HLC data to identify expression traits that were significantly associated with any of the seven CAD-associated SNPs. Given the roughly 40,000 expression traits examined at each of the seven SNPs (280,000 tests in all), we set a nominal p-value threshold of 0.05/280,000 = 1.79 × 10−7 for significance. Only one of the seven SNPs identified in the WTCCC CAD study, rs599839 on Chromosome 1p13.3, was significantly associated with any of the HLC expression traits (Figure 2). Four different expression traits were identified as significantly associated with rs599839 (Table 4). One of the four expression traits corresponded to a gene, PSRC1, that had been identified as a candidate susceptibility gene in the WTCCC CAD study [16].
