Fine mapping of a linkage peak with integration of lipid traits identifies novel coronary artery disease genes on chromosome 5

Background Coronary artery disease (CAD), and one of its intermediate risk factors, dyslipidemia, possess a demonstrable genetic component, although the genetic architecture is incompletely defined. We previously reported a linkage peak on chromosome 5q31-33 for early-onset CAD where the strength of evidence for linkage was increased in families with higher mean low density lipoprotein-cholesterol (LDL-C). Therefore, we sought to fine-map the peak using association mapping of LDL-C as an intermediate disease-related trait to further define the etiology of this linkage peak. The study populations consisted of 1908 individuals from the CATHGEN biorepository of patients undergoing cardiac catheterization; 254 families (N = 827 individuals) from the GENECARD familial study of early-onset CAD; and 162 aorta samples harvested from deceased donors. Linkage disequilibrium-tagged SNPs were selected with an average of one SNP per 20 kb for 126.6-160.2 MB (region of highest linkage) and less dense spacing (one SNP per 50 kb) for the flanking regions (117.7-126.6 and 160.2-167.5 MB) and genotyped on all samples using a custom Illumina array. Association analysis of each SNP with LDL-C was performed using multivariable linear regression (CATHGEN) and the quantitative trait transmission disequilibrium test (QTDT; GENECARD). SNPs associated with the intermediate quantitative trait, LDL-C, were then assessed for association with CAD (i.e., a qualitative phenotype) using linkage and association in the presence of linkage (APL; GENECARD) and logistic regression (CATHGEN and aortas). Results We identified four genes with SNPs that showed the strongest and most consistent associations with LDL-C and CAD: EBF1 , PPP2R2B , SPOCK1 , and PRELID2 . The most significant results for association of SNPs with LDL-C were: EBF1 , rs6865969, p = 0.01; PPP2R2B , rs2125443, p = 0.005; SPOCK1 , rs17600115, p = 0.003; and PRELID2 , rs10074645, p = 0.0002). The most significant results for CAD were EBF1 , rs6865969, p = 0.007; PPP2R2B , rs7736604, p = 0.0003; SPOCK1 , rs17170899, p = 0.004; and PRELID2 , rs7713855, p = 0.003. Conclusion Using an intermediate disease-related quantitative trait of LDL-C we have identified four novel CAD genes, EBF1 , PRELID2 , SPOCK1 , and PPP2R2B . These four genes should be further examined in future functional studies as candidate susceptibility loci for cardiovascular disease mediated through LDL-cholesterol pathways.