Candidate Pathway-Based Genome-Wide Association Studies Identify Novel Associations of Genomic Variants in the Complement System Associated With Coronary Artery Disease

Abstract

Background Genomic variants identified by genome-wide association studies (GWAS) explain <20% of heritability of coronary artery disease (CAD), thus many risk variants remain missing for CAD. Identification of new variants may unravel new biological pathways and genetic mechanisms for CAD. To identify new variants associated with CAD, we developed a candidate pathway-based GWAS by integrating expression quantitative loci (eQTL) analysis and mining of GWAS data with variants in a candidate pathway. Methods and Results Mining of GWAS data was performed to analyze variants in 32 complement system genes for positive association with CAD. Functional variants in genes showing positive association were then identified by searching existing expression quantitative loci databases and validated by RT-PCR. A follow-up case control design was then used to determine whether the functional variants are associated with CAD in two independent GeneID Chinese populations. Candidate pathway-based GWAS identified positive association between variants in C3AR1 and C6 and CAD. Two functional variants, rs7842 in C3AR1 and rs4400166 in C6, were found to be associated with expression levels of C3AR1 and C6, respectively. Significant association was identified between rs7842 and CAD (P=3.99×10−6, OR=1.47) and between rs4400166 and CAD (P=9.30×10−3, OR=1.24) in the validation cohort. The significant findings were confirmed in the replication cohort (P=1.53×10−5, OR=1.37 for rs7842; P=8.41×10−3, OR=1.21 for rs4400166. Conclusions Integration of GWAS with biological pathways and eQTL is effective in identifying new risk variants for CAD. Functional variants increasing C3AR1 and C6 expression were shown to confer significant risk of CAD for the first time.

Genetic Determination of Serum Levels of Diabetes-Associated Adipokines

“…In a candidate pathway-based GWAS in a Chinese population, a variant in the 3'-UTR of C3AR1 (rs7842 A/G) was identified in an eQTL analysis to associate with C3AR1 expression levels and coronary artery disease [171]. In this study, carriers of the minor G-allele exhibited higher C3AR1 expression levels in leukocytes.…”

Functional Genomics Analysis of Big Data Identifies Novel Peroxisome Proliferator–Activated Receptor γ Target Single Nucleotide Polymorphisms Showing Association With Cardiometabolic Outcomes

“…13,14 More recently, investigators have been implementing functional genomics approaches to inform the selection of SNPs for candidate association studies and functional experiments, thus avoiding the multiple comparison burden of GWAS. For example, Xu et al 15 recently used a candidate pathway-based functional genomics approach to identify 2 putative functional SNPs related to cardiovascular disease in Chinese cohorts that would not have reach significance by GWAS thresholds.…”

Compiling the Complement of Genes Implicated in Coronary Artery Disease

“…The study by Xu et al 7 is an initial step toward further extending our understanding of the involvement of the complement system genes and their products in the pathogenesis of CAD using large-scale genetic data in humans. The study was based on a case-control sample of individuals of Han Chinese ancestry.…”

“…The candidate pathway-based approach used by Xu et al 7 for mining extant GWAS data may help illuminate the genetic basis of CAD and bridge the gap in unexplained heritability of the condition. By focusing systematically on known biological pathways previously implicated in atherosclerosis it is conceivable that other novel genetic variants associated with CAD may be identified.…”

“…20 Statistical associations are not necessarily causal and the downstream functional consequences of genetic variation are often unknown. Therefore, integrating multiple forms of functional genomic data beyond the exploration of expression quantitative trait loci data already done by Xu et al, 7 including but not limited to annotation of GWASdiscovered SNP data using Encyclopedia of DNA Elements (ENCODE) project data 21 (eg, targeting noncoding regulatory variation) and other -omics data (ie, metabolomics and proteomics) may help us elucidate the genetic architecture of CAD. The statistical ways of handling pathway-based analyses, including the opportunities and the pitfalls, are beyond the scope of this editorial, but are outlined elsewhere.…”