Identification of 64 Novel Genetic Loci Provides an Expanded View on the Genetic Architecture of Coronary Artery Disease

Abstract

Rationale: Coronary artery disease (CAD) is a complex phenotype driven by genetic and environmental factors. Ninety-seven genetic risk loci have been identified to date, but the identification of additional susceptibility loci might be important to enhance our understanding of the genetic architecture of CAD.

Objective: To expand the number of genome-wide significant loci, catalog functional insights, and enhance our understanding of the genetic architecture of CAD.

Methods and results: We performed a genome-wide association study in 34 541 CAD cases and 261 984 controls of UK Biobank resource followed by replication in 88 192 cases and 162 544 controls from CARDIoGRAMplusC4D. We identified 75 loci that replicated and were genome-wide significant (P<5×10^-8) in meta-analysis, 13 of which had not been reported previously. Next, to further identify novel loci, we identified all promising (P<0.0001) loci in the CARDIoGRAMplusC4D data and performed reciprocal replication and meta-analyses with UK Biobank. This led to the identification of 21 additional novel loci reaching genome-wide significance (P<5×10^-8) in meta-analysis. Finally, we performed a genome-wide meta-analysis of all available data revealing 30 additional novel loci (P<5×10^-8) without further replication. The increase in sample size by UK Biobank raised the number of reconstituted gene sets from 4.2% to 13.9% of all gene sets to be involved in CAD. For the 64 novel loci, 155 candidate causal genes were prioritized, many without an obvious connection to CAD. Fine mapping of the 161 CAD loci generated lists of credible sets of single causal variants and genes for functional follow-up. Genetic risk variants of CAD were linked to development of atrial fibrillation, heart failure, and death.

Conclusions: We identified 64 novel genetic risk loci for CAD and performed fine mapping of all 161 risk loci to obtain a credible set of causal variants. The large expansion of reconstituted gene sets argues in favor of an expanded omnigenic model view on the genetic architecture of CAD.

Keywords: computational biology; coronary artery disease; genetics; genome-wide association study; sample size.

Figure 1.

Network analyses of reconstituted gene sets. The total number of significant gene sets involved in coronary artery disease (CAD) increased to 13.90% since the 1000 Genome genome-wide association studies of CARDIoGRAMplusC4D, considering all possible gene sets. Clustering by modularity using Gephi software indicated that pathways specific for cardiovascular/heart development, inflammation, lipids, kidney and coagulation clustered together. PPI networks & Other indicates a remaining bin predominantly populated by protein–protein interaction networks.

Figure 2.

Heatmap of associations in UK Biobank with novel loci. Heatmap of z scores for different diseases and phenotypes in UK Biobank, aligned to increased risk of coronary artery disease. Only significant associations (false discovery rate<0.01) are shown. The genetic risk score constructed with the known and novel loci, weighted using coefficients of CARDIoGRAMplusC4D, is highlighted by the red rectangle. BMI indicates body mass index; COPD, chronic obstructive pulmonary disease; RBC, red blood cell; and TIA, transient ischemic attack.

Figure 3.

The role of regulatory DNA underlying coronary artery disease (CAD)-associated single-nucleotide polymorphisms (SNPs). Enrichment of genome-wide association analysis P values in Dnase I hypersensitive sites (DHS). CAD SNPs at different genome-wide association study (GWAS) threshold were significantly enriched in DHS footprints (A) and hot spots (B) across many different tissues and cell types. The fold enrichment was highly significant for most tissues and cell types (P<1×10⁻⁸) as indicated by the 4 colored circles next to the labels, 3 colored circles indicate P<1×10⁻⁷. Label sizes of tissue types were downsized because of space limitations; tissue types may be represented by multiple samples, indicated by hash marks of the same color. C, Subsequent prioritization of potential causal annotations underlying the 161 CAD loci also suggested that regions of DHS may be underlying the associations, but coding variants, conservation, 5′ untranslated region (UTR), and H3K4me1 annotations were more likely to be causal. D, Posterior probabilities for causality for each variant in the 164 CAD loci were calculated by an empirical Bayes approach implemented in the Probabilistic Annotation Integrator Framework, taking into account linkage disequilibrium (LD), association statistics, and the potentially causal annotations and summarized in Table 2 and Online Table XX. CTCF indicates transcriptional repressor CTCF; DGF, digital genomic footprint by Dnase1 hypersensitivity; FANTOM5, functional annotation of the mammalian genome V5; TFBS, transcription factor binding site; and TSS, transcription start site.