Genome-Wide Association Study in a Lebanese Cohort Confirms PHACTR1 as a Major Determinant of Coronary Artery Stenosis

The manifestation of coronary artery disease (CAD) follows a well-choreographed series of events that includes damage of arterial endothelial cells and deposition of lipids in the sub-endothelial layers. Genome-wide association studies (GWAS) of multiple populations with distinctive genetic and lifestyle backgrounds are a crucial step in understanding global CAD pathophysiology. In this study, we report a GWAS on the genetic basis of arterial stenosis as measured by cardiac catheterization in a Lebanese population. The locus of the phosphatase and actin regulator 1 gene (PHACTR1) showed association with coronary stenosis in a discovery experiment with genome wide data in 1,949 individuals (rs9349379, OR = 1.37, p = 1.57×10−5). The association was replicated in an additional 2,547 individuals (OR = 1.31, p = 8.85×10−6), leading to genome-wide significant association in a combined analysis (OR = 1.34, p = 8.02×10−10). Results from this GWAS support a central role of PHACTR1 in CAD susceptibility irrespective of lifestyle and ethnic divergences. This association provides a plausible component for understanding molecular mechanisms involved in the formation of stenosis in cardiac vessels and a potential drug target against CAD

Large Scale Association Analysis Identifies Three Susceptibility Loci for Coronary Artery Disease

Genome wide association studies (GWAS) and their replications that have associated DNA variants with myocardial infarction (MI) and/or coronary artery disease (CAD) are predominantly based on populations of European or Eastern Asian descent. Replication of the most significantly associated polymorphisms in multiple populations with distinctive genetic backgrounds and lifestyles is crucial to the understanding of the pathophysiology of a multifactorial disease like CAD. We have used our Lebanese cohort to perform a replication study of nine previously identified CAD/MI susceptibility loci (LTA, CDKN2A-CDKN2B, CELSR2-PSRC1-SORT1, CXCL12, MTHFD1L, WDR12, PCSK9, SH2B3, and SLC22A3), and 88 genes in related phenotypes. The study was conducted on 2,002 patients with detailed demographic, clinical characteristics, and cardiac catheterization results. One marker, rs6922269, in MTHFD1L was significantly protective against MI (OR = 0.68, p = 0.0035), while the variant rs4977574 in CDKN2A-CDKN2B was significantly associated with MI (OR = 1.33, p = 0.0086). Associations were detected after adjustment for family history of CAD, gender, hypertension, hyperlipidemia, diabetes, and smoking. The parallel study of 88 previously published genes in related phenotypes encompassed 20,225 markers, three quarters of which with imputed genotypes The study was based on our genome-wide genotype data set, with imputation across the whole genome to HapMap II release 22 using HapMap CEU population as a reference. Analysis was conducted on both the genotyped and imputed variants in the 88 regions covering selected genes. This approach replicated HNRNPA3P1-CXCL12 association with CAD and identified new significant associations of CDKAL1, ST6GAL1, and PTPRD with CAD. Our study provides evidence for the importance of the multifactorial aspect of CAD/MI and describes genes predisposing to their etiology

Quantile-Quantile plot of the GWAS results.

<p>In this plot, each dot corresponds to a SNP tested for association where the observed –log₁₀ p values, shown by vertical axis, were plotted by the expected –log₁₀ p values under the null hypothesis. Upper right dots with higher observed significance than expected represent candidate variants for association with the phenotype tested (CAD category 1, control subjects; CAD category 2, patients with ≤50% stenosis in any coronary artery; CAD category 3, patients with >50% stenosis in any of the coronary arteries). The genomic control ratio (λ) was 1.033, indicating the lack of strong effect of systematic error such as population stratification.</p

Map around the PHACTR1 locus on chromosome 6 showing strong evidence of association with coronary artery stenosis.

<p>The upper vertical bars correspond to the location of all markers tested from the SNP array chip in the area. The X-axis indicates the chromosomal position in base-pairs on chromosome 6. Recombination rate is presented as a continuous blue line, while individual markers are represented by a circle filled with a color corresponding to the extent of LD with the key marker rs9349379 (in red) from dark blue (r² = 0) to red (r² = 1). Grey filled circles refer to SNPs with no LD information. The lower part represents the location of the genes with corresponding exons and the direction of transcription indicated by arrows. The figure was generated with LocusZoom using CEU from HapMap release 22 as reference.</p

Manhattan plot showing results of a GWA analysis in 1949 Lebanese patients for 513,079 SNPs.

<p> The Y-axis corresponds to the significance of the association (-log₁₀ p-values). The X-axis represents the physical location of the variant colored by chromosome.</p

Association of CAD stenosis categories with conventional risk factors.

<p>Analysis was done in GWA (discovery) and replication phases separately and combined (total). No, mild, and severe correspond to CAD severity categories 1, 2 and 3. <b>¹⁾</b><i>p</i> value indicating association of risk factors with CAD categories. <b>²⁾</b><i>p</i> value indicating association of risk factors with different phases. See Methods section for details.</p