A genome-wide association study of carotid atherosclerosis in HIV-infected men

Abstract

Background: The role of host genetics in the development of subclinical atherosclerosis in the context of HIV-infected persons who are being treated with highly active antiretroviral therapy (HAART) is not well understood.

Methods: The present genome-wide association study (GWAS) is based on 177 HIV-positive Caucasian males receiving HAART who participated in the Fat Redistribution and Metabolic Change in HIV Infection (FRAM) Study. Common and internal carotid intima-media thicknesses (cIMT) measured by B-mode ultrasound were used as a subclinical measure of atherosclerosis. Single nucleotide polymorphisms (SNPs) were assayed using the Illumina HumanCNV370-quad beadchip. Copy Number Variants (CNV) were inferred using a hidden Markov Model (PennCNV). Regression analyses were used to assess the association of common and internal cIMT with individual SNPs and CNVs, adjusting for age, duration of antiretroviral treatment, and principal components to account for potential population stratification.

Results: Two SNPs in tight linkage disequilibrium, rs2229116 (a missense, nonsynonymous polymorphism (IIe to Val)) and rs7177922, located in the ryanodine receptor (RYR3) gene on chromosome 15 were significantly associated with common cIMT (P-value < 1.61 x 10). The RYR gene family has been known to play a role in the etiology of cardiovascular disease and has been shown to be regulated by HIV TAT protein.

Conclusion: These results suggest that in the context of HIV infection and HAART, a functional SNP in a biologically plausible candidate gene, RYR3, is associated with increased common carotid IMT, which is a surrogate for atherosclerosis.

Figure 1

Manhattan plot showing the genome wide association p-values of single nucleotide polymorphism (SNPs) with a) common carotid IMT (cIMT) and b) internal cIMT. The dark blue solid line indicates the Bonferroni threshold, the dotted blue line indicates the threshold based on the effective number of independent tests and the red solid line indicated the threshold at 1.5*10⁻⁵.

Figure 2

Q-Q plot of observed versus expected p-values of association with a) common carotid IMT (cIMT) and b) internal cIMT.

Figure 3

A comprehensive distribution of 122 informative SNPs from the Illumina humanCNV370-quad beadchip in the RYR3 gene spanning from 31,390,469 to 31,945,595 bp genomic location in chromosome 15 and the −log (p-values) (left y-axis) of genomic association with common carotid IMT (cIMT). The blue colored SNP is the functional SNP (rs2229116) that was associated at the genomic significance level after Bonferroni adjustment. The colors of the other SNPs indicate the linkage disequilibrium (LD) (r²) in relation to rs2229116. The right y-axis is the recombination rate shown in blue graphical lines to define recombination hotspots within the RYR3 gene. The dotspot graph at the top represents the log₁₀(p) values of common cIMT residual (after adjusting for age, HAART duration and first principal component) along with mean and median by genotype for rs2229116.