Genome-wide association study identifies a variant in HDAC9 associated with large vessel ischemic stroke

Abstract

Genetic factors have been implicated in stroke risk, but few replicated associations have been reported. We conducted a genome-wide association study (GWAS) for ischemic stroke and its subtypes in 3,548 affected individuals and 5,972 controls, all of European ancestry. Replication of potential signals was performed in 5,859 affected individuals and 6,281 controls. We replicated previous associations for cardioembolic stroke near PITX2 and ZFHX3 and for large vessel stroke at a 9p21 locus. We identified a new association for large vessel stroke within HDAC9 (encoding histone deacetylase 9) on chromosome 7p21.1 (including further replication in an additional 735 affected individuals and 28,583 controls) (rs11984041; combined P = 1.87 × 10(-11); odds ratio (OR) = 1.42, 95% confidence interval (CI) = 1.28-1.57). All four loci exhibited evidence for heterogeneity of effect across the stroke subtypes, with some and possibly all affecting risk for only one subtype. This suggests distinct genetic architectures for different stroke subtypes.

Figure 1. Genome-wide association results at autosomal SNPs in combined British and Germany discovery samples

All ischemic stroke (top panel), large vessel stroke (second panel), small vessel stroke (third panel) and cardioembolic stroke (final panel). Loci previously reported in the literature for particular stoke subtypes (Table 2) are shown in black, with the new HDAC9 locus shown in red. In addition the combined p-values for discovery study and stages one and two of the replication study, at the top SNPs for these loci, are marked with diamonds.

Figure 1. Genome-wide association results at autosomal SNPs in combined British and Germany discovery samples

All ischemic stroke (top panel), large vessel stroke (second panel), small vessel stroke (third panel) and cardioembolic stroke (final panel). Loci previously reported in the literature for particular stoke subtypes (Table 2) are shown in black, with the new HDAC9 locus shown in red. In addition the combined p-values for discovery study and stages one and two of the replication study, at the top SNPs for these loci, are marked with diamonds.

Figure 1. Genome-wide association results at autosomal SNPs in combined British and Germany discovery samples

All ischemic stroke (top panel), large vessel stroke (second panel), small vessel stroke (third panel) and cardioembolic stroke (final panel). Loci previously reported in the literature for particular stoke subtypes (Table 2) are shown in black, with the new HDAC9 locus shown in red. In addition the combined p-values for discovery study and stages one and two of the replication study, at the top SNPs for these loci, are marked with diamonds.

Figure 1. Genome-wide association results at autosomal SNPs in combined British and Germany discovery samples

All ischemic stroke (top panel), large vessel stroke (second panel), small vessel stroke (third panel) and cardioembolic stroke (final panel). Loci previously reported in the literature for particular stoke subtypes (Table 2) are shown in black, with the new HDAC9 locus shown in red. In addition the combined p-values for discovery study and stages one and two of the replication study, at the top SNPs for these loci, are marked with diamonds.

Figure 2. Forest plot for the associations between rs11984041 and large vessel stroke in discovery and replication collections

The blue lines show the 95% confidence intervals of the log odds-ratio (OR) for each cohort, with the area of each square proportional to the inverse of the standard error. The diamonds indicate the 95% confidence interval for, from top to bottom, the discovery summary (combined British and German discovery collections), combined across collections within each of the three replication stages, the replication summary (combined across all three replication stages) and the overall summary (all discovery and replication collections combined). Evidence was combined across collections via an inverse-variance weighted fixed-effect meta-analysis. There was no evidence of heterogeneity of effect across collections (P = 0.92).

Figure 3. Genetic heterogeneity of different stroke sub-types for the 4 loci with significant associations: HDAC9, PITX2, 9p21(CDKN2A/CDKN2B) and ZFHX3

Bar plots show the posterior probabilities on the models of association: no effect in any subtype (Null), same effect in all subtypes, correlated effects across subtypes or subtype specific effects (see main text). Models are a priori assumed to be equally likely. Bayes factors, which compare the evidence (marginal likelihood) between any pair of models, can be calculated as the ratio of the posterior probability assigned to each model as reported under each bar of the plot. Accompanying density plots show the marginal posterior distribution on the odds ratio of the risk allele for each stroke subtype assuming a model of correlated effects (see methods for specification of priors). These analyses were performed using both discovery and replication samples (stage 1 & 2).

Figure 4

Plot of association signals around rs11984041 for large vessel stroke in the combined British and German discovery samples. SNPs are coloured based on their correlation (r²) with the labelled hit SNP which has the smallest P-value in the region. r² is calculated from the WTCCC2 control data. The bottom section of each plot shows the fine scale recombination rates estimated from HapMap data, and genes are marked by horizontal red lines. Arrows on the horizontal red lines denote direction of transcription, and black rectangles are exons.