Loci associated with ischaemic stroke and its subtypes (SiGN): a genome-wide association study

Abstract

Summary Introduction The discovery of disease-associated loci through genome-wide association studies (GWAS) is the leading approach to the identification of novel biological pathways for human disease. To date, GWAS have had been limited by relatively small sample sizes and yielded relatively few loci associated with ischemic stroke The National Institute of Neurological Disorders Stroke Genetics Network (NINDS-SiGN) is an international consortium that has taken a systematic approach to phenotyping and produced the largest ischemic stroke GWAS to date. Methods In order to identify genetic loci associated with ischemic stroke, we performed a two-stage genome-wide association study. The first stage consisted of 16,851 cases with state-of-the-art phenotyping and 32,473 stroke-free controls. Cases were aged 16 to 104 years, recruited between 1989 and 2012, and subtyped by centrally trained and certified investigators using the web-based protocol, Causative Classification of Stroke (CCS). We constructed case-control strata by identify samples genotyped on (nearly) identical arrays and of similar genetic ancestral background. Data was cleaned and imputed using dense imputation reference panels generated from whole-genome sequence data. Genome-wide testing was performed within each stratum for each available phenotype, and summary level results were combined using inverse variance-weighted fixed effects meta-analysis. The second stage consisted of in silico look-ups of 1,372 SNPs in 20,941 cases and 364,736 stroke-free controls, with cases previously subtyped using the TOAST classification system according to local standards. The two stages were then jointly analyzed in a final meta-analysis. Findings We identified a novel locus at 1p13.2 near TSPAN2 associated with large artery atherosclerosis (LAA)-related stroke (stage I OR for the G allele at rs12122341 = 1·21, p = 4.50 × 10−8; stage II OR = 1·19, p = 1·30 × 10−9). We also confirmed four loci robustly associated with ischemic stroke and reported in prior studies, including PITX2 and ZFHX3 for cardioembolic stroke, and HDAC9 for LAA stroke. The 12q24 locus near ALDH2, originally associated with all ischemic stroke but not with any specific subtype, exceeded genome-wide significance in the meta-analysis of small artery stroke. Other loci, including NINJ2, were not confirmed. Interpretation Our results identify a novel LAA-stroke susceptibility gene and now indicate that all loci implicated by GWAS to date are subtype specific. Follow-up studies will be necessary to determine whether the locus near TSPAN2 yields a novel therapeutic approach to stroke prevention. Given the subtype-specificity of these associations, the rich phenotyping available in SiGN is likely to prove vital for further genetic discovery in ischemic stroke. Funding National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health (NIH).

Dutch Parelsnoer Institute-Cerebrovascular Accident (CVA) Study: A Large Multicenter Clinical Biobank with Standardized Collection and Storage

“…The creation of large stroke cohorts is currently of great importance in genetic stroke research, illustrated by genome-wide association studies (GWASs) performed in the last years [20][21][22][23]. Stroke is a heterogeneous disease consisting of several etiological subtypes with different underlying pathophysiological mechanisms.…”

“…Most subtypes are thought to have a specific genetic architecture, as GWASs have found multiple genetic loci to be subtype-specific. Future genetic stroke research may lead to management approaches more tailored to the different subtypes and novel therapeutical targets [20,21,24].…”

“…The ASCO system (where A stands for atherosclerosis, S for small vessel disease, C for Cardiac source, O for other cause) classifies similar subtypes, though both classification schemes have been found to have different characteristics in practice [26,27]. These classifications enable us to investigate associations between genetic risk loci and stroke subtypes and to enable pooling with data of other ongoing genetic stroke studies [20,21,25,27]. Second, besides genetic research the Parelsnoer Institute-CVA Study population is also very well suited for epidemiological studies because of its prospective, multicenter design and large sample size [28].…”

Emerging Risk Factors for Stroke

“…Genome-wide meta-analyses of IS involving >10 000 IS cases have, to date, only identified a few susceptibility loci. 6,7 Furthermore, most genetic associations with IS are subtype specific for which power is more limited. Genetic risk factors for hemorrhagic stroke are summarized elsewhere.…”

“…49 The comparability between Causative Classification of Stroke (CCS) and Trial of ORG 10172 in Acute Stroke Treatment (TOAST) classification of IS subtypes has also been examined and will further facilitate large-scale genetic meta-analyses. 6,50 Exploring genetic factors in different ethnic populations, for example in China where stroke is more common than in the West, will be important for determining the underlying distribution of different stroke subtypes and their risk factors. Studies such as the China Kadoorie Biobank, a prospective study of 500 000 individuals from across China, and the Risk Assessment of Cerebrovascular Events Study (RACE), a study of stroke in South Asians, will facilitate this effort.…”