A genome-wide genotyping study in patients with ischaemic stroke: initial analysis and data release

doi:10.1016/S1474-4422(07)70081-9

The Lancet Neurology

Volume 6, Issue 5, May 2007, Pages 414-420

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https://doi.org/10.1016/S1474-4422(07)70081-9 Get rights and content

Summary

Background

Despite evidence of a genetic role in stroke, the identification of common genetic risk factors for this devastating disorder remains problematic. We aimed to identify any common genetic variability exerting a moderate to large effect on risk of ischaemic stroke, and to generate publicly available genome-wide genotype data to facilitate others doing the same.

Methods

We applied a genome-wide high-density single-nucleotide-polymorphism (SNP) genotyping approach to a cohort of samples with and without ischaemic stroke (n=278 and 275, respectively), and did an association analysis adjusted for known confounders in a final cohort of 249 cases and 268 controls. More than 400 000 unique SNPs were assayed.

Findings

We produced more than 200 million genotypes in 553 unique participants. The raw genotypes of all the controls have been posted publicly in a previous study of Parkinson's disease. From this effort, results of genotype and allele association tests have been publicly posted for 88% of stroke patients who provided proper consent for public release. Preliminary analysis of these data did not reveal any single locus conferring a large effect on risk for ischaemic stroke.

Interpretation

The data generated here comprise the first phase of a genome-wide association analysis in patients with stroke. Release of phase I results generated in these publicly available samples from each consenting individual makes this dataset a valuable resource for data-mining and augmentation.

Introduction

Ischaemic stroke is a common neurological disease and a leading cause of severe disability and death in developed countries.¹ About 85–90% of strokes are ischaemic.2, 3 In most cases, stroke is thought to be a multifactorial disorder or complex trait for which classic patterns of inheritance cannot be shown. However, studies in family and animal models have consistently indicated a genetic influence on stroke risk and prognosis.4, 5, 6

Historically, the two most common approaches to finding genes involved in disease have been linkage and candidate gene association studies. For familial disorders with suitable family structures available for sampling, linkage has been a successful approach. The identification of genetic lesions underlying monogenic disorders has now become routine in many laboratories. In the context of stroke, this approach has provided some success, most notably with the identification of NOTCH3 mutations underlying cerebral autosomal dominant arteriopathy with subcortical infacts and leukoencephalopathy (CADASIL).⁵ Combined linkage and association approaches have led to the identification of putative risk factor loci for ischaemic stroke, namely PDE4D and ALOX5AP in the Icelandic population.7, 8

In the context of diseases with an oligogenic or polygenic basis of genetic risk, population-based association studies provide more statistical power than family-based linkage studies.9, 10 However, similar to other late-onset disorders, the identification of common alleles that affect stroke has been problematic. Until the advent of technology that made feasible the testing of thousands of genetic variants at once, the most practical and widely employed approach to identify disease-associated loci has been candidate gene association analysis. Many candidate genes for ischaemic stroke have been investigated with numerous statistically significant associations reported; however, few associations have been consistently replicated.¹¹

The completion of the International Haplotype Map Project (HapMap), coupled with the availability of high-throughput genotyping methods, affords the opportunity to apply the powerful approach of association testing in a genome-wide manner.12, 13 A handful of genome-wide association studies have so far been published on diseases including age-related macular degeneration, Parkinson's disease, myocardial infarction, and inflammatory bowel disease, and at least two of these have identified novel loci that have been independently replicated.14, 15, 16, 17, 18

In an attempt to define whether there is a common genetic risk factor underlying risk for stroke, and to generate publicly available genome-wide genotypes that can be reanalysed or augmented by others, we did whole-genome genotyping using more than 400 000 unique SNPs from the Illumina Infinium Human-1 and HumanHap300 assays in a cohort of 278 patients with ischaemic stroke and 275 neurologically normal controls. Here we present these data and an initial analysis of this genotyping effort.

Section snippets

Participants

All control samples were from the National Institute of Neurological Disorders and Stroke Neurogenetics Repository. All individuals involved in this study gave written consent for the genetic analysis. As described previously,¹⁶ the panels containing neurologically normal control samples were NDPT002, NDPT006, and NDPT008; these consist of DNA from 275 unique individuals and one replicate sample. Blood samples were drawn from white individuals who were unrelated and neurologically normal at

Results

DNA samples from 278 patients with stroke and 275 control subjects were genotyped using the Human-1 beadchip; 2 stroke cases and 1 control subject were genotyped in replicate to assess reproducibility of the genotyping platform. Ten stroke samples were dropped because of insufficient DNA and nine stroke samples did not reach the quality threshold of 95% call rate, or showed discordance between expected sex and genotype. Thus the ischaemic stroke cohort taken through to the analysis by STRUCTURE

Discussion

We present here an initial genome-wide SNP association study in ischaemic stroke, which compared 408 803 unique SNPs in 249 white patients with ischaemic stroke and 268 white neurologically normal controls. The ischaemic stroke cohort, prospectively ascertained at five US stroke centres, is comparable to population-based cohorts in the United States in terms of its conventional atherosclerotic risk factor profile.³⁶ The control cohort showed a paucity of conventional risk factors relative to

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^‡: These authors contributed equally

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Fast track — ArticlesA genome-wide genotyping study in patients with ischaemic stroke: initial analysis and data release

Summary

Background

Methods

Findings

Interpretation

Introduction

Section snippets

Participants

Results

Discussion

Epidemiology of stroke

Lancet

Change in stroke incidence, mortality, case-fatality, severity, and risk factors in Oxfordshire, UK from 1981 to 2004 (Oxford Vascular Study)

Lancet

Stroke incidence, prevalence, and survival: secular trends in Rochester, Minnesota, through 1989

Stroke

Genetics and ischaemic stroke

Brain

Notch3 mutations in CADASIL, a hereditary adult-onset condition causing stroke and dementia

Nature

New players in the genetics of stroke

N Engl J Med

The gene encoding 5-lipoxygenase activating protein confers risk of myocardial infarction and stroke

Nat Genet

The gene encoding phosphodiesterase 4D confers risk of ischaemic stroke

Nat Genet

Clinical methods in psychiatric genetics. I. Robustness of genetic marker investigative strategies

Acta Psychiatr Scand

The future of genetic studies of complex human diseases

Science

Meta-analysis of genetic studies in ischaemic stroke: thirty-two genes involving approximately 18,000 cases and 58,000 controls

Arch Neurol

The International HapMap Project

Nature

A haplotype map of the human genome

Nature

High-resolution whole-genome association study of Parkinson disease

Am J Hum Genet

Complement factor H polymorphism in age-related macular degeneration

Science

Genome-wide genotyping in Parkinson's disease and neurologically normal controls: first stage analysis and public release of data

Lancet Neurol

Functional SNPs in the lymphotoxin-alpha gene that are associated with susceptibility to myocardial infarction

Nat Genet

A genome-wide association study identifies IL23R as an inflammatory bowel disease gene

Science

Mini-mental state: a practical method for grading the cognitive state of patients for the clinician

J Psychiatr Res

The Ischaemic Stroke Genetics Study (ISGS) Protocol

BMC Neurol

The World Health Organization MONICA Project (monitoring trends and determinants in cardiovascular disease): a major international collaboration

J Clin Epidemiol

Classification of subtype of acute ischaemic stroke. Definitions for use in a multicenter clinical trial. TOAST. Trial of Org 10172 in Acute Stroke Treatment

Stroke

Classification and natural history of clinically identifiable subtypes of cerebral infarction

Lancet

Fast track — Articles
A genome-wide genotyping study in patients with ischaemic stroke: initial analysis and data release