HGVbaseG2P - Study Report

Study Report - GWAS of ischemic stroke (HGVST14)

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HGVbaseG2P identifier

HGVST14

Study name

GWAS of ischemic stroke

Phenotype(s) tested

Ischemic stroke

Study design

Case and control

Genotype Platforms

HumanHap300
Illumina Infinium Human-1

Abstract

Summary-level data and analysis results from the National Institute of Neurological Disorders and Stroke (NINDS) Ischemic Stroke Genetics Study (ISGS) imported from dbGaP. 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

Submission information