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

Mar Matarín, W. Mark Brown, Sonja Scholz, Javier Simón-Sánchez, Hon Chung Fung, Dena Hernandez, J. Raphael Gibbs, Fabienne Wavrant De Vrieze, Cynthia Crews, Angela Britton, Carl D. Langefeld, Thomas G Brott, Robert D Jr. Brown, Bradford B. Worrall, Michael Frankel, Scott Silliman, L. Douglas Case, Andrew Singleton, John A. Hardy, Stephen S. RichJames F Meschia

Research output: Contribution to journalArticle

144 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)414-420
Number of pages7
JournalLancet Neurology
Volume6
Issue number5
DOIs
StatePublished - May 2007

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Stroke
Genome
Genotype
Single Nucleotide Polymorphism
Data Mining
Genome-Wide Association Study
Parkinson Disease
Alleles

ASJC Scopus subject areas

  • Clinical Neurology

Cite this

A genome-wide genotyping study in patients with ischaemic stroke : initial analysis and data release. / Matarín, Mar; Brown, W. Mark; Scholz, Sonja; Simón-Sánchez, Javier; Fung, Hon Chung; Hernandez, Dena; Gibbs, J. Raphael; De Vrieze, Fabienne Wavrant; Crews, Cynthia; Britton, Angela; Langefeld, Carl D.; Brott, Thomas G; Brown, Robert D Jr.; Worrall, Bradford B.; Frankel, Michael; Silliman, Scott; Case, L. Douglas; Singleton, Andrew; Hardy, John A.; Rich, Stephen S.; Meschia, James F.

In: Lancet Neurology, Vol. 6, No. 5, 05.2007, p. 414-420.

Research output: Contribution to journalArticle

Matarín, M, Brown, WM, Scholz, S, Simón-Sánchez, J, Fung, HC, Hernandez, D, Gibbs, JR, De Vrieze, FW, Crews, C, Britton, A, Langefeld, CD, Brott, TG, Brown, RDJ, Worrall, BB, Frankel, M, Silliman, S, Case, LD, Singleton, A, Hardy, JA, Rich, SS & Meschia, JF 2007, 'A genome-wide genotyping study in patients with ischaemic stroke: initial analysis and data release', Lancet Neurology, vol. 6, no. 5, pp. 414-420. https://doi.org/10.1016/S1474-4422(07)70081-9
Matarín, Mar ; Brown, W. Mark ; Scholz, Sonja ; Simón-Sánchez, Javier ; Fung, Hon Chung ; Hernandez, Dena ; Gibbs, J. Raphael ; De Vrieze, Fabienne Wavrant ; Crews, Cynthia ; Britton, Angela ; Langefeld, Carl D. ; Brott, Thomas G ; Brown, Robert D Jr. ; Worrall, Bradford B. ; Frankel, Michael ; Silliman, Scott ; Case, L. Douglas ; Singleton, Andrew ; Hardy, John A. ; Rich, Stephen S. ; Meschia, James F. / A genome-wide genotyping study in patients with ischaemic stroke : initial analysis and data release. In: Lancet Neurology. 2007 ; Vol. 6, No. 5. pp. 414-420.
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T1 - A genome-wide genotyping study in patients with ischaemic stroke

T2 - initial analysis and data release

AU - Matarín, Mar

AU - Brown, W. Mark

AU - Scholz, Sonja

AU - Simón-Sánchez, Javier

AU - Fung, Hon Chung

AU - Hernandez, Dena

AU - Gibbs, J. Raphael

AU - De Vrieze, Fabienne Wavrant

AU - Crews, Cynthia

AU - Britton, Angela

AU - Langefeld, Carl D.

AU - Brott, Thomas G

AU - Brown, Robert D Jr.

AU - Worrall, Bradford B.

AU - Frankel, Michael

AU - Silliman, Scott

AU - Case, L. Douglas

AU - Singleton, Andrew

AU - Hardy, John A.

AU - Rich, Stephen S.

AU - Meschia, James F

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N2 - 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.

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