Evaluation of self-reported ethnicity in a case-control population: the stroke prevention in young women study

• Main Authors: Wozniak Marcella A, O'Connell Jeffery R, Stine Oscar C, MacClellan Leah R, Howard Timothy D, Cole John W, Mez Jesse B, Stern Barney J, Sorkin John D, Mitchell Braxton D, Kittner Steven J
• Format: Article
• Language: English
• Published: BMC 2009-12-01
• Series: BMC Research Notes
• Online Access: http://www.biomedcentral.com/1756-0500/2/260

<p>Abstract</p> <p>Background</p> <p>Population-based association studies are used to identify common susceptibility variants for complex genetic traits. These studies are susceptible to confounding from unknown population substructure. Here we apply a model-based clustering approach to our case-control study of stroke among young women to examine if self-reported ethnicity can serve as a proxy for genetic ancestry.</p> <p>Findings</p> <p>A population-based case-control study of stroke among women aged 15-49 identified 361 cases of first ischemic stroke and 401 age-comparable control subjects. Thirty single nucleotide polymorphisms (SNPs) throughout the genome unrelated to stroke risk and with established ancestry-based allele frequency differences were genotyped in all participants. The <it>Structure </it>program was used to iteratively evaluate for K = 1 to 5 potential genetic-based subpopulations. Evaluating the population as a whole, the <it>Structure </it>output plateaued at K = 2 clusters. 98% of self-reported Caucasians had an estimated probability ≥50% of belonging to Cluster 1, while 94% of self-reported African-Americans had an estimated probability ≥50% of belonging to Cluster 2. Stratifying the participants by self-reported ethnicity and repeating the analyses revealed the presence of two clusters among Caucasians, suggesting that potential substructure may exist.</p> <p>Conclusions</p> <p>Among our combined sample of African-American and Caucasian participants there is no large unknown subpopulation and self-reported ethnicity can serve as a proxy for genetic ancestry. Ethnicity-specific analyses indicate that population substructure may exist among the Caucasian participants indicating that further studies are warranted.</p>