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J.K. Pritchard and N. A. Rosenberg 1999. Use of unlinked genetic markers to detect population stratification in association studies. Am. J. of Hum. Gen. 65: 220-228.

We examine the issue of population stratification in association mapping studies. In case-control studies of association, population subdivision or recent admixture of populations can lead to spurious associations between a phenotype and unlinked candidate loci. Using a model of sampling from a structured population, we show that if population stratification exists, it can be detected using unlinked marker loci. We show that the case-control study design using unrelated control individuals is a valid approach for association mapping, provided that marker loci unlinked to the candidate locus are included in the study in order to test for stratification. We suggest guidelines for how many unlinked marker loci should be used.

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