Measuring European population stratification with microarray genotype data

A proper understanding of population genetic stratification - differences in individual ancestry within a population - is crucial in attempts to find genes for complex traits through association mapping. We report on genomewide typing of similar to 10,000 single-nucleotide polymorphisms in 297 individuals, to explore population structure in Europeans of known and unknown ancestry. The results reveal the presence of several significant axes of stratification, most prominently in a northern-southeastern trend, but also along an east-west axis. We also demonstrate the selection and application of EuroAIMs ( European ancestry informative markers) for ancestry estimation and correction. The Coriell Caucasian and CEPH ( Centre d'E tude du Polymorphisme Humain) Utah sample panels, often used as proxies for European populations, are found to reflect different subsets of the continent's ancestry.