Effects of Population Structure in Genome-Wide Association Studies

A scenario where several slightly genetically different populations are mixed in the same study is frequently the case and a matter of concern in genome-wide associations (GWA) studies. This chapter defines genetic structure and shows how it can be quantified. A major unit of genetic structure is a genetic population. Genetic population is the collection of inter-breeding organisms of a particular species. The effects of population structure on the distribution of genotypes in a study population are considered. An assumption of zero kinship between study participants is made, which allows the formulation of the Hardy-Weinberg principle. When kinship is very low, the effects of kinship on genotypic distribution are minimal. The effects of substructure-that is when the study sample consists of several genetic populations-on genotypic distribution are also considered. Following this, the effects of genetic structure on the standard association tests are discussed. This chapter presents the study data as a 2 * 3 table, where the rows correspond to the case-control status and columns correspond to genotypic groups, and the cells contain counts of events. Finally, specific association tests that take possible genetic structure into account are shown.

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