Genetic association studies in recently admixed populations offer exciting opportunities for the identification of variants underlying phenotypic diversity. At the same time, genetic heterogeneity due to population admixture has to be accounted for in order to ensure validity of association tests. The whole genome sequence data and the genome-wide single nucleotide polymorphism chip data for Mexican American individuals provided by the Genetic Analysis Workshop 18 (GAW18) presents a unique opportunity to evaluate and compare methods for the statistical analysis of admixed genetic data. We summarize here the five contributions from the GAW18 Admixture group. Although group members considered a variety of research topics, the general theme was inference and consideration of ancestry admixture in genetic analyses. The topics considered can be grouped into three categories: (1) global and local ancestry inference and estimation; (2) association and admixture mapping; and (3) genotype imputation in admixed samples. We describe the approaches that were used and the most relevant findings from individual contributions. We also provide insight into the strengths and limitations of the state-of-the-art methods considered for genetic analyses in admixed populations.
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