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Genet Epidemiol. 2010 Dec;34(8):783-91. doi: 10.1002/gepi.20520.

Joint testing of genotype and ancestry association in admixed families.

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  • 1Department of Genetics, School of Medicine, Stanford University, Stanford, California 94305, USA. huatang@stanford.edu


Current genome-wide association studies (GWAS) often involve populations that have experienced recent genetic admixture. Genotype data generated from these studies can be used to test for association directly, as in a non-admixed population. As an alternative, these data can be used to infer chromosomal ancestry, and thus allow for admixture mapping. We quantify the contribution of allele-based and ancestry-based association testing under a family-design, and demonstrate that the two tests can provide non-redundant information. We propose a joint testing procedure, which efficiently integrates the two sources information. The efficiencies of the allele, ancestry and combined tests are compared in the context of a GWAS. We discuss the impact of population history and provide guidelines for future design and analysis of GWAS in admixed populations.

© 2010 Wiley-Liss, Inc.

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