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Hum Mol Genet. 2008 Oct 15;17(R2):R143-50. doi: 10.1093/hmg/ddn268.

Accounting for ancestry: population substructure and genome-wide association studies.

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  • 1Rowe Program in Human Genetics, Departments of Biological Chemistry and Medicine, One Shield Avenue, University of California Davis, Davis, CA 95616, USA.


Accounting for the genetic substructure of human populations has become a major practical issue for studying complex genetic disorders. Allele frequency differences among ethnic groups and subgroups and admixture between different ethnic groups can result in frequent false-positive results or reduced power in genetic studies. Here, we review the problems and progress in defining population differences and the application of statistical methods to improve association studies. It is now possible to take into account the confounding effects of population stratification using thousands of unselected genome-wide single-nucleotide polymorphisms or, alternatively, selected panels of ancestry informative markers. These methods do not require any demographic information and therefore can be widely applied to genotypes available from multiple sources. We further suggest that it will be important to explore results in homogeneous population subsets as we seek to define the extent to which genomic variation influences complex phenotypes.

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