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Review
. 2017 Oct 18:95:1.22.1-1.22.23.
doi: 10.1002/cphg.48.

Population Stratification in Genetic Association Studies

Jacklyn N Hellwege  1 , Jacob M Keaton  1 , Ayush Giri  1 , Xiaoyi Gao  2 , Digna R Velez Edwards  3 , Todd L Edwards  1
Affiliations
Review

Population Stratification in Genetic Association Studies

Jacklyn N Hellwege et al. Curr Protoc Hum Genet. .

Abstract

Population stratification (PS) is a primary consideration in studies of genetic determinants of human traits. Failure to control for PS may lead to confounding, causing a study to fail for lack of significant results, or resources to be wasted following false-positive signals. Here, historical and current approaches for addressing PS when performing genetic association studies in human populations are reviewed. Methods for detecting the presence of PS, including global and local ancestry methods, are described. Also described are approaches for accounting for PS when calculating association statistics, such that measures of association are not confounded. Many traits are being examined for the first time in minority populations, which may inherently feature PS. © 2017 by John Wiley & Sons, Inc.

Keywords: admixture; admixture mapping; association confounding; global ancestry; local ancestry; population stratification.

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Figures

Figure 1
Figure 1. Principal components analysis
These figures show the clustering results using principal components analysis implemented by the Eigensoft v3.0 software with 142,616 genome-wide random autosomal SNP loci from the HapMap project (Phase 3, release 3). Only the first three eigenvectors are shown. Note: CEU, Utah residents with ancestry from northern and western Europe; YRI, Yoruba in Ibadan, Nigeria (West Africa); CHB: Han Chinese in Beijing, China; ASW: African ancestry in Southwest USA. ASW is an admixed population.
Figure 1
Figure 1. Principal components analysis
These figures show the clustering results using principal components analysis implemented by the Eigensoft v3.0 software with 142,616 genome-wide random autosomal SNP loci from the HapMap project (Phase 3, release 3). Only the first three eigenvectors are shown. Note: CEU, Utah residents with ancestry from northern and western Europe; YRI, Yoruba in Ibadan, Nigeria (West Africa); CHB: Han Chinese in Beijing, China; ASW: African ancestry in Southwest USA. ASW is an admixed population.
See this image and copyright information in PMC

References

    1. Abraham G, Inouye M. Fast principal component analysis of large-scale genome-wide data. PLoS One. 2014;9(4):e93766. - PMC - PubMed
    1. Alexander DH, Lange K. Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC Bioinformatics. 2011;12:246. - PMC - PubMed
    1. Alexander DH, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 2009;19(9):1655–64. - PMC - PubMed
    1. Astle W, Balding DJ. Population Structure and Cryptic Relatedness in Genetic Association Studies. Statistical Science. 2009;24(4):451–471.
    1. Bacanu SA, Devlin B, Roeder K. Association studies for quantitative traits in structured populations. Genet Epidemiol. 2002;22(1):78–93. - PubMed

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