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. 2011 Jan 5;2(1):1.
doi: 10.1186/2041-2223-2-1.

Analyses of a set of 128 ancestry informative single-nucleotide polymorphisms in a global set of 119 population samples

Judith R Kidd  1 , Françoise R Friedlaender, William C Speed, Andrew J Pakstis, Francisco M De La Vega, Kenneth K Kidd
Affiliations

Analyses of a set of 128 ancestry informative single-nucleotide polymorphisms in a global set of 119 population samples

Judith R Kidd et al. Investig Genet. .

Abstract

Background: Using DNA to determine an individual's ancestry from among human populations is generally interesting and useful for many purposes, including admixture mapping, controlling for population structure in disease or trait association studies and forensic ancestry inference. However, to estimate ancestry, including possible admixture within an individual, as well as heterogeneity within a group of individuals, allele frequencies are necessary for what are believed to be the contributing populations. For this purpose, panels of ancestry informative markers (AIMs) have been developed.

Results: We are presenting our work on one such panel, composed of 128 ancestry informative single-nucleotide polymorphisms (AISNPs) already proposed in the literature. Compared to previous studies of these AISNPs, we have studied three times the number of individuals (4,871) in three times as many population samples (119). We have validated this panel for many ancestry assignment and admixture studies, especially those that were the rationale for the original selection of the 128 SNPs: African Americans and Mexican Americans. At the same time, the limitations of the panel for distinguishing ancestry and quantifying admixture among Eurasian populations are noted.

Conclusion: We demonstrate the simultaneous importance of the specific set of population samples and their relative sample sizes in the use of the structure program to determine which groups cluster together and consequently influence the ability of a marker panel to infer ancestry. We demonstrate the strengths and weaknesses of this particular panel of AISNPs in a global context.

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Figures

Figure 1
Figure 1
Comparisons of Fst distributions for the 128 ancestry informative single-nucleotide polymorphisms (AISNPs) and for a reference set of 2327 SNPs.
Figure 2
Figure 2
Principal component analysis (PCA) of 119 population samples based on allele frequencies of 128 AISNPs.
Figure 3
Figure 3
Structure analyses at K = 2-8 for 119 population samples.
Figure 4
Figure 4
The different patterns seen more than once in solutions from 20 runs of structure at K = 7 and K = 8.
Figure 5
Figure 5
Average population assignment to clusters for structure analyses at K = 8. The data are the same as the K = 8 analysis in Figures 3 and 4.
See this image and copyright information in PMC

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