Abstract
BackgroundUsing 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.ResultsWe 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.ConclusionWe 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.
Highlights
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
New data The allele frequencies for the 128 ancestry informative single-nucleotide polymorphisms (AISNPs) for all 119 population samples are given in Additional file 2, and the allele frequencies of the 69 population samples tested in our lab have all been entered into the ALFRED database [30] and can be readily accessed using the rs# of each single-nucleotide polymorphisms (SNPs)
Fst The Fst distribution of the 128 AISNPs was compared to the distribution of 2,327 non-AISNPs typed in our lab (Figure 1 and Additional file 3)
Summary
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. 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. Others have focused on distinguishing ancestral origins from three or four continental regions, such as sub-Saharan Africa, Europe, East Asia and the Americas [8,9,10,11,12], or more broadly between many studies attempting to identify markers that provide ancestry information within a region, such as East Asia [24] or Europe [17,18].
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