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

Kidd JR, Friedlaender FR, Speed WC, Pakstis AJ, De La Vega FM, Kidd KK - Investig Genet (2011)

Bottom Line: 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.At the same time, the limitations of the panel for distinguishing ancestry and quantifying admixture among Eurasian populations are noted.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA. Judith.Kidd@yale.edu.

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.

No MeSH data available.


Related in: MedlinePlus

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.
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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.

Mentions: The different patterns at K = 7 and K = 8 show fine distinctions even among the regions that are superficially similar. To make some of these clearer, we have generated the population averages for the best result (highest likelihood) for each of the patterns (Figure 5). These emphasize the variation among individuals in each population sample by showing the population as multiple colors. These figures also emphasize the southwestern Asia through northern Europe cline seen in all patterns.


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

Kidd JR, Friedlaender FR, Speed WC, Pakstis AJ, De La Vega FM, Kidd KK - Investig Genet (2011)

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3025953&req=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.
Mentions: The different patterns at K = 7 and K = 8 show fine distinctions even among the regions that are superficially similar. To make some of these clearer, we have generated the population averages for the best result (highest likelihood) for each of the patterns (Figure 5). These emphasize the variation among individuals in each population sample by showing the population as multiple colors. These figures also emphasize the southwestern Asia through northern Europe cline seen in all patterns.

Bottom Line: 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.At the same time, the limitations of the panel for distinguishing ancestry and quantifying admixture among Eurasian populations are noted.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA. Judith.Kidd@yale.edu.

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.

No MeSH data available.


Related in: MedlinePlus