August 30, 2008

Admixture mapping in Uyghurs

This is a followup to this earlier study. Note that the "European" label for the Caucasoid component in Uyghurs is inappropriate, since this is composed of href="">two distinct "European" and "Caucasoid Central Asian" elements.

From the paper:
Figure 3A shows summary plot of individual admixture proportions based on the highest-probability run of ten STRUCTURE runs. The results show that individuals from the same population often share membership coefficients in the inferred cluster, with the exception that one Japanese outlier shows obvious admixture. Mongola, Adygei, and Russian individuals show some degree of admixture as well.
Most of the EAS admixture in the Adygei from the Caucasus seems mostly spurious, as the Adygei have a substantial "Central Asian" Caucasoid component (38%) rather than Mongoloid admixture (2%).

Note that, as in the previous study, the Uyghur individuals seem to have similar proportions of "Western" and "Eastern" genes, due to the fact that the blend which produced them is fairly old and there are really no individuals in which either of the two components predominate.

The American Journal of Human Genetics, doi:10.1016/j.ajhg.2008.08.001

A Genome-wide Analysis of Admixture in Uyghurs and a High-Density Admixture Map for Disease-Gene Discovery

Shuhua Xu and Li Jin


Following up on our previous study, we conducted a genome-wide analysis of admixture for two Uyghur population samples (HGDP-UG and PanAsia-UG), collected from the northern and southern regions of Xinjiang in China, respectively. Both HGDP-UG and PanAsia-UG showed a substantial admixture of East-Asian (EAS) and European (EUR) ancestries, with an empirical estimation of ancestry contribution of 53:47 (EAS:EUR) and 48:52 for HGDP-UG and PanAsia-UG, respectively. The effective admixture time under a model with a single pulse of admixture was estimated as 110 generations and 129 generations, or admixture events occurred about 2200 and 2580 years ago for HGDP-UG and PanAsia-UG, respectively, assuming an average of 20 yr per generation. Despite Uyghurs' earlier history compared to other admixture populations, admixture mapping, holds promise for this population, because of its large size and its mixture of ancestry from different continents. We screened multiple databases and identified a genome-wide single-nucleotide polymorphism panel that can distinguish EAS and EUR ancestry of chromosomal segments in Uyghurs. The panel contains 8150 ancestry-informative markers (AIMs) showing large frequency differences between EAS and EUR populations (FST > 0.25, mean FST = 0.43) but small frequency differences (7999 AIMs validated) within both populations (FST < 0.05, mean FST < 0.01). We evaluated the effectiveness of this admixture map for localizing disease genes in two Uyghur populations. To our knowledge, our map constitutes the first practical resource for admixture mapping in Uyghurs, and it will enable studies of diseases showing differences in genetic risk between EUR and EAS populations.


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