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Improving Ancestry Distinctions Among Southwest Asian Populations

NCJ Number
253472
Date Published
July 2018
Length
7 pages
Author(s)
Oziem Bulbul; William C. Speed; Cemal Gurkan; Usha Soundararajan; Haseena Rajeevan; Andrew J. Pakstis; Kenneth K. Kidd
Agencies
NIJ-Sponsored
Annotation
Since it is now possible to identify additional SNPs to provide refined discrimination among regional subsets of populations, the current project targeted Southwest Asia and the nearby Mediterranean region (SWA) for such a "second tier" panel.
Abstract
The Kidd Lab panel of 55 AISNPs can provide up to 10 statistically relevant biogeographic groupings of a global set of populations. A second-tier panel would be useful for increasing the accuracy for further differentiation of populations within a specific global grouping. The current project selected the potentially best SNPs from various sources: the authors' own laboratory database (greater than 4600 SNPs), AISNP panels (Kidd 55 and Seldin 128 SNP panels), and published papers reporting European and SW Asian populations. Rosenberg's Informativeness, Fst, and allele frequency heatmap matrices were used to determine the best SNPs for the region. A total of 2,568 individuals from 39 different populations, ranging from North-East Africa through the SW Asia and Europe to the Ural Mountains, were included in the refinement processes and analyses. Heatmap, PCA, Structure (K equals 4), and ancestry inference for selected individuals with an in-lab version of FROG-kb analyses indicate that these 86 AISNPs provide the basis for building an improved, optimized panel of AISNPs that collectively provide additional information on differences among populations in that part of the world. Testing this panel with additional populations from the area and with new SNPs and/or microhaplotypes is expected to improve the panel. (publisher abstracts modified)

Date Created: July 20, 2021