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01-01-2016 | Original Article

A single-tube 27-plex SNP assay for estimating individual ancestry and admixture from three continents

Authors: Yi-Liang Wei, Li Wei, Lei Zhao, Qi-Fan Sun, Li Jiang, Tao Zhang, Hai-Bo Liu, Jian-Gang Chen, Jian Ye, Lan Hu, Cai-Xia Li

Published in: International Journal of Legal Medicine | Issue 1/2016

Abstract

A single-tube multiplex assay of a small set of ancestry-informative markers (AIMs) for effectively estimating individual ancestry and admixture is an ideal forensic tool to trace the population origin of an unknown DNA sample. We present a newly developed 27-plex single nucleotide polymorphism (SNP) panel with highly robust and balanced differential power to perfectly assign individuals to African, European, and East Asian ancestries. Evaluating 968 previously described intercontinental AIMs from three HapMap population genotyping datasets (Yoruban in Ibadan, Nigeria (YRI); Utah residents with Northern and Western European ancestry from the Centre de'Etude du Polymorphism Humain (CEPH) collection (CEU); and Han Chinese in Beijing, China (CHB)), the best set of markers was selected on the basis of Hardy-Weinberg equilibrium (p > 0.00001), population-specific allele frequency (two of three δ values >0.5), according to linkage disequilibrium (r ² < 0.2), and capable of being multiplexed in one tube and detected by capillary electrophoresis. The 27-SNP panel was first validated by assigning the ancestry of the 11 populations in the HapMap project. Then, we tested the 27-plex SNP assay with 1164 individuals from 17 additional populations. The results demonstrated that the SNP panel was successful for ancestry inference of individuals with African, European, and East Asian ancestry. Furthermore, the system performed well when inferring the admixture of Eurasians (EUR/EAS) after analyzing admixed populations from Xinjiang (Central Asian) as follows: Tajik (68:27), Uyghur (49:46), Kirgiz (40:57), and Kazak (36:60). For individual analyses, we interpreted each sample with a three-ancestry component percentage and a population match probability sequence. This multiplex assay is a convenient and cost-effective tool to assist in criminal investigations, as well as to correct for the effects of population stratification for case-control studies.

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Title: A single-tube 27-plex SNP assay for estimating individual ancestry and admixture from three continents
Authors: Yi-Liang Wei
Li Wei
Lei Zhao
Qi-Fan Sun
Li Jiang
Tao Zhang
Hai-Bo Liu
Jian-Gang Chen
Jian Ye
Lan Hu
Cai-Xia Li
Publication date: 01-01-2016
Publisher: Springer Berlin Heidelberg
Published in: International Journal of Legal Medicine / Issue 1/2016
Print ISSN: 0937-9827
Electronic ISSN: 1437-1596
DOI: https://doi.org/10.1007/s00414-015-1183-5

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A single-tube 27-plex SNP assay for estimating individual ancestry and admixture from three continents

Abstract

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