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

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.

Biogeographic origin prediction of three continental populations through 42 ancestry informative SNPs

“…In the current study, we developed the novel multiplex systems of 42 AISNPs for bio‐geographical origin predictions of three continental populations based on the MassARRAY iPLEX platform. In previous studies, some researchers mainly detected selected SNP loci by TaqMan SNP Genotyping Assay . Compared to these researches, there were some shortcomings in this study.…”

“…Wei et al. estimated admixture levels of four central Asian populations (Tajik, Uyghur, Kirgiz, and Kazak) based on a multiplex AISNPs panel, and they found that these populations showed admixture patterns of East Asian and European ancestries . Besides, the same research team re‐analyzed genetic structure of these four populations based on another AISNPs panel and they observed similar results which revealed these populations displayed East Asian and European admixed ancestries .…”

Distinguishing three distinct biogeographic regions with an in‐house developed 39‐AIM‐InDel panel and further admixture proportion estimation for Uyghurs

“…Wei et al. showed that the admixture proportions of East Asian and European ancestral populations for Uyghurs in Xinjiang were 46 and 49% based on a 27‐AIM‐SNP analysis, indicating a higher European ancestral component in Uyghur group from Xinjiang. By analyzing 26 Y‐STR genetic markers, Bian et al.…”

“…Detailed information regarding the overall 16 populations were presented as follows: ESN, Esan in Nigeria ( n = 99); YRI, Yoruba in Ibadan, Nigeria ( n = 108); MSL, Mende in Sierra Leone ( n = 85); GWD, Gambian in Western Division ( n = 113); LWK, Luhya in Webuye, Kenya ( n = 99); TSI, Toscani in Italy ( n = 107); FIN, Finnish in Finland ( n = 99); IBS, Iberian populations in Spain ( n = 107); CEU, Utah residents with Northern and Western European ancestry ( n = 99); GBR, British in England and Scotland ( n = 91); KHV, Kinh in Ho Chi Minh City, Vietnam ( n = 99); CDX, Chinese Dai in Xishuangbanna, China ( n = 93); CHB, Han Chinese in Bejing, China ( n = 103); CHS, Southern Han Chinese, China ( n = 105); JPT, Japanese in Tokyo, Japan ( n = 104); XJU, Uyghurs in Urumchi, China ( n = 517). The other two admixed African populations (ASW, ACB) included in the 1000 Genomes were excluded from the reference dataset for quality control .…”

An ancestral informative marker panel design for individual ancestry estimation of Hispanic population using whole exome sequencing data

“…To further examine the accuracy, we compared our UT-AIM250 panel and two published panels, 34 AIM-panel [14] (termed Phillips-AIM34) and 278 AIM-panel [39] (termed Wei-AIM278), on the Admixed American (AMR) population also from the 1000 Genomes Project. Those panels were generated from three continental populations (with slightly inclusion criterion and samples available at the time): African (AFR), European (EUR), and East Asian (EAS).…”