A set of novel SNP loci for differentiating continental populations and three Chinese populations.

Xiao-Ye Jin,Bo-Feng Zhu,Qiong Lan,Yuan-Yuan Wei,Yu-Xin Guo,Wei Cui,Chong Chen,Ya-Ting Fang

doi:10.7717/peerj.6508

Abstract

In recent years, forensic geneticists have begun to develop some ancestry informative marker (AIM) panels for ancestry analysis of regional populations. In this study, we chose 48 single nucleotide polymorphisms (SNPs) from SPSmart database to infer ancestry origins of continental populations and Chinese subpopulations. Based on the genetic data of four continental populations (African, American, East Asian and European) from the CEPH-HGDP database, the power of these SNPs for differentiating continental populations was assessed. Population genetic structure revealed that distinct ancestry components among these continental populations could be discerned by these SNPs. Another novel population set from 1000 Genomes Phase 3 was treated as testing populations to further validate the efficiency of the selected SNPs. Twenty-two populations from CEPH-HGDP database were classified into three known populations (African, East Asian, and European) based on their biogeographical regions. Principal component analysis and Bayes analysis of testing populations and three known populations indicated these testing populations could be correctly assigned to their corresponding biogeographical origins. For three Chinese populations (Han, Mongolian, and Uygur), multinomial logistic regression analyses indicated that these 48 SNPs could be used to estimate ancestry origins of these populations. Therefore, these SNPs possessed the promising potency in ancestry analysis among continental populations and some Chinese populations, and they could be used in population genetics and forensic research.

Highlights

Ancestry informative markers, which demonstrated distinct allele frequency differences among different populations (Frudakis et al, 2003; Shriver et al, 1997), could be used to infer biogeographical origins of unknown biological samples and discern populationHow to cite this article Jin X-Y, Wei Y-Y, Lan Q, Cui W, Chen C, Guo Y-X, Fang Y-T, Zhu B-F. 2019
After applying Bonferroni correction, the selected 48 single nucleotide polymorphisms (SNPs) all conformed to Hardy-Weinberg equilibrium (HWE) in 25 training populations (Table S2)
The SNPs with distinct color contrasts in pairwise continental populations contributed to differentiating these populations

Summary

Introduction

Ancestry informative markers, which demonstrated distinct allele frequency differences among different populations (Frudakis et al, 2003; Shriver et al, 1997), could be used to infer biogeographical origins of unknown biological samples and discern populationHow to cite this article Jin X-Y, Wei Y-Y, Lan Q, Cui W, Chen C, Guo Y-X, Fang Y-T, Zhu B-F. 2019. Ancestry informative markers, which demonstrated distinct allele frequency differences among different populations (Frudakis et al, 2003; Shriver et al, 1997), could be used to infer biogeographical origins of unknown biological samples and discern population. They are conductive to forensic investigations by providing investigative clues about the biogeographical origins of the unknown suspect. It is noteworthy that AIM panels differentiating different continental populations might not be appropriate to differentiate populations in the same continent, and these panels could even produce prediction errors for ancestry inferences of these populations. The two-tier AIM panels were recommended for this issue: one for estimating ancestry origins of major continental populations and the other for populations in the same continent (Kidd et al, 2014). Pakstis et al (2017) stated that the identification of highly differentiated SNPs in relatively neglected geographical regions or subpopulations from the same continent should be encouraged because these markers could further improve and fine-tune the extant SNP panels

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Conclusion