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

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.

Forensic DNA Phenotyping: a review on SNP panels, genotyping techniques, and prediction models

“…In this sense, several authors believe that it is better to have markers with a strong in uence [110,312], due to the scare amount of DNA in the samples, while others suggest nding genes with weak effects to complement the inference [254,258,316]. Also, in the case of BGA, researchers recommend using a twotier approach: rst, a panel with maximum 100 markers to infer at least 12 global populations, and later other panels to re ne sub-population inference [39,58,121,131]. That is the case of the SNPfor ID 34-plex [90] and its EurasiaPlex [105],…”

Development and Performance Evaluation of a Novel Ancestry Informative DIP Panel for Continental Origin Inference

“…In the last decade, as a new supplementary test, forensic ancestry information analysis provides much valuable information for forensic investigative applications and other forensic fields ( Phillips, 2015 ; Phillips and de la Puente, 2021 ). Most recently, a growing number of AIM panels to estimate ancestry origin of continental and sub-continental populations ( Santos et al, 2016a ; Wei et al, 2016 ; Carvalho Gontijo et al, 2020 ; Xavier et al, 2020 ) or to distinguish population structure of Asian or Chinese populations ( Sun et al, 2016 ; Jin et al, 2019 ; Qu et al, 2019 ) were developed by forensic researchers from abroad and in China, respectively. However, the capacity of these panels to effectively infer the ancestry origins of other populations in China may not be competent enough.…”

Determining the Area of Ancestral Origin for Individuals From North Eurasia Based on 5,229 SNP Markers

“…Other arrays can generate more specific predictions, but the markers they use are geographically limited to large regions or subcontinents, like East or South Asia, Oceania, North Africa, Middle East, and Europe ( Al-Asfi et al, 2018 ; Pereira et al, 2019 ; Lan et al, 2020 ; Xavier et al, 2020 ). One of such panels featuring 48 SNPs has proved to be powerful enough to successfully differentiate between three Chinese populations with very different ancestries: Mongol, Uighur, and Han ( Jin et al, 2019 ). However, it is unclear whether the same set of markers can accurately predict the 40 remaining East Asian Chinese populations.…”