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

Abstract

A biogeographic estimate of a certain population can not only discern population substructure in the whole genome association study, but also provide informative clues for forensic investigations when obtained DNA genotypes do not find a match in the available forensic DNA database. In this study, 100 ancestry informative single nucleotide polymorphisms (AISNPs) were first presented to differentiate three continental ancestries (African, East Asian and European). Ultimately, forty-two AISNPs were chosen from the 100 AISNPs. Distinguishing power of the 100 and 42 AISNPs for differentiating continental populations was further evaluated with population cluster analyses. Results indicated both of AISNP sets could efficiently differentiate 11 training populations from the three continents. Further validation of 42 AISNPs in testing population set indicated these 42 AIS-NPs performed well for ancestry inferences of these testing individuals. Ancestry components of Uyghur group were assessed by comparing with different continental populations based on these 42 AISNPs. Results revealed that East Asian populations contributed more ancestry components to the studied Uyghur group than European populations. In conclusion, our study is expected to provide more AISNP markers and enrich extant reference database.

Comprehensive Understanding the Forensic Systematic Effectiveness in Chinese Yunnan Hani Group and Intercontinental Population Architecture Differentiation Analyses via a Novel Set of Autosomal InDel Markers

“…Except for the American populations, the insertion allele frequency distributions for most of the 57 autosomal InDels were similar in the same intercontinental populations. Previous studies have revealed that allele frequency distributions of the same locus often differ significantly across different regions in various intercontinental populations, and the present results are consistent with these previous findings [36][37][38]. For example, the rs3076465, rs71852971, rs3067397, rs72031009, rs34419736, rs79225518, rs113011930, rs145010051, rs146875868, and rs77635204 loci showed the distinct divergences among populations from different continents, indicating that some loci in this novel system have promising potential as ancestry informative markers (AIMs) [39].…”

Insights into AIM-InDel diversities in Yunnan Miao and Hani ethnic groups of China for forensic and population genetic purposes

“…In recent decades, many sets of AIM-SNP panels and AIM-InDel panels have been constructed to analyze the ancestral origins or genetic patterns within or among continental populations using CE or massively parallel sequencing (MPS) technologies. Incipiently, intercontinental AIM panels mainly focused on specific intercontinental populations (such as populations from Africa, Europe and East Asia) [7][8][9][10]. In recent years, regional AIM panels which concentrated on the inference of ancestral origins in subpopulations or closely related populations have been widely constructed [11][12][13][14].…”

Genetic insights and evaluation of forensic features in Mongolian and Ewenki groups using the InDel variations

“…Whole genome sequencing technology can identify many novel variants and offer tremendous potential for uncovering better genetic markers for more challenging forensic samples [5,6]. The superior feasibility of single nucleotide polymorphisms (SNPs) has already been documented for the individual identification, biogeographic ancestry inference, external visible trait prediction, and genealogical inference [7][8][9][10]. However, the complex experimental procedure of the SNaPshot assay make it timeconsuming and susceptible to contamination, thus hampering the widespread use of SNPs in routine forensic DNA laboratories.…”