Development Of A SNP Ancestry Inference Panel For East Asian Population

Objective:We established a 74-plex SNPs assay to infer the ancestry of unknown individuals in the following ten geographical regions:Sub-Saharan Africa,North Africa,Europe,Pacific,Americas,Southwest Asia,South Asia,North Asia,East Asia and Southeast Asia.We genotyped 3077 individuals from 31 populations of China using this multiplex assay and validated its ability to infer the ancestry in Chinese populations.Next,we selected ancestry informative SNPs of Japanese and northern Han to improve the discrimination power of East Asian population which will facilitate the development of an improved ancestry inference panel within East Asian.Methods:Firstly,we established a 74-plex SNPs assay using MassARRAY system based on our previous 74 AISNPs panel which can differentiate ten geographical regions including the north and south of East Asian.We genotyped 3077 individuals from 31 populations of China using this multiplex assay.The likelihood ratio and ancestry components were analyzed for individual ancestry assignment using the 74-plex SNPs.Then,the accuracy,sensitivity and forensic sample adaptability of 74-plex SNPs detection system was verified.Finally,based on the genotyping of 85 SNPs of 207 individuals from 2 East Asian populations,we selected the differential SNPs between the northern Han and Japanese populations according to F_ST and?values and evaluated its discrimination performance by Structure cluster analysis and heatmap analysis;we used MassARRAY technology to genotype 281 individuals of 3 Han populations and the likelihood ratio and ancestry components were analyzed for individual ancestry assignment using the 53 SNPs panel.Results:The minimum amount of DNA required for a full genotype of the 74 SNPs is 1.5 ng,which is applicable for forensic analysis.The ancestry inference accuracy for East Asia is90.96%and 98.94%for Southeast Asia.The ancestry inference inclusive rate for East Asia is 18.66%and 36.51%for Southeast Asia respectively.The results suggest that this method can be used in forensic investigations of criminal cases.Structure cluster analysis showed that 53 SNPs panel(F_ST?0.05 and??0.16)can be used to make a preliminary distinction between the Japanese and northern Han populations.The ancestry inference results demonstrated that the most likely population of more than 66%of the test individuals are Han Chinese.Conclusion:The 74-plex SNPs assay can be used to test forensic biological evidence,differentiate populations from ten geographic regions worldwide,the result can provide investigative leads for criminal cases.The 53 SNPs panel selected by this study can differentiate Northern Han and Japanese preliminarily,which provide a data bases for the development of a further improved AISNPs panel within East Asian.