Selection Of 111 Ⅱ SNP Loci And Its Forensic Application Research Based On MPS Typing

Background:Single nucleotide polymorphism(SNP)has a promising application in forensic individual identification due to its large number in the genome and ability to genotype by designing short amplicons.Massively parallel sequencing(MPS)is becoming one of the most popular sequencing methods for SNP markers because it could accommodate more SNP markers and detect multitudinous samples at the same time.Several individual identification SNPs(Ⅱ SNPs)show low polymorphisms in East Asian populations.Therefore,to improve the individual identification efficiencies of SNP genetic markers in East Asian populations,the East Asian populations in 1000 Genomes Project phase Ⅲ were selected as the study population,SNP genetic markers with high polymorphism in East Asian populations were systematically selected.And domestic MGI high-throughput sequencing platform provides more efficient,powerful and accurate sequencing tools for SNP genetic marker genotyping.Methods and Contents:(1)Screening of SNP genetic markers:SNP genetic markers with high polymorphisms in East Asian populations from the 1000 Genome Project phase Ⅲ database were selected,and the specific selection criteria were as follows:1)SNP loci conform to Hardy-Weinberg equilibrium and linkage equilibrium;2)SNP loci locate on different chromosomes or physical distances greater than 10Mb on the same chromosome;3)The allele frequency of biallelic SNPs range from 0.4 to 0.6,and the minimum allele frequency of multi-allelic SNPs was greater than 0.01.4)SNP loci are not associated with known diseases;5)The observed heterozygosity of SNP loci was greater than 0.4.(2)Evaluation of forensic medicine application at SNP genetic markers based on MPS technology:Firstly,the genetic polymorphisms of the selected SNP in the East Asian population were preliminarily evaluated,and the cumulative identification efficiencies of SNP loci in East Asian populations and other populations from 1000 Genome Project phase Ⅲ database were compared.Secondly,MPS technology was used to construct library,sequencing and data analysis,and the forensic efficiencies of selected SNP loci in the Chinese Inner Mongolia Manchu(IMM)group were evaluated.Results and conclusions:(1)A total of 111 SNP loci with high polymorphisms in East Asian populations were screened from the 1000 Genome Project phase Ⅲdatabase.The observed heterozygosity and power of discrimination values at 111 SNP loci ranged from 0.4742 to 0.6627 and 0.5838 to 0.8066,respectively,and the average value of polymorphic information content was greater than 0.4.(2)The cumulative matching probability and combined probability of exclusion values at 111 SNPs in East Asian populations were 7.15E-51 and 1-9.96E-13,respectively.The results showed that the accumulative efficiencies of these SNP loci were relatively high,which could be used for individual identification and genetic relationship identification in East Asian populations.Besides,the values of combined discrimination power showed that the cumulative efficiencies of the SNP loci in East Asian populations were higher than that in African,American and European populations.(3)The Q30 values at 111 SNP loci in the IMM population were greater than 85%,and the mean depth of coverage values ranged from 781.7273 to 12374.7059.The mean allele count ratio and noise level values were 0.8672 and 0.0041,respectively.The sequencing results indicated that the SNP genetic marker detection based on the MGI platform had high sequencing performance and could meet the requirements of the Ⅱ SNP genetic marker sequencing in the IMM group.