Population Genetic Diversity and Clustering Analysis for Chinese Dongxiang Group With 30 Autosomal InDel Loci Simultaneously Analyzed

Abstract

In comparison with the most preferred genetic marker utilized in forensic science (STR), insertion/deletion analysis possesses further benefits, like absence of stutter peak, low mutation rate, and enabling mixed stain analysis. At present, a total of 169 unrelated healthy Dongxiang individuals dwelling in Dongxiang Autonomous county of Gansu province were recruited in our study to appraise the forensic usefulness of the panel including 30 autosomal diallelic genetic markers. The insertion allele frequencies were in the range of 0.1598 at HLD 111 to 0.8550 at HLD 118. The cumulative match of probability and the combined probability of exclusion were estimated based on independence of pairwise loci, with the values of 3.96 × 10-11 and 0.9886, respectively, which showed tremendous potential of this panel to be qualified for forensic personal identification in Chinese Dongxiang group. And it could also be used as a complementary tool for forensic parentage testing when combined with standard STR genetic markers. Furthermore, calculation of the DA distance and Fst values of pairwise populations, phylogenetic reconstruction, multidimensional scaling analysis, structure clustering analysis were also conducted to probe the genetic relationships between Dongxiang group and the other 30 reference populations. Results demonstrated that Dongxiang ethnic group might be genetically closer related with most Chinese populations involved in our study, especially Tibet groups, Xibe group, and several Han populations.

Population Genetics and Forensic Efficiency of 30 InDel Markers in Four Chinese Ethnic Groups Residing in Sichuan

“…To comprehensively explore the patterns of genetic affinity between our studied populations and worldwide reference populations, we merged our newly obtained population data with those of 61 worldwide populations. The final database used in the population comparison study included 6483 East Asian individuals from 38 populations [4,5,[8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23][24][25][26], 494 South Asians from three populations [27][28][29], 300 Vietnamese of Southeast Asia [30], 194 West Asians from two populations [31], 621 African individuals from five populations [27,30,32], 984 European individuals from eight populations [4,[31][32][33][34][35] and 1 071 South Americans from eight populations [36,38]. The detailed geographical regions and population sizes of these included populations are submitted in Supplementary Table S1.…”

Genetic diversity and phylogenetic analysis of Chinese Han and Li ethnic populations from Hainan Island by 30 autosomal insertion/deletion polymorphisms

“…To gain an overview of the genetic similarities and differences between our studied populations and 56 global populations (East Asian [8][9][10][11][12][21][22][23][24][25][26][27][28][29][30][31][32][33][34][35], West Asian [36,37], European [33,[37][38][39][40][41][42], American [43][44][45], African [23,46]), we conducted population comparisons along continental divisions through a series of analyses. In the cluster heatmap (Supplementary Figure S1), the HLD101, HLD114, HLD39, HLD48 and HLD111 loci showed high deletion frequencies in most East Asian populations, while the HLD118, HLD99, HLD64 and HLD81 loci showed low deletion frequencies in these groups.…”

“…Chinese populations [8][9][10][11][12]21,22,[24][25][26][27][28][29][30][31][32][33]. Supplementary Figure S4 presents the cluster heatmap of deletion allele frequencies among the 30 populations, and three primary clusters (I, II and III) were easily distinguished.…”

“…With the characteristics of low mutation rate, small amplicon size, length variation as well as absence of stutter peaks and so on, InDels combine the advantages of both short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) markers and are gradually becoming a promising approach in forensic applications (especially for degraded DNA and mixed stain identification), population substructure analysis and biogeographic ancestry inference [2,[4][5][6]. The Investigator DIPplex kit (Qiagen, Valenci, CA, USA), which contains 30 biallelic autosomal InDels and amelogenin, has been validated and studied in some populations to evaluate its efficacy in forensic applications [7][8][9][10][11][12]. However, the genetic polymorphisms and forensic parameters of the 30 InDels in the Hainan Han and Hainan Li populations remain unknown.…”

Genetic Polymorphisms and Forensic Efficiencies of a Set of Novel Autosomal InDel Markers in a Chinese Mongolian Group

“…Additionally, they could also serve as ancestry-informative markers (AIMs) for characterizing population substructure and performing biogeographical origin analyses [5][6][7]. In recent years, more and more studies have found that InDels could be useful in human identification [1], mixed stain identification [8], and so on.…”