GlobalFiler ® Express DNA amplification kit in South Africa: Extracting the past from the present

Abstract

In this study, the GlobalFiler(®) Express amplification kit was evaluated for forensic use in 541 South African individuals belonging to the Afrikaaner, amaXhosa,(1) amaZulu,(1) Asian Indian and Coloured population groups. Allelic frequencies, genetic diversity parameters and forensic informative metrics were calculated for each population. A total of 301 alleles were observed ranging between 5 and 44.2 repeat units, 43 were rarely observed partial repeats and seven were novel. The combined match probability (CMP) ranged from 2.21×10(-26) (Coloured) to 5.21×10(-25) (AmaZulu), and the combined power of exclusion (CPE) 0.9999999978 (Afrikaaner) to 0.99999999979 (AmaZulu) respectively. No significant departures from Hardy-Weinberg equilibrium (HWE) were observed after Bonferroni correction. Strong evidence of genetic structure was detected using the coancestry coefficient θ, Analysis of Molecular Variance (AMOVA) and an unsupervised Bayesian clustering method (STRUCTURE). The efficiency of assignment of individuals to population groups was evaluated by applying likelihood ratios with WHICHRUN, and the individual ancestral membership probabilities inferred by STRUCTURE. Likelihood ratios performed the best in the assignment of individuals to population groups. Signs of positive selection were detected for TH01 and D13S317 and purifying/balancing selection for locus SE33. These three loci also displayed the largest informativeness for assignment (In) values. The results of this study supports the use of the GlobalFiler(®) STR profiling kit for forensic applications in South Africa with the additional capability to predict ethnicity or continental origin of a random sample.

Population Genetic Analysis of Modern and Ancient DNA Variations Yields New Insights Into the Formation, Genetic Structure, and Phylogenetic Relationship of Northern Han Chinese

“…To comprehensively dissect the genetic background of Shanxi northern-Han Chinese, we first integrated our raw genotyping data (23 STRs) with previously published genotype data from 11 Chinese populations from five Chinese ethnic groups (Han, Hui, Tibetan, Yi, and Uyghur) (He et al, 2018b; Wang et al, 2018a; Chen et al, 2019; Liu et al, 2019). To further explore the genetic relationship of Shanxi Han in the context of the genetic variations from the worldwide or nationwide populations, we subsequently combined our allele frequency of 20 STRs with publicly obtained data from 52 worldwide populations (Westen et al, 2012; Gaviria et al, 2013; Park et al, 2013; Fujii et al, 2014; Almeida et al, 2015; Parolin et al, 2015; Aguilar-Velazquez et al, 2016; Hossain et al, 2016; Ng et al, 2016; Park et al, 2016; Ramos-Gonzalez et al, 2016; Ristow et al, 2016; Vullo et al, 2016; Wang, 2016; Zhang et al, 2016a; Zhang et al, 2016b; Choi et al, 2017; Guerreiro et al, 2017; Jin et al, 2017; Liu et al, 2017; Moyses et al, 2017; Ossowski et al, 2017; Singh and Nandineni, 2017; Taylor et al, 2017; Wu et al, 2017; Yang et al, 2017a; He et al, 2018b; He et al, 2018e; Wang et al, 2018a; Liu et al, 2019) and allele frequency of 19 STRs with previously investigated the allele frequency distribution from 60 Chinese populations (Zhang et al, 2011; Zhang, 2012; Liu et al, 2013; Shen, 2013; Zhang, 2013; Wang, 2014; Wang et al, 2014; Xie, 2014; Hu et al, 2015; Li, 2015; Ruan, 2015; Shen et al, 2015; Wang, 2015; Yin, 2015; Zhang and Chen, 2015; Zhao et al, 2015a; Huang, 2016; Meng, 2016; Wang, 2016; Xiang, 2016; Xiao et al, 2016; Zhao, 2016; Chen et al, 2017; Fu et al, 2017; He et al, 2017a; He et al, 2017c; Jin et al, 2017; Liu, 2017; Lu et al, 2017;…”

Design, installation, and performance evaluation of a custom dye matrix standard for automated capillary electrophoresis

“…For this, we evaluated peaks heights in the range 50–30 000 RFU, since 50 RFU is the lowest acceptable threshold in forensic practice . We also evaluated the specific performance of each dye matrix in terms of magnitude of pull‐ups detected in each channel using genotype data generated with Investigator DIPplex , GlobalFiler™ PCR Amplification Kit , AmpFlSTR® Identifiler™ (unpublished), and PowerPlex Y23 . Regression analyses and 95% CI for the estimation of the kits’ critical genotyping point (CGP) were performed using the “stats” package in R version 3.3.1 .…”

Genetic polymorphism and phylogenetic differentiation of the Huaxia Platinum System in three Chinese minority ethnicities

“…We performed locus-by-locus pairwise comparisons (F st ) and calculated Nei’s standard genetic distances (R st ) between our three studied populations and 47 previously published worldwide populations (Asian 9,15–29 , North American 30–32 , European 33–36 , Oceanian 37 , South American 38–41 and South African 42 populations) based on allele frequencies of 20 expanded CODIS loci to infer interpopulation similarity and differentiation (Supplementary Tables S10–S13 and Fig. S1).…”