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

Maria Eugenia D’Amato,Peter Gustav Ristow,Kevin Wesley Cloete

doi:10.1016/j.fsigen.2016.07.007

Maria Eugenia D’Amato, Peter Gustav Ristow + Show 1 more

Open Access

https://doi.org/10.1016/j.fsigen.2016.07.007

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Abstract

In this study, the GlobalFiler® Express amplification kit was evaluated for forensic use in 541 South African individuals belonging to the Afrikaaner, amaXhosa,11Prefixes ama- and isi- are used within Bantu populations to indicate population group and language respectively. 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.

Highlights

IntroductionThe autochthonous population groups of South Africa are the click-speaking Khoisan, and the Bantus (black Africans)
This study has thoroughly evaluated the GlobalFiler1 Express DNA amplification kit for use in forensics applications within South African
The observation of several off-ladder alleles in a small subset of a majority population of South Africa underlines the need for further investigation into African polymorphisms

Summary

Introduction

The autochthonous population groups of South Africa are the click-speaking Khoisan, and the Bantus (black Africans). The Khoisan populations constitute a minority of the total South African population. The Bantu-speaking groups which constitute 79% of the total population [4], entered South Africa via the Eastern coastal routes prior to the fifth century [5]. Both groups have historically been subject to racial killing by indigenous and foreign populations. In 1652, Dutch Europeans moored on the shores of South Africa to set up a refreshment settlement for the Dutch East India Company. The onset of colonisation resulted in the trade of slaves from Central Africa, Eastern Africa and South East Asia [6]

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