Genetic analysis of 27 Y-STR loci in different population groups from South Africa for forensic purposes
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Date
2020-10
Authors
Dooley, Kyla Bianca
Journal Title
Journal ISSN
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Publisher
University of the Free State
Abstract
South Africa has one of the highest rape statistics in the world, with an average of 117 rapes reported daily. Y-STR genotyping is becoming a popular tool in the analysis of DNA evidence collected after a crime of a sexual nature has been committed. Although there are some exceptions, most rape cases involve a male perpetrator and a female victim. By targeting male-specific (perpetrator) DNA, any female (victim) DNA is excluded from analysis, resulting in clear Y-STR profiles that could be used to obtain a match with a male suspect. A reduced genetic diversity at some core Y-STR loci, a limited number of markers investigated, and lack of haplotype frequency data present a challenge in the implementation of Y-STRs in South Africa’s forensic laboratories. This dissertation represents a study aimed at investigating the forensic value of commercial Y-STR PCR Amplification kits in the South African population, as well as provide haplotype frequency data. A total of 308 samples were collected from the African, Asian/Indian, Coloured, and Caucasian populations at the University of the Free State. These samples were amplified using ThermoFisher Scientific’s Y-Filer® Plus PCR Amplification kit, and analysed using the GeneMapperTM ID-X Software. Statistical analysis was performed to estimate several forensic parameters to evaluate the performance of this kit. This set of markers was able to identify 261 unique haplotypes, with an overall discrimination capacity of 98.15%. Discrimination capacities ranged from 91.67% for the Asian/Indian population to 100% for the Coloured population. The haplotype diversity across the four populations is 0.9999, with an average gene diversity across all loci of 0.684. The Coloured population exhibited the highest gene and haplotype diversities, as well as the highest discrimination capacity, most likely due to the high levels of admixture in this population. These values are comparable to those of other populations around the world and are increased from those reported in previous South African studies. This study also used the Y-Filer® Plus kit to genetically characterise the South African population through the use of allelic patterns, genetic distances, AMOVAs, and P-CoAs using the GenAlEx software. The Coloured population exhibited the highest number of different alleles, contributing to the high gene diversity in this population, while, interestingly, the African population was shown to have the highest number of private alleles. It was shown that the most genetic differences occurred between the African and Caucasian populations, while the Coloured population showed a closer affinity to the Caucasian population. The African and Caucasian populations formed two distinct clusters during P-CoA, with the Coloured population distributed across both clusters, albeit closer to the Caucasian cluster. These results are consistent with the history of the South African population. Several profile variations were detected and analysed, including null alleles at DYS390 and DYS448, duplications at DYS458 and DYS449, triplications at DYF387S1, and several intermediate alleles at DYS389II, DYS458, and DYF387S1. Although these variations could introduce some challenges when used in forensic DNA analysis, additional knowledge gained through sequencing regarding the nature of these variations may circumvent these challenges. The forensic parameters estimated in this study provide evidence for the potential use of commercial Y-STR PCR kits in a forensic application in South Africa. Even though this study does provide some haplotype frequency data, it is highly recommended that more haplotypic data is obtained for a more accurate estimation of match probabilities. Future studies should also focus on the performance of the Y-Filer® Plus kit when analysing DNA from closely related males in the South African population.
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Keywords
Dissertation (M.Sc. Forensic Genetics (Genetics))--University of the Free State, 2020, Forensic genetics, Y-STR markers, Y-Filer® Plus PCR Amplification Kit, South African population, Population data, Discrimination capacity, Haplotype diversity, Gene diversity, Sexual assault investigation