Population genetic analysis of forensic markers in the Kuwaiti population

Located in the Arabian Gulf, the nation state of Kuwait is a relatively small country but represents a large geostrategic weight, regionally and globally. However, so far, its genetic diversity has not been extensively studied. This thesis investigates genetic diversity in this population, and evaluates the forensic utility of different classes of forensic markers using both traditional (capillary electrophoresis (CE)) and novel (massively parallel sequencing (MPS)) technologies. Thirty insertion deletion polymorphism (indel) markers were typed in 150 unrelated Kuwaitis. The genotyping results showed that indel markers were highly discriminative, allowing them to be utilised as a stand-alone typing system for human identification in Kuwait. They can be used when additional markers are required, particularly in challenging relationship and paternity cases. Massively parallel sequencing (MPS) offers an improved system in which much larger numbers of different types of forensic markers can be combined in a single assay, with the additional benefit that each marker can be assayed using shorter amplicons, improving performance when DNA samples are degraded. The major benefit of MPS technology in forensic genetics is its ability to determine the actual nucleotide sequences of forensic markers, rather than just their length. The Verogen ForenSeq™ DNA Signature Prep Kit, part of the MiSeq FGx® Forensic Genomics MPS system was used to sequence 376 unrelated Kuwaiti individuals using 153 markers including 27 autosomal STRs, 24 Y-STRs, 7 X-STRs and 94 identity SNPs. The results showed an increased number of genetic variants detected for these markers based on their sequences, when compared to their lengths, which resulted in substantial increases in the discriminatory power of forensic DNA testing, providing high-resolution genotyping for the analysis of DNA evidence. This highlights the potential value of this sequencing technology. Comparison between CE and MPS systems was carried out by comparing the allele length-based genotypes generated using the ForenSeq™ DNA Signature Prep Kit with genotypes generated using the Promega PowerPlex® Fusion 6C kit, and the haplotypes generated using the Promega PowerPlex® Y23 System. The sequencing results were 100% in concordance with the results obtained using CE for both sets of markers, indicating that the profiles generated by the two technologies can be compared and utilised with confidence. The evaluation of the sequenced markers in this thesis provides guidelines and information for data interpretation and the data produced delivers valuable reference datasets for forensic analysis in the Kuwaiti population.Located in the Arabian Gulf, the nation state of Kuwait is a relatively small country but represents a large geostrategic weight, regionally and globally. However, so far, its genetic diversity has not been extensively studied. This thesis investigates genetic diversity in this population, and evaluates the forensic utility of different classes of forensic markers using both traditional (capillary electrophoresis (CE)) and novel (massively parallel sequencing (MPS)) technologies. Thirty insertion deletion polymorphism (indel) markers were typed in 150 unrelated Kuwaitis. The genotyping results showed that indel markers were highly discriminative, allowing them to be utilised as a stand-alone typing system for human identification in Kuwait. They can be used when additional markers are required, particularly in challenging relationship and paternity cases. Massively parallel sequencing (MPS) offers an improved system in which much larger numbers of different types of forensic markers can be combined in a single assay, with the additional benefit that each marker can be assayed using shorter amplicons, improving performance when DNA samples are degraded. The major benefit of MPS technology in forensic genetics is its ability to determine the actual nucleotide sequences of forensic markers, rather than just their length. The Verogen ForenSeq™ DNA Signature Prep Kit, part of the MiSeq FGx® Forensic Genomics MPS system was used to sequence 376 unrelated Kuwaiti individuals using 153 markers including 27 autosomal STRs, 24 Y-STRs, 7 X-STRs and 94 identity SNPs. The results showed an increased number of genetic variants detected for these markers based on their sequences, when compared to their lengths, which resulted in substantial increases in the discriminatory power of forensic DNA testing, providing high-resolution genotyping for the analysis of DNA evidence. This highlights the potential value of this sequencing technology. Comparison between CE and MPS systems was carried out by comparing the allele length-based genotypes generated using the ForenSeq™ DNA Signature Prep Kit with genotypes generated using the Promega PowerPlex® Fusion 6C kit, and the haplotypes generated using the Promega PowerPlex® Y23 System. The sequencing results were 100% in concordance with the results obtained using CE for both sets of markers, indicating that the profiles generated by the two technologies can be compared and utilised with confidence. The evaluation of the sequenced markers in this thesis provides guidelines and information for data interpretation and the data produced delivers valuable reference datasets for forensic analysis in the Kuwaiti population