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Title: Analysis of mitochondrial DNA variation in the Egyptian population and its implications for forensic DNA analysis
Author: Gomaa, R.
Awarding Body: Nottingham Trent University
Current Institution: Nottingham Trent University
Date of Award: 2010
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The genetic sequence of human mitochondrial DNA (mtDNA) is of particular interest to forensic investigations involving human identification, as well as population genetics. The current mtDNA database is lacking sufficient representatives of African mitochondrial DNA sequences compared to European and Asian sequences. The present study was concerned with the analysis of mtDNA in the Egyptian population. FTA cards were used for blood sample collection, storage, and shipment and DNA extraction. An optimised laboratory protocol for rapid PCR amplification of the mitochondrial hypervariable regions was developed. A database of 261 mitochondrial hypervariable region I (HVI) sequences and 78 hypervariable region II (HVII) sequences was established from 261 adult Egyptians. A total of 113 polymorphic sites were reported in the HVI region (nt16024-16365) which identified a total of 187 different haplotypes, of which 151 were unique to single individuals. The most commonly observed HVI haplotype was identical to the Cambridge Reference Sequence (CRS). Analysis of 78 HVII sequences (nt73-340) revealed a total of 42 polymorphic sites that identified 62 different haplotypes, of which 51 were unique to single individuals. Sites that showed the highest variability in the HVI and HVII regions agreed with the previously reported mutational hotspots. Combination of the HVI and HVII data resulted in identification of 207 different mitochondrial haplotypes, of which 183 (~88%) were unique to single individuals. Such a large number of unique mitochondrial haplotypes indicates a high diversity of mtDNA in the Egyptian population, which has a direct impact on forensic applications, since the significance of a match between an evidence sample and a reference sample depends on the population frequency of a profile. The random match probabilities in the HVI and HVII datasets were 2.34% and 3.22%, respectively. Combination of the two datasets reduced the random match probability to 1.28%. The genetic diversities in the HVI and HVII sequences were estimated to be 0.9804 and 0.9803, respectively, whereas, the genetic diversity in the combined dataset was 0.9911. A new strategy was developed to facilitate Restriction Fragment Length Polymorphism (RFLP) analysis of the whole mitochondrial genome for the purpose of haplogroup assignment. All the Egyptian individuals were assigned to well known mitochondrial haplogroups and the frequency distribution of different lineages was estimated. A mixed maternal ancestry of the Egyptian population was reported via detection of a mixture of mitochondrial DNA lineages with varying racial backgrounds. The most frequently reported mitochondrial lineages were haplogroup T (13.8%) followed by haplogroups L3 (12.6%), H (12.3%), U (~10%) and M (8.4%). The genetic relationship between Egypt and its neighbours was revealed, and it was found that present day Egyptians were the closest African population to the Middle East and Europe, with an overall 62.5% European, 25% African, and 12.5% Asian mitochondrial lineages. The data presented here will enrich the limited Egyptian mitochondrial DNA reference data currently available for forensic applications.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available