The Application of Short Tandem Repeats to Paternity Testing in Egypt

Ahmed, Amany Mahmoud (2000) The Application of Short Tandem Repeats to Paternity Testing in Egypt. PhD thesis, University of Glasgow.

Abstract

The project has involved assessing new tools to apply to paternity testing within Egypt. Before examining different genetic markers it was very important to study the Egyptian population for substructure, particularly as the Egyptian population is composed of several ethnic groups and has relatively high levels of consanguineous marriages. In order to examine this 300 blood and buccal samples were collected from unrelated Egyptians living in El-Minia city. Before this could be done a protocol for collecting and preserving biological samples in harsh environmental conditions was developed. Three simple STR loci D3S1358, HUMvWA and MUMFGA were chosen to investigate the population structure, new primers were designed for all three loci and after optimisation 300 samples were typed. A number of parameters were examined in order to assess the degree of population substructure. No deviation from the Hardy Weinberg equilibrium (HWE) was detected at any of the three loci using the exact and heterozygosity tests. The coansectry coefficent (FST) was calculated by comparing the El-Minia data to a Cairo population; the low value (0.001) provided further evidence that there is not a high degree of substructuring in the Egyptian population. The three simple loci alone were of limited value as a tool for paternity testing, therefore three hypervariable STR loci D11S554, ACTBP2 and APOAH were analysed. A new primer was designed for the APOAI1 locus and the three loci were amplified as a triplex. After optimisation of the triplex the 300 Egyptian samples were profiled. As with the simple loci, all three were in HWE and there was no evidence for linkage between loci. Allelic ladders were constructed for all six loci examined to ensure accurate and precise typing. The hypervariable ladders were cloned into plasmids in order to create an inexhaustible stock. The six loci used together were a powerful tool for determining paternity issues, the theoretical value of the loci was compared to the actual value after undertaking 30 cases from Egypt. All the cases were inclusion with high paternity indexes and probabilities of paternity. The hypervariable loci were particularly valuable when assessing motherless cases. To have a complete system for paternity testing, which covers as many case scenarios as possible, as in case of deceased father, a database of seven Y-chromosome STR loci was established using 2 multiplexes. The loci included in multiplex 1 were DYS19, DYS389I, DYS389II and DYS390 and the loci included in multiplex II were DYS39I, DYS392 and DYS393. The study of these loci showed a high power of exclusion of paternity in the Egyptian population. Also an as yet unpublished allele was detected at the DYS392 locus.

• Item Type: Thesis (PhD)
• Qualification Level: Doctoral
• Additional Information: Adviser: Peter Vanezis
• Keywords: Bioinformatics, Forensic anthropology
• Date of Award: 2000
• Depositing User: Enlighten Team
• Unique ID: glathesis:2000-76015
• Copyright: Copyright of this thesis is held by the author.
• Date Deposited: 19 Nov 2019 17:07
• Last Modified: 19 Nov 2019 17:07
• URI: https://theses.gla.ac.uk/id/eprint/76015