The American University in Cairo Biotechnology Program Analysis of the D1S80 VNTR locus polymorphism in the Nubian Population A Thesis Submitted to The Biotechnology Program In partial fulfillment of the requirements for The degree of Master of Science By Soha Rabie Ahmed Bachelor of Science Under supervision of Dr. Hamza El Dorry 1 Table of Content: Contents List of Figures: ............................................................................................................... 4 List of Tables: ................................................................................................................ 6 Abstract .......................................................................................................................... 7 1. Introduction: ............................................................................................................... 8 1.1. Human Races: ..................................................................................................... 8 1.2. Human genetic variation: .................................................................................... 8 2. Literature Review: ..................................................................................................... 9 2.1. Genetic markers importance: .............................................................................. 9 2.2. Genetic markers evolution: ................................................................................. 9 2.2.1. Restriction Fragment Length Polymorphism (RFLP) marker: ................... 10 2.2.2. Polymerase Chain Reaction (PCR) breakthrough: ..................................... 10 2.2.3. PCR based markers:.................................................................................... 11 2.2.4 Single Nucleotide Polymorphism (SNPs): .................................................. 11 2.2.5 Insertion/Deletion (INDELs) markers: ........................................................ 11 2.2.6 VNTRs and STRs ........................................................................................ 12 2.2.6.1 Minisatellites (VNTRs) as polymorphic marker............................…………..13 2.2.6.2 D1S80 VNTR locus as a genetic marker……………………………….…...14 2.3 Nubia as a case study for genetic variation: ....................................................... 15 2.3.1 Geography of Nubia: ................................................................................... 15 2.3.2 Brief History of Nubia: ................................................................................ 16 2.3.3 People of Nubia and the linguistic affiliations: ........................................... 18 2.4 Previous work on genetic variation among contemporary Nubians: ................. 19 2.5 Objective: ........................................................................................................... 20 3. Material, methods and statistical analysis: ............................................................... 26 3.1 Study location and sample size: ......................................................................... 26 3.2 Ethnographic information about samples' donors: ............................................. 26 3.4 Genomic DNA isolation: .................................................................................... 27 3.5 VNTR Analysis: ................................................................................................. 27 3.6 Statistical analysis: ............................................................................................. 33 2 4. Results: ..................................................................................................................... 34 5. Discussion: ............................................................................................................... 55 6. Conclusion and Future perspective: ......................................................................... 58 6.1 Conclusion:......................................................................................................... 58 6.2 Future perspective: ............................................................................................. 58 Acknowledgement: ...................................................................................................... 59 References: ................................................................................................................... 60 3 List of Figures: Figure 1: Diagram of two different alleles in heterozygous individual with primer sites………………………………………………………………………………………......16 Figure 2: D1S80 nucleotide sequence with flanking regions including the underlined primer sites .......................................................................................................................................... 22 Figure 3: Map of Ancient Nubia ............................................................................................. 23 Figure 4: Location of Modern Nubia ....................................................................................... 24 Figure 5: phylogenetic tree of 49 African populations ............................................................ 25 Figure 6: Principal component analysis of 49 African populations ........................................ 26 Figure 7: 24 PCR products detected on 2% (w/v) agarose gel and 1X TBE buffer (Gel 1, Part 1). ............................................................................................................................................. 35 Figure 8: 23 PCR products detected on 2% (w/v) agarose gel and 1X TBE buffer (Gel 1, Part 2). ............................................................................................................................................. 36 Figure 9: 23 PCR products detected on 2% (w/v) agarose gel and 1X TBE buffer (Gel 2, Part 1). ............................................................................................................................................. 37 Figure 10: 23 PCR products detected on 2% (w/v) agarose gel and 1X TBE buffer (Gel 2, Part 2). ............................................................................................................................................. 38 Figure 11: 12 PCR products detected on 2% (w/v) agarose gel and 1X TBE buffer (Gel 3). 39 Figure 12: Allelic distribution chart among the Nubian population ........................................ 42 Figure 13: Non-metric multidimensional scaling of Nubian population with African populations .............................................................................................................................. 44 Figure 14: Cluster dendrogram of Nubian population with African populations .................... 45 Figure 15: Non-metric multidimensional scaling of Nubian population with American populations .............................................................................................................................. 46 Figure 16: Cluster dendrogram of Nubian population with American populations ................ 47 Figure 17: Non-metric multidimensional scaling of Nubian population with Arabian populations .............................................................................................................................. 48 Figure 18: Cluster dendrogram of Nubian population with Arabian populations ................... 49 Figure 19: Non-metric multidimensional scaling of Nubian population with Asian populations ................................................................................................................................................. 50 Figure 20: Cluster dendrogram of Nubian population with Asian populations ....................... 50 Figure 21: Non-metric multidimensional scaling of Nubian population with Caucasian populations .............................................................................................................................. 51 Figure 22: Cluster dendrogram of Nubian population with Caucasian populations................ 52 4 Figure 23: Non-metric multidimensional scaling of Nubian population with European populations .............................................................................................................................. 54 Figure 24: Cluster dendrogram of Nubian population with European populations ................. 55 5 List of Tables: Table1: Differences between RFLP typing method and PCR typing method ............. 12 Table2:Samples number and their ethnic affiliations .................................................. 27 Table 3: Populations included in the study .................................................................. 29 Table 3 cont.: Populations included in the study ......................................................... 30 Table 3 cont.: Populations included in the study ......................................................... 31 Table 3 cont.: Populations included in the study ......................................................... 32 Table 3 cont.: Populations included in the study ......................................................... 33 Table 4: Genotype frequencies of the D1S80 locus among 105 Nubian individual. 75 genotypes were detected .............................................................................................. 39 Table 5: Allele frequencies of the D1S80 locus among 105 Nubian individual. 36 allele were observed ....................................................................................................