Analysis of the genetic landscape of the Palestinian population by using Autosomal and Y-STRsرسالة ماجستير

Abstract

Genetic diversity fosters species ability to evolve and their resilience to adapt. Thus, it has been a research interest for decades. It does not only allow scientists to study the evolutionary process that occurred in the past, but it has many important implications in population genetics and forensic science. Worldwide, forensic testing and legal systems both depend on forensic DNA analysis. According to international forensic regulations and guidelines, each community should create its allele frequency databases to put this branch of science into practice. Thus, we present here one of the first studies that aimed to study the Palestinian population genetic structure, substructure, and the first allele frequency databases that are essential for the Palestinian justice system. Genetic diversity of the Palestinian population was investigated by screening 23 autosomal STRs and 23 Y-STRs. 617 samples were extracted using SwabSolution®. Samples were directly amplified using PowerPlex® Fusion system. Autosomal allelic frequencies ranged from 53.97% to 0.081%, with 336 alleles genotyped along the loci. No significant departure from Hardy-Weinberg equilibrium in the total population was detected at any of the tested loci after applying Bonferroni-type corrections (p-value>0.00217). Moreover, linkage disequilibrium was not detected at any of the loci co-located on the same chromosome. Observed heterozygosity ranged from 58% (TPOX) to 92.5% (SE33). Combined random match probability (CMP), combined power of discrimination (CPD), and combined power of exclusion (CPE) were 4.20677E-30, 1, and 0.999999999, respectively. Deviations from HWE were detected at the subpopulation level with the Samaritan subpopulation (p-value=0.0006) indicating a higher degree of inbreeding. For Y-STRs genotyping, 303 samples were successfully amplified using PowerPlex® Y23, 288 different haplotypes were detected. 275 were unique haplotypes (90.8% of samples). Y-STRs V Allelic frequencies ranged from 79.2% to 0.33% with 156 different alleles among all loci. The average gene diversity for the 23 Y-STRs was 65%. Haplotype match probability, haplotype diversity, and discrimination capacity were 0.39%., 99.9%, and 95%, respectively. Our analysis revealed relatedness to the surrounding countries and our In-silico analysis predicted haplogroup Q to be widespread in the Palestinian population. We reveal that the Palestinian population is quite diverse, moreover, our results indicate that both autosomal and Y STRs systems presented in this study are useful forensically and can be implemented in the West Bank-Palestine. In case of encountering a Samaritan Autosomal DNA profile or a sample of unknown sources, a theta (ϴ) correction factor of 0.03 needs to be applied to correct for the deviation.