Genetic diversity and haplotypic structure of a Saudi population sample using Investigator Argus X-12 amplification kit

Abstract

Background:X-chromosome short tandem repeat (X-STR) markers have shown a great capability in forensic identity investigations and paternity testing involving kinship analysis. Material and methods:In the current study, the distribution of 12 X-STR loci (DXS10148, and HPRTB) located in four linkage groups (LG)s was evaluated using Investigator ® Argus X-12 Amplification Kit in 200 unrelated healthy individuals (105 males, and 95 females) from the central region of the Saudi Arabia in order to create a DNA database. Results:No significant difference was recorded in the allele frequencies of males and females.Our results indicated that DXS10146 locus was the most informative with 21 alleles while DXS8378 locus was the least with 5 alleles. Hardy-Weinberg equilibrium (HWE) was applied and confirmed for all loci in the female samples, except for DXS10074, DXS10101, DXS10135 and DXS10148 (p > 0.05/12 = 0.0042). Forensic parameters showed that all X-STRs loci either as individual markers or as linkage groups provide genetic information with high discrimination that is appropriate for forensic purposes with Paternity Informed Consent (PIC), Power of exclusion (PE), and Paternity index (PI) varied from 0.61211 to 0.917979, 0.38722 to 0.842949, and 0.038416 to 0.16367, respectively. A significant Linkage disequilibrium (LD) with p-value after Bonferroni correction p ≤ 0.05/66= 0.0008 was observed for 17 pairs of loci in male samples and 4 pairs of loci in female. In the male group, LG3 showed relatively high values of Haplotype diversity (HD). This indicated that these LGs were quite informative in the studied Saudi group and would have high application value in forensic sciences. The pairwise genetic distance fixation index (Fst) results showed that the Saudi population is genetically close to the Egyptian and Emirati populations and distant to the Turkish population. Genetic distances were represented in a non-metric MDS plot representing that Saudis cluster with Middle East populations and are clearly separated from European and East Asian populations. Conclusion:The current study revealed that Investigator® Argus 12 X-STR kit would support forensic application, kinship testing involving female offspring, and human identification in Saudi populations.

Population Genetic Analysis of 12 X-Chromosomal Short Tandem Repeats in a Bahraini Population Sample

“…Interpopulation pairwise genetic distances based on Fst between the population of Bahrain and the rest of populations extracted from the literature that included Saudi, 15 Filipino, 16 Emiratis, 17 Bengali, 18 Egyptian, 19 Turkish, 20 Indian, 21 Algerian, 22 and Jewish 23 were calculated using POPTREE2 software 24 and represented by a nonmetric multidimensional scaling (NM-MDS) analysis using IBM SPSS Statistics v21.0 software to investigate the populations' structure between Bahraini population and the already mentioned populations based on Fst's genetic distances. Phylogenetic tree was constructed from allele frequency data by using the neighbor-joining (NJ) method 25 via MEGA X: Molecular Evolutionary Genetics Analysis.…”

“…20 Jewish and Saudi populations shared the highest frequency with allele 19 (DXS10103). 15,23 The Bengali population showed the highest allele frequency in allele 11 (DXS8378). 18 Regarding the interpopulation diversity, the phylogenetic tree was constructed based upon the data from the nine populations, which were consistent with other population data from the region based upon the Fst values obtained.…”

“…We used nine populations that are Saudi, 15 Filipino, 16 Emiratis, 17 Bengali, 18 Egyptian, 19 Turkish, 20 Indian, 21 Algerian, 22 and Jewish. 23 Fst and p-values for allele frequency distribution between Bahraini population and the published groups are given in Table 4.…”

Population genetic analysis of 12 X-STRs in a Bahraini population sample (Allele and haplotype frequencies of 12 X-STRs in Bahraini population)

“…Turkish population gave the highest allele frequency in allele 13 in HPRTB (23). Jewish and the Saudi populations shared highest frequency with allele 19 in DXS10103(19,26). Bengali population showed the highest allele frequency in allele 11 in locus DXS8378…”