Analysis of 21 autosomal STRs in Saudi Arabia reveals population structure and the influence of consanguinity

Khubrani, Yahya M.; Wetton, Jon H.; Jobling, Mark A.

doi:10.1016/j.fsigen.2018.12.006

Cited by 16 publications

(23 citation statements)

References 24 publications

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“…Other applications include population genetics, anthropology, and epidemiology studies investigating the risk of prostate cancer (Paracchini et al 2003;Hameed et al 2015). Because of its crucial geographical location in the Arabian Peninsula and in the Gulf of Oman, several authors have studied Y chromosome diversity in native Saudi population employing Y-STR technology (Cadenas et al 2008;Abu-Amero et al 2009;Alshamali et al 2009;Khurbani et al 2018Khurbani et al , 2019. The current report presents the population data for 17 Y-STR loci among 125 adult, native, Saudi male volunteers recruited from different geographic regions of Saudi Arabia (Fig.…”

Section: Resultsmentioning

confidence: 98%

“…Other studies have shown that sample selection bias can affect population structure analysis of genotype data, genetic ancestry of individuals, and evolutionary history of a certain population (Rosenberg et al 2002;Patterson et al 2006). Most of the studies carried out in the Saudi population (Cadenas et al 2008;Abu-Amero et al 2009;Alshamali et al 2009;Khurbani et al 2018Khurbani et al , 2019 are based upon the sample collected either from Saudi blood banks, hospitals, forensic casework samples, or from native Saudis living abroad who are mostly self-declared and are not subjected to any type of further verification therefore, lacking the reliable ethnic or demographic originality that may affect, to some extent, the outcome of population genetic parameters.…”

Section: Resultsmentioning

confidence: 99%

“…Studies regarding Y chromosome genetic lineage and population genetic structure in Saudi Arabia are limited (Abu-Amero et al 2009;Alshamali et al 2009;Khurbani et al 2018Khurbani et al , 2019. In the present paper, we present analysis of Y chromosome haplotypes in 125 native Saudi males from different geographic regions of Saudi Arabia, using the AmpFℓSTR® YFiler® Amplification kit (Life Technologies, USA).…”

Section: Introductionmentioning

confidence: 97%

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Population data and genetic diversity analysis of 17 Y-STR loci in Saudi population

Kassab

Alaqeel

Messaoudi

et al. 2020

Egypt J Forensic Sci

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Background The Y chromosome polymorphism has been widely studied for human migrations, population genetics, forensic applications, and paternity analysis. However, studies regarding genetic lineage and population genetic structure of the Y chromosome in different regions of Saudi Arabia are limited. Aim This study aimed to analyze the distribution of Y chromosome haplotypes in a sample of 125 native Saudi males from different geographic regions of Saudi Arabia and compare to previously published Y chromosome haplotype data from Saudi Arabia and some neighboring Arab populations. Materials and methods Buccal swabs were collected from 125 healthy unrelated native Saudi males from different geographic regions of Saudi Arabia. Genomic DNA was extracted by Chelex®100; 17 Y-STR loci were amplified using the AmpFℓlSTR Yfiler PCR amplification kit and detected on the 3130 Genetic AnalyzerTM. Allele frequency and gene diversity were calculated with online tool STRAF. The Saudi population data were compared with the neighboring populations using pairwise genetic distances and associated probability values were calculated using the Y Chromosome Haplotype Reference Database Website (YHRD) software. Results and conclusion One hundred six YSTR haplotypes and 102 YSTR alleles (excluding 4 null alleles) were identified having a discrimination capacity (DC) of 85.8%. The highest haplotype diversity (HD) and gene diversity (GD) were observed at the loci DYS 458 (0.817) and DYS385b (0.807), respectively. According to our results, the Iraqi and Qena (Egypt) populations appeared to have closer relatedness to the Saudi population as compared with Yemen. The UAE and Kuwait populations showed the same degree of relatedness to the Saudi population followed by Bahrain. On the contrary, the Adnanit and Qahtanit populations of Jordan demonstrated low genetic distance from the Saudi population. In short, studying a population sample of pure Saudi ethnicity enabled us to identify a unique set of haplotypes which may help in establishing genetic relatedness between Saudi and the neighboring Arab populations. The present paper, therefore, highlights the importance of ensuring ethnic originality of the study sample while conducting population genetics studies.

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Section: Resultsmentioning

confidence: 98%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 97%

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Population data and genetic diversity analysis of 17 Y-STR loci in Saudi population

Kassab

Alaqeel

Messaoudi

et al. 2020

Egypt J Forensic Sci

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“…Data from Lebanon (LEB) and an Indian (IND) population from Madhya Pradesh typed for the 23 autosomal loci 24 were also included in the analysis. Genetic distance was also assessed at a regional level using allele frequencies for the 13 of the 23 autosomal loci (CSF1PO, D13S317, D16S539, D18S51, D21S11, D3S1358, D5S818, D7S820, D8S1179, FGA, TH01, TPOX, vWA) that are shared between the data reported in this study and other studies of Kuwait and neighbouring counties: Kuwait (KW1 3 and KW2 2 ), Iran (IRN 25 and IRN1 2 ), Saudi Arabia (SA 26 and SA1 27 ), Qatar (QAT 28 ), Oman (OMN 29 ), Yemen (YEM 29 ), United Arab Emirates (UAE 30 ), Bahrain (BAH 31 ), and Iraq (IRQ 32 and IRQ1 2 ). PCA analysis was conducted using R software 33 and visualised using the factoextra package 34 .…”

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confidence: 77%

Population genetics and forensic utility of 23 autosomal PowerPlex Fusion 6C STR loci in the Kuwaiti population

Haidar

Abbas

Alsaleh

et al. 2021

Sci Rep

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This study evaluates the forensic utility of 23 autosomal short tandem repeat markers in 400 samples from the Kuwaiti population, of which four markers (D10S1248, D22S1045, D2S441 and SE33) are reported for the first time for Kuwait. All the markers were shown to exhibit no deviation from Hardy–Weinberg equilibrium, nor any linkage disequilibrium between and within loci, indicating that these loci are inherited independently, and their allele frequencies can be used to estimate match probabilities in the Kuwaiti population. The low combined match probability of 7.37 × 10–30 and the high paternity indices generated by these loci demonstrate the usefulness of the PowerPlex Fusion 6C kit for human identification in this population, as well as to strengthen the power of paternity testing. Off-ladder alleles were seen at several loci, and these were identified by examining their underlying nucleotide sequences. Principal component analysis (PCA) and STRUCTURE showed no genetic structure within the Kuwaiti population. However, PCA revealed a correlation between geographic and genetic distance. Finally, phylogenetic trees demonstrated a close relationship between Kuwaitis and Middle Easterners at a global level, and a recent common ancestry for Kuwait with its northern neighbours of Iraq and Iran, at a regional level.

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“…Saudi Arabia is the largest country in the Arabian Peninsula with a population exceeding 32 million where people are non-uniformly distributed [12]. Nearly half of the population resides in two major administrative provinces, Riyadh and Mecca [13].…”

Section: Introductionmentioning

confidence: 99%

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

Messaoudi

Babu

Alsaleh

et al. 2019

Preprint

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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.

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Analysis of 21 autosomal STRs in Saudi Arabia reveals population structure and the influence of consanguinity

Cited by 16 publications

References 24 publications

Population data and genetic diversity analysis of 17 Y-STR loci in Saudi population

Population data and genetic diversity analysis of 17 Y-STR loci in Saudi population

Population genetics and forensic utility of 23 autosomal PowerPlex Fusion 6C STR loci in the Kuwaiti population

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

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