Population genetic data for 21 autosomal STR loci for the Saudi Arabian population using the GlobalFiler ®  PCR amplification kit

Alsafiah, Hussain M; Goodwin, William; Hadi, Sibte; Alshaikhi, Mohammed A; Wepeba, Pet-Paul

doi:10.1016/j.fsigen.2017.09.014

Cited by 18 publications

(22 citation statements)

References 12 publications

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“…We have compared Bahraini population data to the nearest available populations using the accessible loci. It is shown that the Bahraini population shares similar results with the study conducted of Saudi Arabia and UAE populations using the GlobalFiler STR loci [19, 22] . As the above-mentioned populations share the most informative and polymorphic locus is SE33 and the least informative locus is TPOX.…”

Section: Discussionsupporting

confidence: 71%

Population genetic data of the 21 autosomal STRs included in GlobalFiler kit of a population sample from the Kingdom of Bahrain

et al. 2019

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Bahrain’s population consists mainly of Arabs, Baharna and Persians leading Bahrain to become ethnically diverse. The exploration of the ethnic origin and genetic structure within the Bahraini population is fundamental mainly in the field of population genetics and forensic science. The purpose of the study was to investigate and conduct genetic studies in the population of Bahrain to assist in the interpretation of DNA-based forensic evidence and in the construction of appropriate databases. 24 short-tandem repeats in the GlobalFiler PCR Amplification kit including 21 autosomal STR loci and three gender determination loci were amplified to characterize different genetic and forensic population parameters in a cohort of 543 Bahraini unrelated healthy men. Samples were collected during the year 2017. The genotyping of the 21 autosomal STRs showed all of the loci were in Hardy-Weinberg Equilibrium (HWE) after applying Bonferroni’s correction. We also found out no significant deviations from LD between pairwise STR loci in Bahraini population except when plotting for D3S1358-CSF1PO, CSF1PO-SE33, D19S433-D12S391, FGA-D2S1338, FGA-SE33, FGA-D7S820 and D7S820-SE33. The SE33 locus was the most polymorphic for the studied population and THO1 locus was the less polymorphic. The Allele 8 in TPOX scored the highest allele frequency of 0.496. The SE33 locus showed the highest power of discrimination (PD) in Bahraini population, whereas TPOX showed the lowest PD value. The 21 autosomal STRs showed a value of combined match probability (CMP) equal to 4.5633 E-27 , and a combined power of discrimination (CPD) of 99.99999999%. Off-ladders and tri-allelic variants were observed in various samples at D12S391, SE33 and D22S1045 loci. Additionally, pairwise genetic distances based on FST were calculated between Bahraini population and other populations extracted from the literature. Genetic distances were represented in a non-metric MDS plot and clustering of populations according to their geographic locations was detected. Phylogenetic tree was constructed to investigate the genetic relatedness between Bahraini population and the neighboring populations. Our study indicated that the twenty-one autosomal STRs are highly polymorphic in the Bahraini population and can be used as a powerful tool in forensics and population genetic analyses including paternity testing and familial DNA searching.

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Section: Discussionsupporting

confidence: 71%

Population genetic data of the 21 autosomal STRs included in GlobalFiler kit of a population sample from the Kingdom of Bahrain

et al. 2019

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“…Sample# 520 showed 3 variants in D2S441 (10,11,12) with sizes of 85.03 bp, 89.15 bp and 93.30 bp respectively (Figure 2B). Whereas the adjacent locus D19S433 was of homozygous allele (13,13) and it was observed and previously reported in STRbase (http://strbase.nist.gov/index.htm) (16). 8…”

Section: Rare Variants Off-ladder and Null Allelessupporting

confidence: 73%

Population genetic data of the 21 autosomal STRs included in GlobalFiler^TM kit of a population sample from the Kingdom of Bahrain

Al-Snan

Messaoudi

Babu

et al. 2019

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Introduction: Bahrain's population consists mainly of Arabs, Baharna and Persians leadingBahrain to become ethnically diverse. The exploration of the ethnic origin and genetic structure within the Bahraini population is fundamental mainly in the field of population genetics and forensic science. Aim:The purpose of the study was to investigate and conduct genetic studies in the population of Bahrain to assist in the interpretation of DNA-based forensic evidence and in the construction of appropriate databases. Materials and Methods: 24 short-tandem repeats in the GlobalFiler™ PCR Amplification kit including 21 autosomal STR loci and three gender determination loci were amplified to characterize different genetic and forensic population parameters in a cohort of 543 Bahraini unrelated healthy men. Samples were collected during the year 2017. 2Results: The genotyping of the 21 autosomal STRs showed that most loci were in Hardy-Weinberg Equilibrium (HWE) except for three markers; D3S1358, D19S433 and D5S818 which showed deviation from HWE. We also found out no significant deviations from LD between pairwise STR loci in Bahraini population except when plotting for D3S1358-CSF1PO, CSF1PO-SE33, D19S433-D12S391, FGA-D2S1338, FGA-SE33, FGA-D7S820 and D7S820-SE33. The SE33 locus was the most polymorphic for the studied population and THO1 locus was the less polymorphic. The Allele 8 in TPOX scored the highest allele frequency of 0.496. The SE33 locus showed the highest power of discrimination (PD) in Bahraini population, whereas TPOX showed the lowest PD value. The 21 autosomal STRs showed a value of combined match probability (CMP) equal to 4.5633 E-27 , and a combined power of discrimination (CPD) of 99.99999999%.Off-ladders and tri-allelic variants were observed in various samples at D12S391, SE33 and D22S1045 loci. Conclusion:Our study indicated that the twenty-one autosomal STRs are highly polymorphic in the Bahraini population and can be used as a powerful tool in forensics and population genetic analyses including paternity testing and familial DNA searching.Kingdom of Bahrain is a country of 33 islands located in the Arabian Peninsula. The location of Bahrain had affected the diversity of its population, which is mainly divided into four main ethnic groups: Arabs, Baharna and Persians. Genetic studies on Bahraini population are very limited and little has been done to characterize population structure within Kingdom of Bahrain. Here, we used 21 autosomal STRs included in the GlobalFiler TM Amplification Kit to amplify DNA from 543 non-related males from Bahraini population. We conducted statistical analysis using two main different software such as STRAF and GenAlEx. Different forensic and population parameters 3 were obtained to characterize Bahraini population. Some of the significant results obtained were the following: most of the loci were in Hardy-Weinberg Equilibrium, the most polymorphic and informative marker was SE33. Allele 8 in TPOX presented the highest allele frequency for the studied population. We ...

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“…The SE33 and D1S1656 loci are highly informative for the population of Saudi Arabia and showed a power of discrimination of 0.993 and 0.970 respectively . The SE33 alleles detailed here have not been reported in STRBase; the D1S1656 alleles 7 and 8 have been reported in the STRBase , but no sequence data were available (Figs.…”

Section: Introductionmentioning

confidence: 87%

“…An electropherogram showing allele 2 at the SE33 locus. The figure shows an unusual SE33 allele situated under the D7S820 allelic window; this allele was previously demonstrated to belong to the SE33 locus and was called as allele 2 based on its size . This short allele could be due to a complete loss in the repeat region or due to a deletion in the flanking regions.…”

Section: Introductionmentioning

confidence: 96%

Sequence data of six unusual alleles at SE33 and D1S1656 STR Loci

et al. 2018

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When profiling a reference dataset of 500 DNA samples for the population of Saudi Arabia, using the GlobalFiler® PCR amplification kit, six unusual alleles were detected. At the SE33 locus, four novel alleles were found: 2, 14.3, 20.3, and 38; two alleles, at the D1S1656 locus: 7 and 8, had been previously reported, but no published sequence data was available.The D1S1656 alleles were sequenced using ForenSeq™ DNA Signature Prep with the MiSeq FGx System (Illumina, USA). As the SE33 is not reported by available Massively Parallel Sequencing (MPS) systems, samples that exhibited the unreported alleles were sequenced using BigDye™ Terminator v3.1 Cycle Sequencing Kit. Here we present the sequence and structure of the previously uncharacterized alleles.

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Population genetic data for 21 autosomal STR loci for the Saudi Arabian population using the GlobalFiler ® PCR amplification kit

Abstract:  GlobalFiler® PCR amplification kit was used to generate a reference dataset for the population of Saudi Arabia.  SE33, D12S391, and D1S1656 in this kit are more informative for the population of Saudi Arabia than any locus in the AmpFlSTR® Identifiler® PCR amplification kit.

Cited by 18 publications

References 12 publications

Population genetic data of the 21 autosomal STRs included in GlobalFiler kit of a population sample from the Kingdom of Bahrain

Population genetic data of the 21 autosomal STRs included in GlobalFiler kit of a population sample from the Kingdom of Bahrain

Population genetic data of the 21 autosomal STRs included in GlobalFiler^TM kit of a population sample from the Kingdom of Bahrain

Sequence data of six unusual alleles at SE33 and D1S1656 STR Loci

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Population genetic data for 21 autosomal STR loci for the Saudi Arabian population using the GlobalFiler ® PCR amplification kit

Abstract:  GlobalFiler® PCR amplification kit was used to generate a reference dataset for the population of Saudi Arabia.  SE33, D12S391, and D1S1656 in this kit are more informative for the population of Saudi Arabia than any locus in the AmpFlSTR® Identifiler® PCR amplification kit.

Cited by 18 publications

References 12 publications

Population genetic data of the 21 autosomal STRs included in GlobalFiler kit of a population sample from the Kingdom of Bahrain

Population genetic data of the 21 autosomal STRs included in GlobalFiler kit of a population sample from the Kingdom of Bahrain

Population genetic data of the 21 autosomal STRs included in GlobalFilerTM kit of a population sample from the Kingdom of Bahrain

Sequence data of six unusual alleles at SE33 and D1S1656 STR Loci

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Population genetic data of the 21 autosomal STRs included in GlobalFiler^TM kit of a population sample from the Kingdom of Bahrain