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Population genetics data of 23 autosomal STR loci for three Populations in United Arab Emirates

Published:November 01, 2019DOI:https://doi.org/10.1016/j.fsigss.2019.09.073

      Abstract

      In the present study, forensic parameters were estimated for three populations residing in the United Arab Emirates (UAE) including UAE Arabs, Pakistanis and Indians based on the population data of 23 autosomal short tandem repeats (STRs). The UAE Arabs is a vital population to study due to high rates of consanguineous marriages. Therefore, it is essential to estimate the allele distribution and frequencies within this population. In addition, it is crucial to study the largest communities living in the UAE such as Indians and Pakistanis. A total of 1272 blood samples were collected on FTA® cards, comprising of 571 UAE Arabs, 352 Indians and 349 Pakistanis. All of these samples were amplified directly using Verifiler® Express PCR Amplification Kit that focuses on 23 autosomal STR loci, namely D3S1358, vWA, D16S539, CSF1PO, TPOX, D8S1179, D21S11, D18S51, D2S441, D19S433, TH01, FGA, D22S1045, D5S818, D13S317, D7S820, D10S1248, D1S1656, D12S391, D2S1338, D6S1043, Penta D and Penta E loci. The PCR products were electrophoresed on ABI 3500 Genetic Analyzer and analyzed using GeneMapper ID-X v1.4 software. Arlequin v3.5 and PowerStats software were utilized to determine the forensic parameters and population structure using AMOVA. Gene diversity, ranged from 0.67406 (TPOX) to 0.9226 (Penta E) in the UAE Arabs, 0.69955 (TPOX) to 0.9214 (Penta E) in Indian and 0.69853 (TPOX) to 0.921 (Penta E) in Pakistani population. The most discriminating autosomal STR loci observed was Penta E (PD = 0.985), (PD = 0.986), (PD = 0.986) in the UAE Arabs, Indian and Pakistani population, respectively. The obtained results showed the 23 STR loci had a relatively high genetic variation, confirming the suitability for forensic identification and kinship analysis, in the relevant populations. The significance of this study is to build an allelic frequency database for one of the most powerful commercially available STR amplification kits by using the current forensic workflow.

      Keywords

      1. Introduction

      UAE, is an Arab country located in the southeast region of the Arabian Peninsula. It’s considered as home to over 200 nationalities [
      • Al-Khouri A.M.
      Population growth and government modernisation efforts.
      ]. The population of UAE is approximately 9.4 million out of which Emirati nationals constitute 1.1 million according to the Federal Competitiveness and Statistical Authority. The Indian community is considered as the largest community in the UAE, followed by the Pakistanis, Bangladeshis and other Asians [
      • Vora N.
      Unofficial citizens: indian entrepreneurs and the state-effect in Dubai, United Arab Emirates.
      ]. This study aims to evaluate the allelic frequencies of the two largest communities; Indian and Pakistani alongside the UAE Arabs by utilizing one of the most powerful commercially available STR amplification kits (VeriFiler™ Express PCR Amplification Kit) and consequently to build an allelic frequency database.

      2. Materials and methods

      2.1 Samples collection

      Consented blood samples were randomly collected from a total of 1272 unrelated individuals. This consisted of three populations residing in UAE; UAE Arabs (n =n571), Indian (n = 352), Pakistani (n = 349). Ethical approval was granted from Dubai scientific research ethics committee in (DHA)

      2.2 DNA extraction

      An FTA® card (Whatman, UK) was punched using the micro-puncher (Harries®) measuring (0.5 mm diameter). The disc was placed in 0.2ml PCR tubes. Quarter the volume of reagents suggested in the manufacturer’s protocol was utilized.

      2.3 DNA amplification and detection

      The extracted DNA samples were amplified with the Verifiler® Express PCR Amplification Kit, based on 23 autosomal STRs: D3S1358, vWA, D16S539, CSF1PO, TPOX, D8S1179, D21S11, D18S51, D2S441, D19S433, TH01, FGA, D22S1045, D5S818, D13S317, D7S820, D10S1248, D1S1656, D12S391, D2S1338, D6S1043, Penta D and Penta E loci. Amplification was performed on Veriti™ PCR Thermocycler using 25 cycles as per the conditions stated in the manufacturer’s protocol (ThermoFisher Scientific). 1 μl of amplified product was added to 9.5μl Hi-Di Formamide and electrophoresed on an ABI3500 Genetic Analyzer (ThermoFisher Scientific). GeneMapper ID-X software V1.4 was used for analyzing and interpreting the data achieved.

      2.4 Forensic and statistical analysis

      PowerStats v1.2 software (Promega Corporation, Madison, WI, USA) was used to calculate allele frequencies, Random Match Probability (PM), Power of Discrimination (PD), Power of Exclusion (PE), observed homozygosity and observed heterozygosity. Arlequin v3.5 was used to test Hardy Weinberg equilibrium, calculate expected heterozygosity, perform AMOVA to investigate genetic diversity between the three geographical regions as well as to undertake population differentiation tests for UAE and other countries.

      3. Results

      Penta E locus represented the highest number of different alleles in UAE Arabs and Indian population (25 and 21 alleles, respectively). Whereas, FGA locus showed the topmost number of different alleles in the Pakistani population (24 alleles). The TH01 locus exhibited the least number of different alleles (6 alleles) in UAE Arabs, while TPOX locus showed the lowest number of different alleles (5 and 7 alleles) in the Indian and Pakistani population, respectively. Thereupon, the following results revealed that Penta E and FGA are the most polymorphic loci and TH01 and TPOX are the least polymorphic loci among the three studied populations. The highest genetic diversity was achieved in Penta E loci (0.915, 0.921 and 0.921) in UAE Arabs, Indian and Pakistani population, respectively as displayed in Table 1, Table 2; whereas the lowest genetic diversity in all the populations was shown for TPOX loci. The combined match probability attained was 2.9 × 10−29 for UAE Arabs, 5.4 × 10−29 for Indian and 2.9 × 10−29 for the Pakistani population.
      Table 1Forensic efficiency parameters, genetic diversity and heterozygosity for 23 AUTOSOMAL -STR markers from UAE Arabs Population.
      UAED3S1358vWAD16S539CSF1POTPOXD8S1179D21S11D18S51Penta ED2S441D19S433TH01
      FGAD22S1045D5S818D13S317D7S820D6S1043D10S1248D1S1656D12S391D2S1338Penta D
      PD0.9000.9280.9100.8620.8500.9530.9540.9720.9850.9040.9580.918
      0.9690.8830.8940.9220.9300.9470.9140.9730.9740.9730.960
      PE0.5710.5430.5430.4600.4100.6660.6290.7460.8030.5550.6760.524
      0.7010.4180.4020.5680.5580.6060.4710.7180.7460.7570.653
      GD0.7630.7950.7710.7140.6740.8400.8420.8820.9150.7610.8430.782
      0.8700.7170.7400.7840.7990.8220.7720.8810.8850.8830.850
      He0.7850.7690.7690.7200.6880.8350.8160.8760.9040.7760.8410.758
      0.8530.6940.6830.7830.7780.8040.7270.8620.8760.8810.828
      Table 2Forensic efficiency parameters, genetic diversity and heterozygosity for 23 AUTOSOMAL -STR markers from Indian Population.
      IndianD3S1358vWAD16S539CSF1POTPOXD8S1179D21S11D18S51Penta ED2S441D19S433TH01
      FGAD22S1045D5S818D13S317D7S820D6S1043D10S1248D1S1656D12S391D2S1338Penta D
      PD0.8870.9300.9300.8590.8560.9590.9610.9640.9860.8630.9480.924
      0.9670.8880.8890.9370.9340.9520.9170.9740.9630.9710.942
      PE0.5290.5800.50.4440.4220.6770.6660.7220.820.4580.6330.534
      0.7160.4010.4950.5800.5440.6770.5650.7330.7970.7220.606
      GD0.7460.8050.7950.7110.7000.8520.8580.8580.9210.7120.8260.790
      0.8700.7320.7440.8130.8080.8360.7840.8880.8650.8800.824
      He0.7610.7900.7440.7100.6960.8410.8350.8640.9120.7190.8180.764
      0.8610.6820.7410.7900.7700.8410.7810.8690.9010.8640.804

      4. Conclusion

      The primary objective of this study was to determine the genetic structure of three populations residing in United Arab Emirates, including; UAE Arabs, Pakistani and Indian population as well as to evaluate the usefulness of these loci for forensic genetic purposes. The combined analysis of the 23 STR loci in VeriFiler™ Express PCR Amplification Kit showed high power of discrimination and genetic diversity. Consequently, the results obtained can be utilized for the establishment of a database and contribute to other studies in the region, pertaining to the genetic diversities of populations.

      Declaration of Competing Interest

      The authors declared no conflicts of interest

      Acknowledgement

      The authors would like to express their deepest appreciation and thanks to Dubai Police General Head Quarter for providing us with the facilities during our work in this study. In addition, I would like to thank Dubai Health Authority for providing us with the blood samples.

      Appendix A. Supplementary data

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