Ali Alhmoudi, Osamah

Alsafar, Habiba

Hadi, Ss

Jones, Rebecca J

Tay, Guan K

CLoK

ArticlePopulation genetics data for 21 autosomal STR loci for United Arab Emirates (UAE) population using next generation multiplex STR kitAli Alhmoudi, Osamah, Jones, Rebecca J, Tay, Guan K, Alsafar, Habiba and Hadi, SsAvailable at http://clok.uclan.ac.uk/13862/Ali Alhmoudi, Osamah, Jones, Rebecca J, Tay, Guan K, Alsafar, Habiba and Hadi, Ss (2015) Population genetics data for 21 autosomal STR loci for United Arab Emirates (UAE) population using next generation multiplex STR kit. Forensic Science International: Genetics, 19 . pp. 190­191. ISSN 18724973  It is advisable to refer to the publisher’s version if you intend to cite from the work.http://dx.doi.org/10.1016/j.fsigen.2015.07.009For more information about UCLan’s research in this area go to http://www.uclan.ac.uk/researchgroups/ and search for <name of research Group>.For information about Research generally at UCLan please go to http://www.uclan.ac.uk/research/ All outputs in CLoK are protected by Intellectual Property Rights law, includingCopyright law.  Copyright, IPR and Moral Rights for the works on this site are retained by the individual authors and/or other copyright owners. Terms and conditions for use of this material are defined in the http://clok.uclan.ac.uk/policies/CLoKCentral Lancashire online Knowledgewww.clok.uclan.ac.uk1    Forensic Population Genetics-Letter to Editor 1 Dear JM, 2 DNA samples were analysed from 519 healthy, unrelated and consenting individuals who 3 reside in the United Arab Emirates (UAE) and were randomly chosen for this study. The 4 UAE is one of the middle-eastern countries located on the Arabian Gulf. It shares a border 5 with Iran, Saudi Arabia and Oman. The UAE was founded in 1971, and consists of seven 6 Emirates: Abu Dhabi, Dubai, Sharjah, Ajman, Ra’s Al-Khaymah, Al-Fujairah and Umm Al-7 Quwain [1]. According to the National Bureau of Statistics, (2012), the total UAE 8 population was reported to be around 8.26 million in 2010 [2]. The statistics showed that 9 some 11.5% of the total population comprised of native Arabs, with majority of the 10 population being of Indian and Pakistani ethnicities. In the early part of the twentieth 11 century, the different Arabic tribes migrated in different directions in search of suitable 12 locations to colonize. Some moved into coastal regions, while others inhabited the desert. 13 Despite the modernization throughout the union, the basic family structure and pattern of 14 native UAE Arab population has remained unchanged. Culturally, the preference for 15 consanguineous marriages remains embedded in the society [3].  However, as the 16 awareness of the social and medical impact of consanguinity increases and with 17 diversification, non-consanguineous marriages appear to be on the increase, which has 18 possibly resulted in greater genetic diversity throughout the population [4, 5]. The 19 increase in genetic diversity in the population is of interest to assess whether STR 20 markers can be used for forensic and paternity purposes. This study expands on previous 21 publications with regards to the analysis of UAE populations with the amplification of 22 additional STR markers and a larger population sample size [6]. 23 The DNA samples analysed in the current study were obtained from indigenous UAE 24 nationals residing in Abu Dhabi, UAE in accordance with approval from the Ethics 25 committee of the Ministry of Health of the United Arab Emirates (2011). Informed consent 26 was received from every volunteer during this collection process and de-identified data is 27 presented. This study was also approved by the Ethics committee of the University of 28 Central Lancashire (2014) as it was carried out as part of Masters Project in DNA profiling. 29 2    The DNA samples provided for this study were collected and extracted using the 30 Genotek’s Oragene-DNA kit (Genotek, Ottawa, Canada) in accordance with 31 manufacturer’s guidelines. The quantities of extracted DNA samples were determined 32 using a NanoDrop spectrophotometer (Thermo Scientific, Wilmington DE, USA).    33 Using half volume (7.5 µl) reactions, samples were amplified using the GlobalFiler® 34 PCR amplification kit (Life Technologies, Foster City CA, USA) and alleles were called 35 using the allelic ladder provided by the manufacturer. The PCR was performed in the 36 GeneAmp® PCR System 9700 (Life Technologies). The GlobalFiler® PCR amplification 37 kit (Life Technologies) amplifies 21 autosomal STR loci, a Y-STR locus DYS 391, a Y-38 indel marker and Amelogenin. The 21 autosomal STR loci within this amplification kit 39 were of interest for the purposes of this study. The 21 autosomal loci amplified and 40 focused on within this study were D3S1358, vWA, D16S539, CSF1PO, TPOX, 41 D8S1179, D21S11, D18S51, D2S441, D19S433, TH01, FGA, D22S1045, D5S818, 42 D13S317, D7S820, SE33, D10S1248, D1S1656, D12S391, D2S1338.       43 The PCR products   were analysed using an 8 capillary ABI 3500 DNA Genetic 44 Analyser with POP-4™ polymer (Life Technologies). GeneMapper® Software version 45 4.0 (Life Technologies) was then used for analysis.    LIZ-600 was used as internal 46 Standard (Life Technologies). 47 The alleles from all loci reported here were designated using the allelic ladder supplied 48 by the manufacturer, according to the published nomenclatures and the guidelines of 49 the International Society for Forensic Genetics (ISFG) for performing STR analyses [7]. 50 The STR allele frequencies along with the parameters of population genetics: observed  51 and expected heterozygosity (Ho and He, respectively), power of discrimination (PD), 52 probability of exclusion (PE), and polymorphic information content (PIC) were estimated 53 using PowerStats version 1.2 (Promega, Madison, USA) (Supplementary Table 1). 54 Version 3.11 of the Arlequin software was used to perform an exact test to investigate 55 any departures from the Hardy-Weinberg equilibrium (HWE) [8].  The theoretical profile 56 frequency range was estimated signifying the rarest and most common heterozygous 57 genotypes. Furthermore, the number of possible genotypes was also calculated 58 (Supplementary Table 2).  59 3    The data generated from this study was compared to 5 published population data sets 60 for available loci [9]. Exact test comparisons were made between this current study of 61 the UAE population in this study and data from Kuwaiti, India, Saudi Arabia, Egypt, and 62 Iran.    63 Data is available upon request from shadi@uclan.ac.uk 64 Through the analysis of allele frequency data, allele 8 of TPOX was found to exhibit the 65 highest allele frequency with 49.4% in the total samples analysed for the population. 66 During analysis, two off ladder allelic variants were observed at locus SE33. These 67 variants were allele 7.3 (within 3 samples) and allele 17.3 (within 1 sample). Both of these 68 variants have been previously reported on STRBase [9]. A tri-allelic pattern (allele 6, 8, 69 10) was observed for TPOX during analysis which has also been previously reported on 70 STRBase [10]. The SE33 locus showed the largest number of different alleles (50 alleles) 71 and D13S1358, D16S539 and CSF1PO loci showed the smallest number of different 72 alleles (8 alleles). The heterozygosity (Ho) of the 21 autosomal STR loci ranged from 65% 73 (TPOX) to 92% (SE33). The power of discrimination values (PD) for all tested loci was 74 above 85%; the highest observed at SE33 with 99.3% and the least at TPOX with 85%. 75 The combined probability of exclusion (CPE), power of discrimination (CPD) and 76 matching probability (CMP) for all 21 STR loci were 0.999999999999999999999999994, 77 99.999x10-2 and 6.2468x10-27 respectively. When HWE was tested, there was no 78 statistical significance observed for 19 out of 21 autosomal STR loci. Bonferroni correction 79 was applied to the two loci (D8S1179 and D22S1045) that showed deviation from HWE 80 after which no significant departure was observed. The data for the most common STR 81 profile from the UAE population (based on this dataset) showed that even using a very 82 conservative value of 0.05 for FST leads to a discrimination power in the order of 1015, 83 which translates into a value which is much higher than 1 in a billion. These estimates 84 indicate that UAE might like to adopt a match probability estimates to be reported by the 85 laboratories (in case of a full match) based on statistics generated using its own 86 population allele frequency data. Further work is indicated in this area in order to develop 87 guidelines for forensic DNA laboratories in UAE. 88 Some significant differences were identified between the obtained UAE population data 89 and the other published data. The populations from Iran and Saudi Arabia showed 90 4    significant differences at fewer loci when compared with populations from Kuwait, Egypt 91 and India (P > 0.05). This is also supported by low FST value for the Iranian and Saudi 92 Arabian populations. These results support the development of population or location 93 specific databases even when considering populations that are geographically close such 94 as within the Middle East (Supplementary Table 3).  95 This current dataset establishes the characteristics of the 21 STR loci panel for the 96 identification of individuals, in paternity testing and for crime scene analysis in the UAE.  97 This manuscript of population data follows the journal guidelines for publication of data 98 described [11, 12 and 13].  99 Acknowledgments    100 We acknowledge Khalifa University, Abu Dhabi for hosting the project and the Abu 101 Dhabi Police General Head Quarter for sponsoring the studies of AAO through a 102 scholarship.  103  104 Appendix A. Supplementary data 105 Publication\Supplementary Table 1.xlsx 106 Publication\Supplementary Table 2.xlsx 107 Publication\Supplementary Table 3.xlsx 108 References 109 [1] S.B. Miles. The countries and tribes of the Persian Gulf, London, Harrison and Sons 110 (1919). 111   112 [2] National Bureau of Statistics. Demographic and Social Statistics. Internet. 19-1- 113 2012. 19-12-2011. 114   115 [3] G.O. Tadmouri, P. Nair, T. Obeid, M.T. Al Ali, N. Al Khaja, H.A. Hamamy, 116  Consanguinity and reproductive health among Arabs, Reprod Health. 6 (2009) 17. 117 [4] I. Abed, P. Hellyer. United Arab Emirates, a New Perspective, London, Trident Press 118  (2001). 119  120 [5] T. Mohammad, Y. Xue, M. Evison, & C. Tyler-Smith, Genetic structure of nomadic 121  Bedouin from Kuwait, Heredity. 103 (5) (2009) 425-433. 122 5      123 [6] R. Garcia-Bertrand, T.M Simms, A.M Cadenas, R.J Herrera, United Arab Emirates: 124  Phylogenetic relationships and ancestral population s, Gene. 533 (2014) 411-419. 125  126 [7] P.M. Schneider, Scientific standards for studies in forensic genetics, Forensic Sci. 127  Int. 165 (2007) 238-243. 128  129 [8] L. Excoffier, G. Laval, & S. Scnheider, Arlequin ver. 3.0: An integrated software 130  package for population genetics data analysis, Evol Bioinform. 1 (2005) 47-50. 131  132 [9] M. Al-Enizi, J. Ge, S. Ismael, H. Al-Enezi, A. Al-Awadhi, W. Al-Duaij, B. Al-Saleh, Z. 133  Ghulloom, B. Budowle, Population genetic analyses of 15 STR loci from seven 134  forensically-relevant populations residing in the state of Kuwait, Forensic Sci Int- Gen. 135  7(4) (2013) e106-e107. 136  137 [10] C.M. Ruitberg, D.J. Reeder, J.M. Butler, STRBase: A short tandem repeat DNA 138  database for the human identity testing community, Nucl. Acids Res. 29 (1) (2001) 320- 139 322. 140  141 [11] A. Carracedo, J.M Butler, L. Gusmão, A. Linacre, W. Parson, L. Roewer, P.M, 142  Schneider, Update of the guidelines for the publication of genetic population data, 143  Forensic Sci. Int. Gen. 10( 2014) A1 - A2. 144   145 [12] A. Carracedo, J.M Butler, L. Gusmão, A. Linacre, W. Parson, L. Roewer, P.M, 146  Schneider, New guidelines for the publication of genetic population data, Forensic Sci. 147  Int. Gen. 7 (2013) 217-220. 148     149 [13] P. Lincoln, A. Carracedo, Publication of population data of human polymorphisms, 150  Forensic Sci Int. 110 (2000) 3-5.  151 

Population genetics data for 21 autosomal STR loci for United Arab Emirates (UAE) population using next generation multiplex STR kit

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