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Genetic profile of 17 Y-chromosome STR haplotypes in East of Iran
G Model
FSIGEN-1249; No. of Pages 2 Forensic Science International: Genetics xxx (2014) e1–e2
Contents lists available at ScienceDirect
Forensic Science International: Genetics journal homepage: www.elsevier.com/locate/fsig
Letter to the Editor Genetic profile of 17 Y-chromosome STR haplotypes in East of Iran Dear Editor-in-Chief, Due to lack of proper Y chromosome STR data from eastern population of Iran, we have conducted a study to determine the 17 Y chromosome STR loci (DYS19, DYS385a, DYS385b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, and YGATA H4) haplotypes in 259 random unrelated male individuals from three eastern provinces of Iran (129 samples of Razavi Khorasan, 27 samples of South Khorasan and 103 samples of Sistan and Baluchestan) comprising 24% and 12% of Iran geographical area and Iranian population, respectively. This study was approved and supported by Iranian Legal Medicine Research Center and collaboration of three referral centers in the capital city of Razavi Khorasan province (Mashhad) and capital cities of South Khorasan and Sistan and Baluchestan provinces (Birjand and Zahedan), respectively. Blood samples were collected from consented participants on Whatman1 FTATM Classic papers. For DNA extraction, a punch of 1.2 mm2 was used following manufacturer’s standard protocol. The 17 Y-STR loci (AmpFlSTR YfilerTM kit, Life Technologies) were amplified simultaneously according to the kit recommendations using TC-512 Thermal cycler (Techne, Bibby Scientific, UK). Electrophoresis of amplified PCR products was carried out using capillary electrophoresis on automated ABI 3130 Genetic Analyzer (Applied Biosystems, Foster City, CA). Quality assessment for Y chromosome STR typing was guaranteed by correct typing of 17 Y-STR markers for five blind DNA samples provided by YHRD in 2012 (YC000268) [1]. Haplotype analysis was performed via Genemapper ID1 V3.2 software (Applied Biosystems, Foster City, CA). The obtained Y-STR data were submitted to the Y chromosome Haplotype Reference Database (accession number of YA003903 for Mashhad and accession numbers of YA003902 and YA003901 for Birjand and Zahedan, respectively) [1]. Haplotypes and gene diversities were determined based on Nei formula [2]. Haplotype discrimination capacity (DC) was calculated by dividing the total number of different haplotypes in analyzed population by the total number of individuals in the sample size [3]. Using YHRD and GenAlEx V6.5, Analysis of molecular variance (AMOVA) and FST values were calculated, respectively [1,4,5]. Haplotype diversities (HD) were calculated using HapYDive [6,7]. Haplotype match probability (HMP) was calculated according to HMP = 1 HD formula. A total of 256 different haplotypes were detected from male individuals living in Razavi Khorasan, South Khorasan and Sistan and Baluchestan provinces and three obtained haplotypes were occurred twice. In comparison to Tehran and Isfahan published data, total population HD in our study was greater than Tehran and
Isfahan Populations (0.9999 vs. 0.997 and 0.997, respectively) [8] which represented the HMP for our population to be 0.0001. The estimated DC of 17 Y-STRs in this population was 0.9884 which was higher than the calculated DC for Tehran (0.9) and Isfahan (0.938) populations [8]. The variation range of genetic diversity values were from 0.313 (DYS391 in South Khorasan) to 0.866 (DYS385b in Razavi Khorasan) [5]. The Eastern Iranian population is consisted of three provinces and comparative analysis indicated that the Razavi Khorasan population had statistically insignificant differences from Sistan and Baluchestan population (FST = 0.0001, p = 0.8004) and South Khorasan population (FST = 0.0002, p = 0.2553). Population pairwise comparisons using Eastern Iranian haplotypes and registered Iranian haplotypes in YHRD revealed the same results of close relationships between these regions within Iran (FST = 0.0014, p = 1.0000) [1,9]. Results of comparison among our population and twelve other Iranian populations showed insignificant genetic distance between the eastern Iranian population and most of the other socio-geographical populations within Iran except for Masal, Izeh, Sari, Qashqaee and central region of Iran which had low genetic distance with our population (Supplementary Table 1) [9]. An AMOVA analysis of the Eastern Iranian population 17 Y-STR haplotypes obtained from this study was compared to data from the neighboring countries Afghanistan (consisting Afghan, Pathan, North and South populations) and Pakistan (Pathan) which have shown small genetic discrimination between populations living in this close region (Supplementary Table 1) [1,10–12]. There was a significant difference between our studied population and adjacent populations from Afghanistan (FST = 0.0022, p = 0.0000) and Pakistan (FST = 0.0027, p = 0.0000). Our results have shown that the Y-STR markers included in AmpFlSTR YfilerTM kit had a high discriminatory power for the purpose of regional/national forensic casework investigations in the eastern Iranian population, human identification purposes and haplotype comparisons among relevant neighbor populations. This study follows the updated guidelines for publication of population data requested by the journal [13]. Acknowledgments We would also like to extend our thanks to all the contributors in this study, including sample donors and our colleagues in South Khorasan and Sistan and Baluchestan legal medicine organization. This study was granted by Legal Medicine Research Center, Tehran, Iran. Appendix A. Supplementary data Supplementary data associated with this article can be found, in the online version, at doi:10.1016/j.fsigen.2014.10.010.
http://dx.doi.org/10.1016/j.fsigen.2014.10.010 1872-4973/ß 2014 Elsevier Ireland Ltd. All rights reserved.
Please cite this article in press as: A.A. Tabrizi, et al., Genetic profile of 17 Y-chromosome STR haplotypes in East of Iran, Forensic Sci. Int. Genet. (2014), http://dx.doi.org/10.1016/j.fsigen.2014.10.010
G Model
FSIGEN-1249; No. of Pages 2 e2
Letter to the Editor / Forensic Science International: Genetics xxx (2014) e1–e2
References [1] S. Willuweit, L. Roewer, Y chromosome haplotype reference database (YHRD): update, Forensic Sci. Int. Genet. 1 (2) (2007) 83–87. [2] M. Nei, Molecular Evolutionary Genetics, Columbia University Press, New York, 1987. [3] M. Kayser, et al., Evaluation of Y-chromosomal STRs: a multicenter study, Int. J. Legal Med. 110 (3) (1997) 125–133. [4] L. Roewer, et al., Online reference database of European Y-chromosomal short tandem repeat (STR) haplotypes, Forensic Sci. Int. 118 (2) (2001) 106–113. [5] R. Peakall, P.E. Smouse, GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research – an update, Bioinformatics 28 (19) (2012) 2537–2539. [6] C. Alves, et al., Making the most of Y-STR haplotypes. The HapYDive, Progr. Forensic Genet. 11 (2006) 201–203. [7] C. Alves, et al., Evaluating the informative power of Y-STRs: a comparative study using European and new African haplotype data, Forensic Sci. Int. 134 (2–3) (2003) 126–133. [8] I. Nasidze, H. Schadlich, M. Stoneking, Haplotypes from the Caucasus: Turkey and Iran for nine Y-STR loci, Forensic Sci. Int. 137 (1) (2003) 85–93. [9] L. Roewer, et al., A Y-STR database of Iranian and Azerbaijanian minority populations, Forensic Sci. Int. Genet. 4 (1) (2009) 53–55. [10] H. Lacau, et al., Y-STR profiling in two Afghanistan populations, Leg. Med. (Tokyo) 13 (2) (2011) 103–108. [11] C. A¨lgena¨s, A.O. Tillmar, Population genetics of 29 autosomal STRs and 17 Ychromosomal STRs in a population sample from Afghanistan, Int. J. Legal Med. 128 (2) (2014) 279–280. [12] N.M. Achakzai, et al., Y-chromosomal STR analysis in the Pashtun population of Southern Afghanistan, Forensic Sci. Int. Genet. 6 (4) (2012) e103–e105. [13] A. Carracedo, et al., Update of the guidelines for the publication of genetic population data, Forensic Sci. Int. Genet. 10 (2014) A1–A2.
Arash Alipour Tabrizi Arya Hedjazi* Iranian Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran Mohammad Amin Kerachian Department of Medical Genetics, School of Medicine, Mashhad University of Medical Science, Mashhad, Iran Zohreh Honarvar Iranian Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran Maliheh Dadgarmoghaddam Department of Community Medicine, School of Medicine, Mashhad University of Medical Science, Mashhad, Iran Reza Raoofian Iranian Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran *Corresponding author E-mail address: [email protected] (A. Hedjazi).
1 August 2014
Please cite this article in press as: A.A. Tabrizi, et al., Genetic profile of 17 Y-chromosome STR haplotypes in East of Iran, Forensic Sci. Int. Genet. (2014), http://dx.doi.org/10.1016/j.fsigen.2014.10.010
FSIGEN-1249; No. of Pages 2 Forensic Science International: Genetics xxx (2014) e1–e2
Contents lists available at ScienceDirect
Forensic Science International: Genetics journal homepage: www.elsevier.com/locate/fsig
Letter to the Editor Genetic profile of 17 Y-chromosome STR haplotypes in East of Iran Dear Editor-in-Chief, Due to lack of proper Y chromosome STR data from eastern population of Iran, we have conducted a study to determine the 17 Y chromosome STR loci (DYS19, DYS385a, DYS385b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, and YGATA H4) haplotypes in 259 random unrelated male individuals from three eastern provinces of Iran (129 samples of Razavi Khorasan, 27 samples of South Khorasan and 103 samples of Sistan and Baluchestan) comprising 24% and 12% of Iran geographical area and Iranian population, respectively. This study was approved and supported by Iranian Legal Medicine Research Center and collaboration of three referral centers in the capital city of Razavi Khorasan province (Mashhad) and capital cities of South Khorasan and Sistan and Baluchestan provinces (Birjand and Zahedan), respectively. Blood samples were collected from consented participants on Whatman1 FTATM Classic papers. For DNA extraction, a punch of 1.2 mm2 was used following manufacturer’s standard protocol. The 17 Y-STR loci (AmpFlSTR YfilerTM kit, Life Technologies) were amplified simultaneously according to the kit recommendations using TC-512 Thermal cycler (Techne, Bibby Scientific, UK). Electrophoresis of amplified PCR products was carried out using capillary electrophoresis on automated ABI 3130 Genetic Analyzer (Applied Biosystems, Foster City, CA). Quality assessment for Y chromosome STR typing was guaranteed by correct typing of 17 Y-STR markers for five blind DNA samples provided by YHRD in 2012 (YC000268) [1]. Haplotype analysis was performed via Genemapper ID1 V3.2 software (Applied Biosystems, Foster City, CA). The obtained Y-STR data were submitted to the Y chromosome Haplotype Reference Database (accession number of YA003903 for Mashhad and accession numbers of YA003902 and YA003901 for Birjand and Zahedan, respectively) [1]. Haplotypes and gene diversities were determined based on Nei formula [2]. Haplotype discrimination capacity (DC) was calculated by dividing the total number of different haplotypes in analyzed population by the total number of individuals in the sample size [3]. Using YHRD and GenAlEx V6.5, Analysis of molecular variance (AMOVA) and FST values were calculated, respectively [1,4,5]. Haplotype diversities (HD) were calculated using HapYDive [6,7]. Haplotype match probability (HMP) was calculated according to HMP = 1 HD formula. A total of 256 different haplotypes were detected from male individuals living in Razavi Khorasan, South Khorasan and Sistan and Baluchestan provinces and three obtained haplotypes were occurred twice. In comparison to Tehran and Isfahan published data, total population HD in our study was greater than Tehran and
Isfahan Populations (0.9999 vs. 0.997 and 0.997, respectively) [8] which represented the HMP for our population to be 0.0001. The estimated DC of 17 Y-STRs in this population was 0.9884 which was higher than the calculated DC for Tehran (0.9) and Isfahan (0.938) populations [8]. The variation range of genetic diversity values were from 0.313 (DYS391 in South Khorasan) to 0.866 (DYS385b in Razavi Khorasan) [5]. The Eastern Iranian population is consisted of three provinces and comparative analysis indicated that the Razavi Khorasan population had statistically insignificant differences from Sistan and Baluchestan population (FST = 0.0001, p = 0.8004) and South Khorasan population (FST = 0.0002, p = 0.2553). Population pairwise comparisons using Eastern Iranian haplotypes and registered Iranian haplotypes in YHRD revealed the same results of close relationships between these regions within Iran (FST = 0.0014, p = 1.0000) [1,9]. Results of comparison among our population and twelve other Iranian populations showed insignificant genetic distance between the eastern Iranian population and most of the other socio-geographical populations within Iran except for Masal, Izeh, Sari, Qashqaee and central region of Iran which had low genetic distance with our population (Supplementary Table 1) [9]. An AMOVA analysis of the Eastern Iranian population 17 Y-STR haplotypes obtained from this study was compared to data from the neighboring countries Afghanistan (consisting Afghan, Pathan, North and South populations) and Pakistan (Pathan) which have shown small genetic discrimination between populations living in this close region (Supplementary Table 1) [1,10–12]. There was a significant difference between our studied population and adjacent populations from Afghanistan (FST = 0.0022, p = 0.0000) and Pakistan (FST = 0.0027, p = 0.0000). Our results have shown that the Y-STR markers included in AmpFlSTR YfilerTM kit had a high discriminatory power for the purpose of regional/national forensic casework investigations in the eastern Iranian population, human identification purposes and haplotype comparisons among relevant neighbor populations. This study follows the updated guidelines for publication of population data requested by the journal [13]. Acknowledgments We would also like to extend our thanks to all the contributors in this study, including sample donors and our colleagues in South Khorasan and Sistan and Baluchestan legal medicine organization. This study was granted by Legal Medicine Research Center, Tehran, Iran. Appendix A. Supplementary data Supplementary data associated with this article can be found, in the online version, at doi:10.1016/j.fsigen.2014.10.010.
http://dx.doi.org/10.1016/j.fsigen.2014.10.010 1872-4973/ß 2014 Elsevier Ireland Ltd. All rights reserved.
Please cite this article in press as: A.A. Tabrizi, et al., Genetic profile of 17 Y-chromosome STR haplotypes in East of Iran, Forensic Sci. Int. Genet. (2014), http://dx.doi.org/10.1016/j.fsigen.2014.10.010
G Model
FSIGEN-1249; No. of Pages 2 e2
Letter to the Editor / Forensic Science International: Genetics xxx (2014) e1–e2
References [1] S. Willuweit, L. Roewer, Y chromosome haplotype reference database (YHRD): update, Forensic Sci. Int. Genet. 1 (2) (2007) 83–87. [2] M. Nei, Molecular Evolutionary Genetics, Columbia University Press, New York, 1987. [3] M. Kayser, et al., Evaluation of Y-chromosomal STRs: a multicenter study, Int. J. Legal Med. 110 (3) (1997) 125–133. [4] L. Roewer, et al., Online reference database of European Y-chromosomal short tandem repeat (STR) haplotypes, Forensic Sci. Int. 118 (2) (2001) 106–113. [5] R. Peakall, P.E. Smouse, GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research – an update, Bioinformatics 28 (19) (2012) 2537–2539. [6] C. Alves, et al., Making the most of Y-STR haplotypes. The HapYDive, Progr. Forensic Genet. 11 (2006) 201–203. [7] C. Alves, et al., Evaluating the informative power of Y-STRs: a comparative study using European and new African haplotype data, Forensic Sci. Int. 134 (2–3) (2003) 126–133. [8] I. Nasidze, H. Schadlich, M. Stoneking, Haplotypes from the Caucasus: Turkey and Iran for nine Y-STR loci, Forensic Sci. Int. 137 (1) (2003) 85–93. [9] L. Roewer, et al., A Y-STR database of Iranian and Azerbaijanian minority populations, Forensic Sci. Int. Genet. 4 (1) (2009) 53–55. [10] H. Lacau, et al., Y-STR profiling in two Afghanistan populations, Leg. Med. (Tokyo) 13 (2) (2011) 103–108. [11] C. A¨lgena¨s, A.O. Tillmar, Population genetics of 29 autosomal STRs and 17 Ychromosomal STRs in a population sample from Afghanistan, Int. J. Legal Med. 128 (2) (2014) 279–280. [12] N.M. Achakzai, et al., Y-chromosomal STR analysis in the Pashtun population of Southern Afghanistan, Forensic Sci. Int. Genet. 6 (4) (2012) e103–e105. [13] A. Carracedo, et al., Update of the guidelines for the publication of genetic population data, Forensic Sci. Int. Genet. 10 (2014) A1–A2.
Arash Alipour Tabrizi Arya Hedjazi* Iranian Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran Mohammad Amin Kerachian Department of Medical Genetics, School of Medicine, Mashhad University of Medical Science, Mashhad, Iran Zohreh Honarvar Iranian Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran Maliheh Dadgarmoghaddam Department of Community Medicine, School of Medicine, Mashhad University of Medical Science, Mashhad, Iran Reza Raoofian Iranian Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran *Corresponding author E-mail address: [email protected] (A. Hedjazi).
1 August 2014
Please cite this article in press as: A.A. Tabrizi, et al., Genetic profile of 17 Y-chromosome STR haplotypes in East of Iran, Forensic Sci. Int. Genet. (2014), http://dx.doi.org/10.1016/j.fsigen.2014.10.010