- Email: [email protected]
An autosomal STR database of Muslims: The largest minority community, Uttar Pradesh, India
Forensic Science International: Genetics 5 (2011) e117–e118
Contents lists available at ScienceDirect
Forensic Science International: Genetics journal homepage: www.elsevier.com/locate/fsig
Forensic Population Genetics—Letter to the Editor An autosomal STR database of Muslims: The largest minority community, Uttar Pradesh, India
Dear Editor, The population of India is unique in its size and level of subdivision, with fifteen major languages and six main religions [1]. A lot of work has been done to genetically explore the different tribes and castes in the majority Hindu community; however, there is very little data on the minority groups in India. Muslims constitute the largest minority group (13.4%) and are similarly subdivided into Sunni, Shia, Ismaili and Dawoodi Bohra communities, and biraderis (patrilineages) that are based on traditional, social and occupational divisions. These biraderis are of known historical provenance and are identified as endogamous units [2]. Muslims in general belong to two major sects: Sunni and Shia, and each sect have different biraderis, which are grouped under Ashraf and Ajlaf [3]. The Ashraf include higher rank Muslims, such as the Syed, Sheikh, Pathan, and Mughal, whereas the Ajlaf include the Qureshi, Ansari, and other groups of lower occupations [4]. In the present study, genetic polymorphism of the 15 autosomal STR loci was studied in four Muslim biraderis of Uttar Pradesh, the heartland of Indian Muslims. The populations were selected on the basis of their socio-cultural affiliation, two of them namely, Syed and Yusufzai Pathan belonging to Ashraf and the other two, Ansari and Qureshi belonging to the Ajlaf group (Fig. 1). 354 blood samples (Syed 59, Yusufzai Pathan 104, Ansari 117 and Qureshi 74) from unrelated healthy individuals were collected with informed consent following the guidelines of the Institutional Ethics Committee. Genomic DNA was extracted from blood samples using the standard phenol chloroform extraction followed by ethanol precipitation method [5]. DNA was quantified by Quantifiler1 Human DNA Quantification Kit according to the manufacturer’s protocol using 7500 Real-Time PCR System (Applied Biosystems, Foster city, CA). PCR amplification was performed for fifteen tetranucleotide repeat loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, THO1, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA) and amelogenin using AmpFlSTR1 Identifiler1 PCR Amplification kit following the manufacturer’s guidelines and GeneAmp1 PCR System 9700 (Applied Biosystems, Foster City, CA). The amplified products were genotyped on ABIPRISM1 3100 Genetic Analyzer with POP-4TM polymer, GeneScanTM 500 LIZTM Size Standard and the data was analyzed using GeneMapper1 ID Software v3.2 (Applied Biosystems, Foster City, CA). The alleles of all loci were determined according to the number of repeat units present as recommended by International Society of Forensic Genetics [6]. Allele frequencies, observed heterozygosity (H), gene diversity (GD), polymorphic information content (PIC), likelihood ratio pvalues and exact tests for the possible deviation from the Hardy– Weinberg equilibrium were computed by Power Marker [7]. 1872-4973/$ – see front matter ß 2011 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.fsigen.2011.03.012
Population pairwise Fst genetic distances among the populations were estimated using Arlequin v3.11 [8]. Several parameters of forensic importance, like probability of match (PM), power of discrimination (PD), power of exclusion (PE) and typical paternity index (TPI) were calculated using Excel Powerstats spread sheet from Promega v1.2. The allele frequencies and various statistical parameters including the combined probabilities of match, combined powers of exclusion and most common profile frequencies for the 4 populations are shown in Tables 1–4 (supplementary data). The observed heterozygosity (H) oscillates between 0.5763 for TPOX to 0.9322 for D21S11 in Syed, 0.6154 for TPOX to 0.8942 for D8S1179 in Yusufzai Pathan, 0.6581 for CSF1PO to 0.8803 for D18S51 in Ansari and 0.6622 for D13S317 to 0.8649 for D2S1338 in Qureshi populations. FGA was found to be most polymorphic with 17 alleles each in Syed and Ansari, and 18 alleles in Yusufzai Pathan population; D2S1338 was found to be most polymorphic in Qureshi population with 12 alleles; whereas TPOX was found to be least polymorphic with 5 alleles each in Syed and Ansari and 6 alleles in Yusufzai Pathan population; D5S8188 was found to be least polymorphic with 7 alleles in Qureshi population. The combined probabilities of match for the 15 STR loci ranged from 6.3 10 18 in Yusufzai Pathan population to 2.8 10 17 in Syed population. The combined powers of exclusion varied among the populations from 0.999996707 to 0.999999761 in Qureshi and Syed populations, respectively. The most common profile frequencies for the populations ranged from 5.15 10 16 to 3.05 10 14 in Syed and Yusufzai Pathan populations, respectively. Deviations from the Hardy–Weinberg Equilibrium after applying Bonferroni’s adjustment for the number of loci tested (p < 0.0033) were observed at D7S820, CSF1PO and FGA loci in Syed, D18S51 in Yusufzai Pathan, TPOX and FGA in Qureshi populations which can be attributed to the excess of homozygotes; however, in Ansari population, none of the tested loci showed significant deviation. In order to ascertain the genetic diversity within the Muslim community of Uttar Pradesh, comparative analysis with other four reference Muslim groups has also been carried out [9,10]. The population pairwise Fst genetic distance matrix with the p-values for the studied populations is given in Table 5 (supplementary data). Analysis of molecular variance (AMOVA) reveals significant or high genetic distances between all the studied populations. However, Syed, Yusufzai Pathan and Qureshi populations show non-significant p-values when compared with the Shia reference population. This paper follows the guidelines for publication of population data as required by the journal [11,12]. To the best of our knowledge, Muslim biraderis have not been explored genetically for generating forensic data on STR markers. Therefore, the data generated from the present study is a valuable contribution to the existing DNA database on Indian population. It also provides additional information on the high degree of genetic variation prevalent within the Muslim community of Uttar Pradesh.
[()TD$FIG]
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Letter to the Editor / Forensic Science International: Genetics 5 (2011) e117–e118
Fig. 1. Map of Uttar Pradesh, India and location of the analyzed populations.
This work was supported by Directorate of Forensic Science, Ministry of Home Affairs, Government of India, New Delhi. Sincere thanks to all the donors of blood samples for the present study. We would also like to thank M. Eaaswarkhanth for providing the allele frequency data of the reference populations. Appendix A. Supplementary data Supplementary data associated with this article can be found, in the online version, at doi:10.1016/j.fsigen.2011.03.012.
[8] L. Excoffier, G. Lavel, S. Schneider, Arlequin ver 3.0: an integrated software package for population genetics data analysis, Evol. Bioinform. Online 1 (2005) 47–50. [9] M. Eaaswarkhanth, B. Dubey, P.R. Meganathan, S. Noor, I. Haque, Microsatellite diversity delineates genetic relationships of Shia and Sunni Muslim populations of Uttar Pradesh, India, Hum. Biol. 81 (2009) 427–445. [10] M. Eaaswarkhanth, B. Dubey, P.R. Meganathan, Z. Ravesh, F.A. Khan, L. Singh, K. Thangaraj, I. Haque, Diverse genetic origin of Indian Muslims: evidence from autosomal STR loci, J. Hum. Genet. 54 (2009) 340–348. [11] A. Carracedo, J.M. Butler, L. Gusma˜o, W. Parson, L. Roewer, P.M. Schneider, Publication of population data for forensic purposes, Forensic Sci. Int. Genet. 4 (2010) 145–147. [12] B. Olaisen, W. Ba¨r, B. Brinkmann, B. Budowle, A. Carracedo, P. Gill, P. Lincoln, W.R. Mayr, S. Rand, DNA recommendations 1997 of the International Society for Forensic Genetics, Vox Sang. 74 (1998) 61–63.
References [1] M.K. Bhasin, H. walter, H. Danker-Hopfe, The Distribution of Genetical Morphological and Behavioural Traits among the People of Indian Region, Kamal-Raj Publication, Delhi, 1992, pp. 14–35. [2] S.A. Shami, J.C. Grant, A.H. Bittles, Consanguineous marriage within social/occupational class boundaries in Pakistan, J. Biosoc. Sci. 26 (1994) 91–96. [3] G. Ansari, Muslim castes in U.P., in: Ethnographic and Folk Culture and Society, Lucknow, 1959. [4] I. Ahmad, Endogamy and status mobility among the Siddique, Sheikhs of Allahabad, U.P., in: Caste and Stratification among the Muslims of India, Manohar Publication, Delhi, 1978, pp. 171–206. [5] J. Sambrook, E.F. Fritch, T. Maniatis, Molecular Cloning. A Laboratory Manual, 2nd ed., Cold Spring Harbour Laboratory Press, New York, NY, 1989. [6] P.M. Schneider, Scientific standards for studies in forensic genetics, Forensic Sci. Int. 165 (2007) 238–243. [7] K. Liu, S.V. Muse, PowerMarker: integrated analysis environment for genetic marker data, Bioinformatics 21 (2005) 2128–2129.
Sabahat Noor Soma Roy Ikramul Haque* Center of Excellence in Forensic Biology, Central Forensic Science laboratory, Directorate of Forensic Science, 30 Gorachand Road, Kolkata 700014, India *Corresponding
author. Tel.: +91 33 22841638; fax: +91 33 22849442 E-mail address: [email protected] (I. Haque). 24 November 2010
Contents lists available at ScienceDirect
Forensic Science International: Genetics journal homepage: www.elsevier.com/locate/fsig
Forensic Population Genetics—Letter to the Editor An autosomal STR database of Muslims: The largest minority community, Uttar Pradesh, India
Dear Editor, The population of India is unique in its size and level of subdivision, with fifteen major languages and six main religions [1]. A lot of work has been done to genetically explore the different tribes and castes in the majority Hindu community; however, there is very little data on the minority groups in India. Muslims constitute the largest minority group (13.4%) and are similarly subdivided into Sunni, Shia, Ismaili and Dawoodi Bohra communities, and biraderis (patrilineages) that are based on traditional, social and occupational divisions. These biraderis are of known historical provenance and are identified as endogamous units [2]. Muslims in general belong to two major sects: Sunni and Shia, and each sect have different biraderis, which are grouped under Ashraf and Ajlaf [3]. The Ashraf include higher rank Muslims, such as the Syed, Sheikh, Pathan, and Mughal, whereas the Ajlaf include the Qureshi, Ansari, and other groups of lower occupations [4]. In the present study, genetic polymorphism of the 15 autosomal STR loci was studied in four Muslim biraderis of Uttar Pradesh, the heartland of Indian Muslims. The populations were selected on the basis of their socio-cultural affiliation, two of them namely, Syed and Yusufzai Pathan belonging to Ashraf and the other two, Ansari and Qureshi belonging to the Ajlaf group (Fig. 1). 354 blood samples (Syed 59, Yusufzai Pathan 104, Ansari 117 and Qureshi 74) from unrelated healthy individuals were collected with informed consent following the guidelines of the Institutional Ethics Committee. Genomic DNA was extracted from blood samples using the standard phenol chloroform extraction followed by ethanol precipitation method [5]. DNA was quantified by Quantifiler1 Human DNA Quantification Kit according to the manufacturer’s protocol using 7500 Real-Time PCR System (Applied Biosystems, Foster city, CA). PCR amplification was performed for fifteen tetranucleotide repeat loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, THO1, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA) and amelogenin using AmpFlSTR1 Identifiler1 PCR Amplification kit following the manufacturer’s guidelines and GeneAmp1 PCR System 9700 (Applied Biosystems, Foster City, CA). The amplified products were genotyped on ABIPRISM1 3100 Genetic Analyzer with POP-4TM polymer, GeneScanTM 500 LIZTM Size Standard and the data was analyzed using GeneMapper1 ID Software v3.2 (Applied Biosystems, Foster City, CA). The alleles of all loci were determined according to the number of repeat units present as recommended by International Society of Forensic Genetics [6]. Allele frequencies, observed heterozygosity (H), gene diversity (GD), polymorphic information content (PIC), likelihood ratio pvalues and exact tests for the possible deviation from the Hardy– Weinberg equilibrium were computed by Power Marker [7]. 1872-4973/$ – see front matter ß 2011 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.fsigen.2011.03.012
Population pairwise Fst genetic distances among the populations were estimated using Arlequin v3.11 [8]. Several parameters of forensic importance, like probability of match (PM), power of discrimination (PD), power of exclusion (PE) and typical paternity index (TPI) were calculated using Excel Powerstats spread sheet from Promega v1.2. The allele frequencies and various statistical parameters including the combined probabilities of match, combined powers of exclusion and most common profile frequencies for the 4 populations are shown in Tables 1–4 (supplementary data). The observed heterozygosity (H) oscillates between 0.5763 for TPOX to 0.9322 for D21S11 in Syed, 0.6154 for TPOX to 0.8942 for D8S1179 in Yusufzai Pathan, 0.6581 for CSF1PO to 0.8803 for D18S51 in Ansari and 0.6622 for D13S317 to 0.8649 for D2S1338 in Qureshi populations. FGA was found to be most polymorphic with 17 alleles each in Syed and Ansari, and 18 alleles in Yusufzai Pathan population; D2S1338 was found to be most polymorphic in Qureshi population with 12 alleles; whereas TPOX was found to be least polymorphic with 5 alleles each in Syed and Ansari and 6 alleles in Yusufzai Pathan population; D5S8188 was found to be least polymorphic with 7 alleles in Qureshi population. The combined probabilities of match for the 15 STR loci ranged from 6.3 10 18 in Yusufzai Pathan population to 2.8 10 17 in Syed population. The combined powers of exclusion varied among the populations from 0.999996707 to 0.999999761 in Qureshi and Syed populations, respectively. The most common profile frequencies for the populations ranged from 5.15 10 16 to 3.05 10 14 in Syed and Yusufzai Pathan populations, respectively. Deviations from the Hardy–Weinberg Equilibrium after applying Bonferroni’s adjustment for the number of loci tested (p < 0.0033) were observed at D7S820, CSF1PO and FGA loci in Syed, D18S51 in Yusufzai Pathan, TPOX and FGA in Qureshi populations which can be attributed to the excess of homozygotes; however, in Ansari population, none of the tested loci showed significant deviation. In order to ascertain the genetic diversity within the Muslim community of Uttar Pradesh, comparative analysis with other four reference Muslim groups has also been carried out [9,10]. The population pairwise Fst genetic distance matrix with the p-values for the studied populations is given in Table 5 (supplementary data). Analysis of molecular variance (AMOVA) reveals significant or high genetic distances between all the studied populations. However, Syed, Yusufzai Pathan and Qureshi populations show non-significant p-values when compared with the Shia reference population. This paper follows the guidelines for publication of population data as required by the journal [11,12]. To the best of our knowledge, Muslim biraderis have not been explored genetically for generating forensic data on STR markers. Therefore, the data generated from the present study is a valuable contribution to the existing DNA database on Indian population. It also provides additional information on the high degree of genetic variation prevalent within the Muslim community of Uttar Pradesh.
[()TD$FIG]
e118
Letter to the Editor / Forensic Science International: Genetics 5 (2011) e117–e118
Fig. 1. Map of Uttar Pradesh, India and location of the analyzed populations.
This work was supported by Directorate of Forensic Science, Ministry of Home Affairs, Government of India, New Delhi. Sincere thanks to all the donors of blood samples for the present study. We would also like to thank M. Eaaswarkhanth for providing the allele frequency data of the reference populations. Appendix A. Supplementary data Supplementary data associated with this article can be found, in the online version, at doi:10.1016/j.fsigen.2011.03.012.
[8] L. Excoffier, G. Lavel, S. Schneider, Arlequin ver 3.0: an integrated software package for population genetics data analysis, Evol. Bioinform. Online 1 (2005) 47–50. [9] M. Eaaswarkhanth, B. Dubey, P.R. Meganathan, S. Noor, I. Haque, Microsatellite diversity delineates genetic relationships of Shia and Sunni Muslim populations of Uttar Pradesh, India, Hum. Biol. 81 (2009) 427–445. [10] M. Eaaswarkhanth, B. Dubey, P.R. Meganathan, Z. Ravesh, F.A. Khan, L. Singh, K. Thangaraj, I. Haque, Diverse genetic origin of Indian Muslims: evidence from autosomal STR loci, J. Hum. Genet. 54 (2009) 340–348. [11] A. Carracedo, J.M. Butler, L. Gusma˜o, W. Parson, L. Roewer, P.M. Schneider, Publication of population data for forensic purposes, Forensic Sci. Int. Genet. 4 (2010) 145–147. [12] B. Olaisen, W. Ba¨r, B. Brinkmann, B. Budowle, A. Carracedo, P. Gill, P. Lincoln, W.R. Mayr, S. Rand, DNA recommendations 1997 of the International Society for Forensic Genetics, Vox Sang. 74 (1998) 61–63.
References [1] M.K. Bhasin, H. walter, H. Danker-Hopfe, The Distribution of Genetical Morphological and Behavioural Traits among the People of Indian Region, Kamal-Raj Publication, Delhi, 1992, pp. 14–35. [2] S.A. Shami, J.C. Grant, A.H. Bittles, Consanguineous marriage within social/occupational class boundaries in Pakistan, J. Biosoc. Sci. 26 (1994) 91–96. [3] G. Ansari, Muslim castes in U.P., in: Ethnographic and Folk Culture and Society, Lucknow, 1959. [4] I. Ahmad, Endogamy and status mobility among the Siddique, Sheikhs of Allahabad, U.P., in: Caste and Stratification among the Muslims of India, Manohar Publication, Delhi, 1978, pp. 171–206. [5] J. Sambrook, E.F. Fritch, T. Maniatis, Molecular Cloning. A Laboratory Manual, 2nd ed., Cold Spring Harbour Laboratory Press, New York, NY, 1989. [6] P.M. Schneider, Scientific standards for studies in forensic genetics, Forensic Sci. Int. 165 (2007) 238–243. [7] K. Liu, S.V. Muse, PowerMarker: integrated analysis environment for genetic marker data, Bioinformatics 21 (2005) 2128–2129.
Sabahat Noor Soma Roy Ikramul Haque* Center of Excellence in Forensic Biology, Central Forensic Science laboratory, Directorate of Forensic Science, 30 Gorachand Road, Kolkata 700014, India *Corresponding
author. Tel.: +91 33 22841638; fax: +91 33 22849442 E-mail address: [email protected] (I. Haque). 24 November 2010