- Email: [email protected]
Population data of 17 Y-STR loci in Nanyang Han population from Henan Province, Central China
Forensic Science International: Genetics 13 (2014) 145–146
Contents lists available at ScienceDirect
Forensic Science International: Genetics journal homepage: www.elsevier.com/locate/fsig
Forensic Population Genetics – Letter to the Editor Population data of 17 Y-STR loci in Nanyang Han population from Henan Province, Central China Dear Editor, Nanyang is a prefecture-level city in the southwest of Henan province, bordering the province of Shaanxi to the west, and the province of Hubei to the south (Fig. S1). It is the largest administrative area in Henan and spans over 26,591 km2. The city has 10,263,006 inhabitants at the 2010 census, with a majority of the Han population (97.6%) and a total of 43 ethnic compositions (2.4%), such as Hui, Mongolian, Manchu and so forth. Its local dialect is known as Nanyang Hua, which is a branch of Henan dialect, spoken by about 15 million people around the area. Supplementary Fig. S1 related to this article can be found, in the online version, at doi:10.1016/j.fsigen.2014.07.013. Venous blood was collected from 413 unrelated healthy male individuals living in Nanyang city, and informed consent was signed by all the donors. DNA was extracted using the Chelex-100 protocol [1]. PCR amplification was performed on GeneAmp1 PCR 9700 (Life Technologies, CA, USA) using the AmpFISTR1 Y-filerTM PCR Amplification kit (Life Technologies) according to the manufacturer’s recommendations. Amplification products were separated and detected on Applied BiosystemsTM 3500 Series Genetic Analyzer (Life Technologies). Raw data was analyzed using GeneMapper ID-X v1.2 Software (Life Technologies). The experimental procedures were guided in keeping with laboratory internal control standards and kit controls. The control DNA 007 (Life Technologies) was employed as positive control, and the control DNA 9947A (Life Technologies) and ddH2O were as negative control. Haplotype frequencies and allele frequencies were calculated using the ARLEQUIN Version 3.5 software [2]. Haplotype diversity (HD) and gene diversity (GD) were calculated according to the formula described by Nei [3]. Haplotype discrimination capacity (DC) was determined as the proportion of different haplotypes in the sample. Genetic distances (Rst) between our data and 10 published populations were measured by analysis of molecular variance (AMOVA) in YHRD database (http:// www.yhrd.org/Analyse/AMOVA), and visualized in two multidimensional scaling (MDS) plot using SPSS 19.0 software (IBM, NY, USA). A total of 391 different haplotypes were found from 413 individuals, of which 370 were unique, 20 were shared in 2 individuals, and 1 was shared in 3 individuals (see Table S1). Null alleles were observed in 3 individuals at DYS448 (Ht4 and Ht241), 1 individual at DYS438 (Ht131), and 1 individual at DYS19 (Ht321). At DYS385a/b, we confirmed four tri-allelic patterns (13, 16, 20 in Ht102; 13, 16, 19 in Ht104; 13, 17, 18 in Ht295; 13, 18, 20 in Ht348), one quadri-allelic pattern (13, 17, 18, 21 in Ht48), and two variant alleles (18.2 in Ht165 and 9.1 in Ht300). The HD was calculated as 0.9997 with the DC of 0.9467. http://dx.doi.org/10.1016/j.fsigen.2014.07.013 1872-4973/ß 2014 Elsevier Ireland Ltd. All rights reserved.
The GD values across 17 loci ranged from 0.4119 (DYS391) to 0.9689 (DYS385) with allele frequencies from 0.0024 to 0.7385 (Table S2). Pairwise Rst and p-value were performed between Nanyang Han and ten populations submitted to the YHRD database (Table S3), namely Northern Han (YA003756), Shanxi Han [4], Yunnan Han [5,6], Zhejiang Han [7], Gansu Hui (YA003841), Liaoning Manchu [8], Qinghai Tibetan [9], Guangxi Zhuang (YA003542), South Korean [10,11], and Japanese [12], where Nanyang Han had no significant distances after Bonferroni correction (p > 0.0029) with Northern Han (Rst = 0.0006, p = 0.5702), Shanxi Han (Rst = 0.0070, p = 0.0092), Manchu (Rst = 0.0015, p = 0.1190) or Yunnan Han (Rst = 0.0068, p = 0.0999). The same conclusion could be observed in Fig. S2, which might be associated with a large migration of Han population from the Henan province into Northwest China, Manchuria and Yunnan in the first half of the twentieth century. Supplementary Table S1 related to this article can be found, in the online version, at doi:10.1016/j.fsigen.2014.07.013. Supplementary Table S2 related to this article can be found, in the online version, at doi:10.1016/j.fsigen.2014.07.013. Supplementary Table S3 related to this article can be found, in the online version, at doi:10.1016/j.fsigen.2014.07.013. Supplementary Fig. S2 related to this article can be found, in the online version, at doi:10.1016/j.fsigen.2014.07.013. We have strictly followed International Society for Forensic Genetics (ISFG) recommendations on the analysis of the DNA polymorphisms and nomenclature [13] and guidelines for publication of population data requested by the journal [14,15]. The YHRD QC and population accession number are YC000234 (2012-07-18) and YA003925 (Nanyang, China (Han)), respectively.
References [1] P.S. Walsh, D.A. Metzger, R. Higuchi, Chelex100 as a medium for simple extraction of DNA for PCR-based from forensic material, Biotechniques 10 (1991) 506–513. [2] L. Excoffier, H.E.L. Lischer, Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows, Mol. Ecol. Resour. 10 (2010) 564–567. [3] M. Nei, Molecular Evolutionary Genetics, Columbia University Press, New York, 1987, p. 178. [4] R. Bai, Z. Zhang, Q. Liang, D. Lu, L. Yuan, X. Yang, M. Shi, Haplotype diversity of 17 Y-STR loci in a Chinese Han population sample from Shanxi Province, Northern China, Forensic Sci. Int. Genet. 7 (2012) 214–216. [5] Y. Yanmei, G. Tao, Z. Yubao, X. Chunjie, C. Bifeng, L. Shi, X. Bingying, J. Qiang, Z. Qinyong, Z. Wen, L. Shengjun, N. Shengjie, Genetic polymorphism of 11 Y-chromosomal STR loci in Yunnan Han Chinese, Forensic Sci. Int. Genet. 4 (2009) e67–e69. [6] Y.J. Kim, D.J. Shin, J.M. Kim, H.J. Jin, K.D. Kwak, M.S. Han, S.K. Choi, W. Kim, Y-chromosome STR haplotype profiling in the Korean population, Forensic Sci. Int. 115 (2001) 231–237. [7] W. Wu, L. Pan, H. Hao, X. Zheng, J. Lin, D. Lu, Population genetics of 17 Y-STR loci in a large Chinese Han population from Zhejiang Province, Eastern China, Forensic Sci. Int. Genet. 5 (2011) e11–e13. [8] J. He, F. Guo, Population genetics of 17 Y-STR loci in Chinese Manchu population from Liaoning Province, Northeast China, Forensic Sci. Int. Genet. 7 (2013) e84– e85.
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Forensic Population Genetics – Letter to the Editor / Forensic Science International: Genetics 13 (2014) 145–146
[9] B. Zhu, Y. Wu, C. Shen, T. Yang, Y. Deng, X. Xun, Y. Tian, J. Yan, T. Li, Genetic analysis of 17 Y-chromosomal STRs haplotypes of Chinese Tibetan ethnic group residing in Qinghai province of China, Forensic Sci. Int. 175 (2008) 238–243. [10] K.M. Seong, S.Y. Yoo, J.H. Hwang, S.H. Kim, K.W. Chung, N.S. Cho, Population genetic polymorphisms of 17 Y-chromosomal STR loci in South Koreans, Forensic Sci. Int. Genet. 5 (2010) 122–123. [11] S.H. Kim, M.S. Han, W. Kim, W. Kim, Y chromosome homogeneity in the Korean population, Legal Med. 124 (2010) 653–657. [12] N. Mizuno, H. Nakahara, K. Sekiguchi, K. Yoshida, M. Nakano, K. Kasai, 16 Y chromosomal STR haplotypes in Japanese, Forensic Sci. Int. 174 (2008) e71–e76. [13] L. Gusma˜o, J.M. Butler, A. Carracedo, P. Gill, M. Kayser, W.R. Mayr, N. Morling, M. Prinz, L. Roewer, C. Tyler-Smith, P.M. Schneider, DNA Commission of the International Society of Forensic Genetics (ISFG): an update of the recommendations on the use of Y-STRs in forensic analysis, Int. J. Legal Med. 120 (2006) 191–200. [14] 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. [15] A. Carracedo, J.M. Butler, L. Gusma˜o, A. Linacre, W. Parson, L. Roewer, P.M. Schneider, New guidelines for the publication of genetic population data, Forensic Sci. Int. Genet. 7 (2013) 217–220.
Yanyan Yang Department of Forensic Genetics, Wannan Medical College, No. 22, Wenchang West Road, Yijiang District, Wuhu, Anhui 241000, China
Wanliu Yuan Fangcheng County Public Security Bureau, No. 158, Zhangqian Road, Fangcheng County, Nanyang, Henan 473200, China Fei Guo Department of Forensic Medicine, China Criminal Police College, No. 38, Tawan Street, Huanggu District, Shenyang, Liaoning 110854, China Xianhua Jiang* Liaoning Province Criminal Science and Technology Institute, No. 2, Qishan Middle Road, Huanggu District, Shenyang, Liaoning 110032, China *Corresponding
author. Tel.: +86 24 8699 2025; fax: +86 24 8684 2058 E-mail address: [email protected] (X. Jiang). 14 June 2014
Contents lists available at ScienceDirect
Forensic Science International: Genetics journal homepage: www.elsevier.com/locate/fsig
Forensic Population Genetics – Letter to the Editor Population data of 17 Y-STR loci in Nanyang Han population from Henan Province, Central China Dear Editor, Nanyang is a prefecture-level city in the southwest of Henan province, bordering the province of Shaanxi to the west, and the province of Hubei to the south (Fig. S1). It is the largest administrative area in Henan and spans over 26,591 km2. The city has 10,263,006 inhabitants at the 2010 census, with a majority of the Han population (97.6%) and a total of 43 ethnic compositions (2.4%), such as Hui, Mongolian, Manchu and so forth. Its local dialect is known as Nanyang Hua, which is a branch of Henan dialect, spoken by about 15 million people around the area. Supplementary Fig. S1 related to this article can be found, in the online version, at doi:10.1016/j.fsigen.2014.07.013. Venous blood was collected from 413 unrelated healthy male individuals living in Nanyang city, and informed consent was signed by all the donors. DNA was extracted using the Chelex-100 protocol [1]. PCR amplification was performed on GeneAmp1 PCR 9700 (Life Technologies, CA, USA) using the AmpFISTR1 Y-filerTM PCR Amplification kit (Life Technologies) according to the manufacturer’s recommendations. Amplification products were separated and detected on Applied BiosystemsTM 3500 Series Genetic Analyzer (Life Technologies). Raw data was analyzed using GeneMapper ID-X v1.2 Software (Life Technologies). The experimental procedures were guided in keeping with laboratory internal control standards and kit controls. The control DNA 007 (Life Technologies) was employed as positive control, and the control DNA 9947A (Life Technologies) and ddH2O were as negative control. Haplotype frequencies and allele frequencies were calculated using the ARLEQUIN Version 3.5 software [2]. Haplotype diversity (HD) and gene diversity (GD) were calculated according to the formula described by Nei [3]. Haplotype discrimination capacity (DC) was determined as the proportion of different haplotypes in the sample. Genetic distances (Rst) between our data and 10 published populations were measured by analysis of molecular variance (AMOVA) in YHRD database (http:// www.yhrd.org/Analyse/AMOVA), and visualized in two multidimensional scaling (MDS) plot using SPSS 19.0 software (IBM, NY, USA). A total of 391 different haplotypes were found from 413 individuals, of which 370 were unique, 20 were shared in 2 individuals, and 1 was shared in 3 individuals (see Table S1). Null alleles were observed in 3 individuals at DYS448 (Ht4 and Ht241), 1 individual at DYS438 (Ht131), and 1 individual at DYS19 (Ht321). At DYS385a/b, we confirmed four tri-allelic patterns (13, 16, 20 in Ht102; 13, 16, 19 in Ht104; 13, 17, 18 in Ht295; 13, 18, 20 in Ht348), one quadri-allelic pattern (13, 17, 18, 21 in Ht48), and two variant alleles (18.2 in Ht165 and 9.1 in Ht300). The HD was calculated as 0.9997 with the DC of 0.9467. http://dx.doi.org/10.1016/j.fsigen.2014.07.013 1872-4973/ß 2014 Elsevier Ireland Ltd. All rights reserved.
The GD values across 17 loci ranged from 0.4119 (DYS391) to 0.9689 (DYS385) with allele frequencies from 0.0024 to 0.7385 (Table S2). Pairwise Rst and p-value were performed between Nanyang Han and ten populations submitted to the YHRD database (Table S3), namely Northern Han (YA003756), Shanxi Han [4], Yunnan Han [5,6], Zhejiang Han [7], Gansu Hui (YA003841), Liaoning Manchu [8], Qinghai Tibetan [9], Guangxi Zhuang (YA003542), South Korean [10,11], and Japanese [12], where Nanyang Han had no significant distances after Bonferroni correction (p > 0.0029) with Northern Han (Rst = 0.0006, p = 0.5702), Shanxi Han (Rst = 0.0070, p = 0.0092), Manchu (Rst = 0.0015, p = 0.1190) or Yunnan Han (Rst = 0.0068, p = 0.0999). The same conclusion could be observed in Fig. S2, which might be associated with a large migration of Han population from the Henan province into Northwest China, Manchuria and Yunnan in the first half of the twentieth century. Supplementary Table S1 related to this article can be found, in the online version, at doi:10.1016/j.fsigen.2014.07.013. Supplementary Table S2 related to this article can be found, in the online version, at doi:10.1016/j.fsigen.2014.07.013. Supplementary Table S3 related to this article can be found, in the online version, at doi:10.1016/j.fsigen.2014.07.013. Supplementary Fig. S2 related to this article can be found, in the online version, at doi:10.1016/j.fsigen.2014.07.013. We have strictly followed International Society for Forensic Genetics (ISFG) recommendations on the analysis of the DNA polymorphisms and nomenclature [13] and guidelines for publication of population data requested by the journal [14,15]. The YHRD QC and population accession number are YC000234 (2012-07-18) and YA003925 (Nanyang, China (Han)), respectively.
References [1] P.S. Walsh, D.A. Metzger, R. Higuchi, Chelex100 as a medium for simple extraction of DNA for PCR-based from forensic material, Biotechniques 10 (1991) 506–513. [2] L. Excoffier, H.E.L. Lischer, Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows, Mol. Ecol. Resour. 10 (2010) 564–567. [3] M. Nei, Molecular Evolutionary Genetics, Columbia University Press, New York, 1987, p. 178. [4] R. Bai, Z. Zhang, Q. Liang, D. Lu, L. Yuan, X. Yang, M. Shi, Haplotype diversity of 17 Y-STR loci in a Chinese Han population sample from Shanxi Province, Northern China, Forensic Sci. Int. Genet. 7 (2012) 214–216. [5] Y. Yanmei, G. Tao, Z. Yubao, X. Chunjie, C. Bifeng, L. Shi, X. Bingying, J. Qiang, Z. Qinyong, Z. Wen, L. Shengjun, N. Shengjie, Genetic polymorphism of 11 Y-chromosomal STR loci in Yunnan Han Chinese, Forensic Sci. Int. Genet. 4 (2009) e67–e69. [6] Y.J. Kim, D.J. Shin, J.M. Kim, H.J. Jin, K.D. Kwak, M.S. Han, S.K. Choi, W. Kim, Y-chromosome STR haplotype profiling in the Korean population, Forensic Sci. Int. 115 (2001) 231–237. [7] W. Wu, L. Pan, H. Hao, X. Zheng, J. Lin, D. Lu, Population genetics of 17 Y-STR loci in a large Chinese Han population from Zhejiang Province, Eastern China, Forensic Sci. Int. Genet. 5 (2011) e11–e13. [8] J. He, F. Guo, Population genetics of 17 Y-STR loci in Chinese Manchu population from Liaoning Province, Northeast China, Forensic Sci. Int. Genet. 7 (2013) e84– e85.
146
Forensic Population Genetics – Letter to the Editor / Forensic Science International: Genetics 13 (2014) 145–146
[9] B. Zhu, Y. Wu, C. Shen, T. Yang, Y. Deng, X. Xun, Y. Tian, J. Yan, T. Li, Genetic analysis of 17 Y-chromosomal STRs haplotypes of Chinese Tibetan ethnic group residing in Qinghai province of China, Forensic Sci. Int. 175 (2008) 238–243. [10] K.M. Seong, S.Y. Yoo, J.H. Hwang, S.H. Kim, K.W. Chung, N.S. Cho, Population genetic polymorphisms of 17 Y-chromosomal STR loci in South Koreans, Forensic Sci. Int. Genet. 5 (2010) 122–123. [11] S.H. Kim, M.S. Han, W. Kim, W. Kim, Y chromosome homogeneity in the Korean population, Legal Med. 124 (2010) 653–657. [12] N. Mizuno, H. Nakahara, K. Sekiguchi, K. Yoshida, M. Nakano, K. Kasai, 16 Y chromosomal STR haplotypes in Japanese, Forensic Sci. Int. 174 (2008) e71–e76. [13] L. Gusma˜o, J.M. Butler, A. Carracedo, P. Gill, M. Kayser, W.R. Mayr, N. Morling, M. Prinz, L. Roewer, C. Tyler-Smith, P.M. Schneider, DNA Commission of the International Society of Forensic Genetics (ISFG): an update of the recommendations on the use of Y-STRs in forensic analysis, Int. J. Legal Med. 120 (2006) 191–200. [14] 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. [15] A. Carracedo, J.M. Butler, L. Gusma˜o, A. Linacre, W. Parson, L. Roewer, P.M. Schneider, New guidelines for the publication of genetic population data, Forensic Sci. Int. Genet. 7 (2013) 217–220.
Yanyan Yang Department of Forensic Genetics, Wannan Medical College, No. 22, Wenchang West Road, Yijiang District, Wuhu, Anhui 241000, China
Wanliu Yuan Fangcheng County Public Security Bureau, No. 158, Zhangqian Road, Fangcheng County, Nanyang, Henan 473200, China Fei Guo Department of Forensic Medicine, China Criminal Police College, No. 38, Tawan Street, Huanggu District, Shenyang, Liaoning 110854, China Xianhua Jiang* Liaoning Province Criminal Science and Technology Institute, No. 2, Qishan Middle Road, Huanggu District, Shenyang, Liaoning 110032, China *Corresponding
author. Tel.: +86 24 8699 2025; fax: +86 24 8684 2058 E-mail address: [email protected] (X. Jiang). 14 June 2014