Forensic Science International 171 (2007) 222–225 www.elsevier.com/locate/forsciint
Announcement of Population Data
Analysis of 15 STR loci in Chinese population from Sichuan in West China Haijun Zhang a,b, Yingbi Li a, Jiping Jiang b, Ji Zhang a, Jing Wu a, Hong Du a,b, Jing Yan a, Yuehua Shen b, Yiping Hou a,* a
Institute of Forensic Medicine, Sichuan University (West China University of Medical Sciences), Chengdu 610041, Sichuan, PR China b Center of Forensic Sciences, Public Security Bureau of Sichuan Province, Chengdu 610041, Sichuan, PR China Received 5 April 2006; received in revised form 17 May 2006; accepted 21 May 2006 Available online 27 June 2006
Abstract Allele frequencies for 15 STR loci found in PowerPlex 16 System kit were determined in a sample of 200 unrelated individuals living in Sichuan area in west China. The values of observed heterozygosity (Ho), power of discrimination (PD), probability of paternity exclusion (PE) and polymorphism information content (PIC) were calculated. All loci were in accordance with Hardy–Weinberg equilibrium ( p < 0.05). The obtained frequency distributions were compared with other previously reported population data. # 2006 Elsevier Ireland Ltd. All rights reserved. Keywords: Short tandem repeat (STR); Allele frequency; PowerPlex 16; Population genetics; China
1. General information on the studied population Sichuan area is located in a basin in west China. This area is relatively isolated from other parts of China. People residing in this area speak in unique dialect and have distinct lifestyle. 2. Population samples Blood samples were obtained from 200 unrelated, autochthonous healthy individuals living in Sichuan area with known ancestors until at least the third generation (Fig. 1). 3. DNA extraction Genomic DNA was isolated from blood by standard organic phenol/chlorophorm extraction. Extracted DNA was quantified using UV spectrophotometry and was adjusted concentrations to approximately 1 ng/ml. 4. PCR Amplification was performed using 1 ng genomic DNA template according to manufacture’s protocol (PowerPlex 16 * Corresponding author. Tel.: +86 28 86303084; fax: +86 28 86301631. E-mail address:
[email protected] (H. Zhang). 0379-0738/$ – see front matter # 2006 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.forsciint.2006.05.039
System kit, Promega, USA). The cycling conditions provided with the kit were exactly followed. 5. Typing The PCR product of 1 ml was mixed with 0.3 ml internal size standard (ILS600, Promega) and 8.7 ml Hi-Di formamide (Applied Biosystems, USA), Electrophoresis, detection of PCR products and genotyping were carried out on the ABI PRISM 310 Genetic Analyzer (Applied Biosystems) using the ABI PRISM 310 data collection software and Genescan analysis and Genotyper software. 6. Quality control Laboratory internal control standards and kit control were employed. 7. Analysis of data Hardy–Weinberg equilibrium was assessed according to Hou’s method [1]. Allelic frequencies, the power of discrimination (PD), the probability of paternity exclusion (PE), the polymorphic information content (PIC), and the
H. Zhang et al. / Forensic Science International 171 (2007) 222–225
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Fig. 1. Distribution of Sichuan in China.
observed heterozygosity (Ho) were calculated using the PowerStatesV12 (http://www.promega.com). RxC chi-square test was employed for pairwise population comparisons. Excel program and SPSS 11.5 for windows software were used analysis of data.
8. Results No deviation from Hardy–Weinberg equilibrium was observed ( p > 0.05). All results are shown in Tables 1 and 2 in detail.
Table 1 Allele frequencies of 15 STR loci of Sichuan population from West China (n = 200) Allele D3S1358 TH01 D18S51 Penta E D5S818 D13S317 D7S820 D16S539 CSF1PO Penta D VWA D8S1179 TPOX Allele D21S11 FGA 5 6 7 8 9 9.3 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
0.045 0.098 0.273 0.075 0.470 0.003 0.058 0.028 0.003
0.030 0.320 0.323 0.273 0.050 0.005
0.038 0.198 0.183 0.190 0.118 0.083 0.045 0.050 0.038 0.020 0.020 0.010 0.005
0.013 0.008 0.063 0.135 0.115 0.055 0.073 0.115 0.055 0.080 0.075 0.065 0.040 0.028 0.023 0.008 0.003 0.005
0.003 0.025 0.003 0.070 0.205 0.320 0.248 0.113 0.015
0.005 0.303 0.148 0.143 0.210 0.143 0.040 0.008 0.003
0.090
0.003 0.005 0.085 0.338
0.223 0.195 0.370 0.088 0.020 0.013
0.130 0.158 0.150 0.103 0.023 0.008
0.003 0.160 0.040
0.020 0.285
0.128 0.430 0.215 0.025 0.003
0.103 0.253 0.223 0.105 0.013
0.003 0.590 0.090
0.003 0.005 0.300 0.033 0.165 0.225 0.170 0.093 0.008
0.160 0.083 0.150 0.200 0.168 0.135 0.080 0.023 0.003
0.013 0.293 0.013
17 18 19 20 21 21.2 22 22.2 23 23.2 24 24.2 25 25.2 26 27 28 29 30 30.2 30.3 31 31.2 32
0.045 0.245 0.268 0.015 0.008 0.093 0.075 0.023
0.003 0.028 0.065 0.048 0.118 0.003 0.210 0.005 0.175 0.003 0.175 0.005 0.113 0.003 0.033 0.013 0.005
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Table 1 (Continued ) Allele D3S1358 TH01 D18S51 Penta E D5S818 D13S317 D7S820 D16S539 CSF1PO Penta D VWA D8S1179 TPOX Allele D21S11 FGA
PD PIC PE Ho P
0.863 0.662 0.460 0.720 0.943
0.853 0.641 0.383 0.670 0.596
0.966 0.848 0.705 0.855 0.683
0.983 0.913 0.826 0.915 0.754
0.905 0.742 0.695 0.850 0.140
0.928 0.772 0.646 0.825 0.421
0.880 0.686 0.501 0.745 0.559
0.919 0.750 0.536 0.765 0.482
0.911 0.724 0.476 0.730 0.301
0.936 0.780 0.581 0.790 0.578
0.925 0.763 0.618 0.810 0.612
0.954 0.834 0.735 0.870 0.523
0.736 0.491 0.246 0.560 0.985
32.2 33 33.2 34.2
0.175 0.005 0.048 0.003
PD PIC PE He P
0.941 0.795 0.666 0.835 0.595
0.957 0.844 0.755 0.880 0.456
H, observed heterozygosity; PD, power of discrimination; PE, probability of paternity exclusion; PIC, polymorphic information content; p, the p-values of the exact test for Hardy–Weinberg equilibrium.
Table 2 Population comparison ( p-value) between Sichuan population (west China) and nine populations No.
Loci
Hong Kong (South China)
East China
Beijing (North China)
Singapore
Thai
Korean
Japan
West African
Argentina
1 2 3 4 5 6 7 8 9 10 11 12 13
D3S1358 TH01 D21S11 D18S51 D5S818 D13S317 D7S820 D16S539 CSF1PO vWA D8S1179 TPOX FGA
0.769 0.052 0.365 0.880 0.011 0.029 0.333 0.074 0.000 0.278 0.061 0.488 0.942
0.040 0.202 0.021 0.001 0.245 0.296 0.144 0.845 0.362 0.239 0.432 0.045 0.051
0.024 0.078 0.016 0.058 0.807 0.467 0.262 0.005 0.062 0.868 0.003 0.378 0.142
0.250 0.123 0.760 0.611 0.389 0.667 0.040 0.034 0.032 0.290 0.076 0.078 0.298
0.131 0.000 0.013 0.001 0.400 0.931 0.026 0.014 0.000 0.426 0.962 0.157 0.128
0.028 0.000 0.001 0.061 0.194 0.062 0.076 0.000 0.132 0.015 0.501 0.007 0.230
0.003 0.000 0.007 0.364 0.000 0.113 0.001 0.000 0.003 0.000 0.004 0.000 0.014
0.006 0.000 0.000 0.000 0.000 0.000 0.000 0.167 0.000 0.000 0.000 0.000 0.103
0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
The statistically significant p-values ( p < 0.05) are indicated in bold.
9. Access to the data The complete data are available to any interested researchers via e-mail: zhhaijun@ 126.com. 10. Other remarks In these samples, the observed heterozygosity (Ho) ranges from 0.560 (TPOX) to 0.915 (Penta E). The power of discrimination (PD) varies between 0.763(TPOX) and 0.983 (Penta E), and the combined power of discrimination for the 15 STR loci is 0.9999999999999999. The probability of excluding paternity (PE) varies between 0.246 (TPOX) and 0.755 (Penta E), and the combined probability of excluding paternity for the 15 loci is 0.9999994. The polymorphic information content varies between 0.491 (TPOX) and 0.913 (Penta E). All the loci show highly polymorphic. We also compared our results with those of other populations from Asia, Africa and America at the same loci. The statistically significant differences ( p < 0.05) were found between the studied population and Argentina population [2] at 13 STR loci, West African population [3] and Japanese population [4] at 11 STR loci, Korean population [5] and Thai population [6] at 6 STR loci. Between Singapore population [7] and this population, statistically significant differences were found at D7S820
( p = 0.040), D16S539 ( p = 0.034) and CSF1PO ( p = 0.032), Beijing (North China) population [8] at D3S1358 ( p = 0.024), D21S11 ( p = 0.016) and D8S1179 ( p = 0.003), the populations from east China [9] at D3S1358 ( p = 0.040), D21S11 ( p = 0.021) and TPOX ( p = 0.045). Only three STR loci (D5S818 ( p = 0.011), D13S317 ( p = 0.029) and CSF1PO ( p = 0.000) showed statistically significant differences between Hong Kong (South China) [10] and this studied population. To our knowledge, this report of allele frequencies would serve as a reference database for individual identification in Sichuan, West China. This database also has value for other population genetics and diversity studies. This paper follows the guidelines for publication data requested by the journal [11]. Acknowledgement This study was supported by the Grants from National Nature Science Foundation of China (30572088). References [1] Y.P. Hou, M. Prinz, M. Staak, Comparison of different test for deviation from Hardy–Weinberg equilibrium of AMPFLP population data, Adv. Forensic Genet. 5 (1994) 511–514.
H. Zhang et al. / Forensic Science International 171 (2007) 222–225 [2] M. Marino, A. Sala, D. Corach, Population genetic analysis of 15 autosomal STRs loci in the central region of Argentina, Forensic Sci. Int. 161 (2006) 72–77. [3] R.G. Alves, J. Jesus, A.T. Fernandes, A. Brehm, Genetic profile of a multiethnic population from Guine’-Bissau (west African coast) using the new PowerPlex1 16 System kit, Forensic Sci. Int. 129 (2002) 78–80. [4] M. Hashiyada, Y. Itakura, M. Nata, PowerPlex, 16 analysis in the Japanese population, Int. Congress Ser. 1239 (2003) 125–130. [5] Y.L. Kim, J.Y. Hwang, Y.J. Kim, S. Lee, N.G. Chung, H.G. Goh, C.C. Kim, D.W. Kim, Allele frequencies of 15 STR loci using AmpF/STR Identifiler kit in a Korean population, Forensic Sci. Int. 136 (2003) 92–95. [6] B. Rerkamnuaychoke, T. Rinthachai, J. Shotivaranon, U. Jomsawat, T. Siriboonpiputtana, K. Chaiatchanarat, E. Pasomsub, W. Chantratita, Thai population data on 15 tetrameric STR loci—D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433,
[7]
[8]
[9]
[10]
[11]
225
vWA, TPOX, D18S51, D5S818 and FGA, Forensic Sci. Int. 158 (2006) 234–237. R.Y. Yong, L.T. Aw, E.P.H. Yap, Allele frequencies of 15 STR loci of three main ethnic populations in Singapore using an in-house marker panel, Forensic Sci. Int. 141 (2004) 175–183. Y. Liu, Z.Y. Huo, H. Tang, J. Wang, Z. Jiao, W. Ma, J. Yan, J. Yang, Sh. Jia, X. Zhu, Frequency data for 15 STR loci and forensic use in a Beijing-Han population, Int. Congress Ser. 1239 (2003) 267–270. Y.Z. Gao, Z.X. Zhang, Z.F. Wang, S.Z. Bian, Genetic data of 15 STR forensic loci in eastern Chinese population, Forensic Sci. Int. 154 (2005) 78–80. K.M. Chan, C.T. Chiu, P. Tsui, D.M. Wong, W.K. Fung, Population data for the IdentifierTM 15 STR loci in Hong Kong Chinese, Forensic Sci. Int. 152 (2005) 307–309. P. Lincoln, A. Carracedo, Publication of population data of human polymorphisms, Forensic Sci. Int. 110 (2000) 3–5.