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Analysis of STR polymorphisms in the northeast Chinese population
Forensic Science International 132 (2003) 161–163
Announcement of population data
Analysis of STR polymorphisms in the northeast Chinese population Xiuling Wang*, Toshiko Sawaguchi, Akiko Sawaguchi Department of Legal Medicine, Tokyo Women’s Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo, Japan Received 18 November 2002; received in revised form 13 December 2002; accepted 18 December 2002
Abstract The distribution of allele frequencies for 12 short tandem repeats (STR) loci were determined in 300 unrelated healthy Chinese individuals living in northeast of China, using AmpF‘STR Profiler Plus kit and AmpF‘STR Green I kit (PE, Applied Biosystems). In these samples, 123 alleles and 399 genotypes were observed for 12 STR loci. The distribution of these observed genotypes were not significantly different from the expected distribution according to Hardy–Weinberg equilibrium. # 2003 Elsevier Science Ireland Ltd. All rights reserved. Keywords: Short tandem repeats; Population data; Northeast Chinese
Population: The DNA samples were obtained from 300 unrelated healthy Chinese individuals living in northeast of China. Extraction: The DNA was extracted from whole blood using John’s method [1]. The DNA concentration was determined by a spectrophotometer. PCR: A 2 ng target DNA following manufacturer’s instructions (AmpF‘STR Profiler Plus PCR amplification kit and AmpF‘STR Green I PCR amplification kit, PE Applied Biosystems). TM
Typing: ABI PRISM 310 Genetic Analyzer and reference sequenced ladders (PE Applied Biosystems). Results: See Table 1. Quality control: Laboratory internal control standards and kit controls.
Analysis of data: Hardy–Weinberg equilibrium was assessed by means of Chi-square test [2]. DP was calculated from the frequency of each distinct phenotype and the number of distinct phenotypes for each locus [3]. Ho (observed heterozygosity), He (expected heterozygosity), PIC and CE were calculated from the frequency of each distinct allele and the number of distinct alleles for each locus [4–6]. Access to the data: [email protected]. Other remarks: Differentiation tests between northeast Chinese and other Chinese [7–10] samples were not significant for STR loci. These STR loci are useful genetic markers for identification and paternity tests as well as anthropological studies in Chinese population. This paper follows the guidelines for publication of population data requested by the journal [11].
* Corresponding author. Tel.: þ81-3-32078690; fax: þ81-3-52697300. E-mail address: [email protected] (X. Wang).
0379-0738/03/$ – see front matter # 2003 Elsevier Science Ireland Ltd. All rights reserved. doi:10.1016/S0379-0738(03)00007-0
162
X. Wang et al. / Forensic Science International 132 (2003) 161–163
Table 1 Allele frequencies for 12 STR loci in the northeast Chinese population (n ¼ 300) Allele
D3S1358 vWA
FGA
D8S1179
D21S11
D18S51
D5S818
D13S317
D7S820
TH01
TPOX
CSF1PO
6 7 8 9 9.3 10 11 12 13 14 15 16 17 18 19 20 21 21.2 22 22.2 23 23.2 24 24.2 25 25.2 26 26.2 27 28 28.2 29 29.2 30 30.2 31 31.2 32 32.2 33 33.2 34 34.2
– – – – – – – 0.002 0.003 0.035 0.445 0.273 0.177 0.057 0.007 0.002 – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – – – – – 0.023 0.248 0.045 0.175 0.275 0.150 0.070 0.014 – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – – – – – – – – – 0.003 0.022 0.043 0.072 0.124 0.002 0.153 0.008 0.235 0.003 0.165 0.005 0.113 0.005 0.037 0.002 0.002 0.003 – 0.003 – – – – – – – – – – –
– – 0.003 0.010 – 0.087 0.098 0.110 0.305 0.172 0.140 0.062 0.013 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – – – – – – – – – – – – – – – – – – – – – 0.007 – – – – 0.057 0.008 0.208 0.002 0.228 0.012 0.170 0.062 0.045 0.118 0.003 0.065 0.007 0.008
– – – – – 0.003 0.007 0.028 0.207 0.218 0.198 0.100 0.072 0.040 0.045 0.030 0.022 – 0.012 – 0.012 – 0.003 – 0.002 – 0.001 – – – – – – – – – – – – – – – –
0.002 0.016 0.005 0.072 – 0.187 0.296 0.237 0.175 0.007 0.003 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– 0.002 0.290 0.132 – 0.162 0.236 0.135 0.035 0.008 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– 0.003 0.118 0.063 – 0.200 0.347 0.227 0.037 0.005 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
0.107 0.273 0.083 0.502 0.017 0.018 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
0.003 – 0.488 0.139 – 0.042 0.313 0.015 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– 0.008 0.022 0.078 – 0.225 0.217 0.341 0.087 0.022 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
Ho He PD CE PIC P
0.692 0.694 0.853 0.431 0.657 0.968
0.802 0.805 0.932 0.574 0.793 0.786
0.857 0.860 0.965 0.660 0.857 0.563
0.825 0.827 0.949 0.622 0.815 0.665
0.848 0.851 0.960 0.644 0.848 0.738
0.849 0.852 0.961 0.663 0.840 0.865
0.785 0.788 0.919 0.535 0.765 0.822
0.797 0.800 0.930 0.565 0.788 0.818
0.769 0.772 0.913 0.529 0.747 0.936
0.655 0.657 0.832 0.397 0.648 0.902
0.642 0.644 0.813 0.366 0.633 0.887
0.771 0.774 0.913 0.536 0.753 0.698
Ho (observed heterozigosity), He (expected heterozigosity), PD (power of discrimination), CE (a priori chance of exclusion), PIC (polymorphic information content), P (exact test of Hardy–Weinberg equilibrium).
X. Wang et al. / Forensic Science International 132 (2003) 161–163
Acknowledgements This study was supported by grants from the Japan China Medical Association—the Japan Foundation.
References [1] S.W.M. John, G. Weitzner, R. Rozen, C.R. Scriver, A rapid procedure for extracting genomic DNA from leukocytes, Nudeic Acids Res. 19 (1991) 408. [2] S.W. Guo, E.A. Thompson, Performing the exact test of Hardy–Weinberg population for multiples alleles, Biometrics 48 (1992) 361–372. [3] B.W. Grunbaum, S. Selvin, N. Pace, D.M. Black, Frequency distribution and discrimination probability of twelve protein genetic variants in human blood as functions of race, J. Forensic Sci. 23 (1978) 577–587. [4] M. Nei, A.K. Roychoudhury, Sampling variances of heterozygosity and genetic distance, Genetic 76 (1974) 379– 390.
163
[5] D. Botstein, R.L. White, M. Skolnick, R.W. Davis, Construction of a genetic linkage map in man using restriction fragment length polymorphisms, Am. J. Hum. Genet. 32 (1980) 314–331. [6] Y. Ohno, I.M. Sebetan, S. Akaishi, A simple method for calculating the probability of excluding paternity with any number of codominant alleles, Forensic Sci. Int. 19 (1982) 93–98. [7] W.K. Fung, K.L. Leong, C.L. Wong, Chinese population data in Macau at nine STR loci, Forensic Sci. Int. 126 (2002) 95–96. [8] Y.L. Ma, B.C. Gong, J.H. Xia, H.X. Deng, Q. Pan, Q. Li, H.P. Dai, S. Wen, K. Xia, Han Chinese population data for ten STR loci in Changsha, China, J. Forensic Sci. 47 (2002) 404–405. [9] L. Gusmao, M.J. Prata, P. Sanchez-Diz, M.V. Lareu, A. Carracedo, C. Alves, N. Martins, A. Amorim, Str data for AmpF‘STR profiler plus loci from Macau (China), Forensic Sci. Int. 123 (2001) 74–75. [10] Y. Hou, Y. Li, J. Wu, J. Tang, M. Prinz, Polymorphisms of 13 STR markers in population, Prog. Forensic Genet. 8 (2000) 242–244. [11] P. Lincoln, A. Carracedo, Publication of population data of human polymorphisms, Forensic Sci. Int. 110 (2000) 3–5.
Announcement of population data
Analysis of STR polymorphisms in the northeast Chinese population Xiuling Wang*, Toshiko Sawaguchi, Akiko Sawaguchi Department of Legal Medicine, Tokyo Women’s Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo, Japan Received 18 November 2002; received in revised form 13 December 2002; accepted 18 December 2002
Abstract The distribution of allele frequencies for 12 short tandem repeats (STR) loci were determined in 300 unrelated healthy Chinese individuals living in northeast of China, using AmpF‘STR Profiler Plus kit and AmpF‘STR Green I kit (PE, Applied Biosystems). In these samples, 123 alleles and 399 genotypes were observed for 12 STR loci. The distribution of these observed genotypes were not significantly different from the expected distribution according to Hardy–Weinberg equilibrium. # 2003 Elsevier Science Ireland Ltd. All rights reserved. Keywords: Short tandem repeats; Population data; Northeast Chinese
Population: The DNA samples were obtained from 300 unrelated healthy Chinese individuals living in northeast of China. Extraction: The DNA was extracted from whole blood using John’s method [1]. The DNA concentration was determined by a spectrophotometer. PCR: A 2 ng target DNA following manufacturer’s instructions (AmpF‘STR Profiler Plus PCR amplification kit and AmpF‘STR Green I PCR amplification kit, PE Applied Biosystems). TM
Typing: ABI PRISM 310 Genetic Analyzer and reference sequenced ladders (PE Applied Biosystems). Results: See Table 1. Quality control: Laboratory internal control standards and kit controls.
Analysis of data: Hardy–Weinberg equilibrium was assessed by means of Chi-square test [2]. DP was calculated from the frequency of each distinct phenotype and the number of distinct phenotypes for each locus [3]. Ho (observed heterozygosity), He (expected heterozygosity), PIC and CE were calculated from the frequency of each distinct allele and the number of distinct alleles for each locus [4–6]. Access to the data: [email protected]. Other remarks: Differentiation tests between northeast Chinese and other Chinese [7–10] samples were not significant for STR loci. These STR loci are useful genetic markers for identification and paternity tests as well as anthropological studies in Chinese population. This paper follows the guidelines for publication of population data requested by the journal [11].
* Corresponding author. Tel.: þ81-3-32078690; fax: þ81-3-52697300. E-mail address: [email protected] (X. Wang).
0379-0738/03/$ – see front matter # 2003 Elsevier Science Ireland Ltd. All rights reserved. doi:10.1016/S0379-0738(03)00007-0
162
X. Wang et al. / Forensic Science International 132 (2003) 161–163
Table 1 Allele frequencies for 12 STR loci in the northeast Chinese population (n ¼ 300) Allele
D3S1358 vWA
FGA
D8S1179
D21S11
D18S51
D5S818
D13S317
D7S820
TH01
TPOX
CSF1PO
6 7 8 9 9.3 10 11 12 13 14 15 16 17 18 19 20 21 21.2 22 22.2 23 23.2 24 24.2 25 25.2 26 26.2 27 28 28.2 29 29.2 30 30.2 31 31.2 32 32.2 33 33.2 34 34.2
– – – – – – – 0.002 0.003 0.035 0.445 0.273 0.177 0.057 0.007 0.002 – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – – – – – 0.023 0.248 0.045 0.175 0.275 0.150 0.070 0.014 – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – – – – – – – – – 0.003 0.022 0.043 0.072 0.124 0.002 0.153 0.008 0.235 0.003 0.165 0.005 0.113 0.005 0.037 0.002 0.002 0.003 – 0.003 – – – – – – – – – – –
– – 0.003 0.010 – 0.087 0.098 0.110 0.305 0.172 0.140 0.062 0.013 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – – – – – – – – – – – – – – – – – – – – – 0.007 – – – – 0.057 0.008 0.208 0.002 0.228 0.012 0.170 0.062 0.045 0.118 0.003 0.065 0.007 0.008
– – – – – 0.003 0.007 0.028 0.207 0.218 0.198 0.100 0.072 0.040 0.045 0.030 0.022 – 0.012 – 0.012 – 0.003 – 0.002 – 0.001 – – – – – – – – – – – – – – – –
0.002 0.016 0.005 0.072 – 0.187 0.296 0.237 0.175 0.007 0.003 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– 0.002 0.290 0.132 – 0.162 0.236 0.135 0.035 0.008 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– 0.003 0.118 0.063 – 0.200 0.347 0.227 0.037 0.005 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
0.107 0.273 0.083 0.502 0.017 0.018 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
0.003 – 0.488 0.139 – 0.042 0.313 0.015 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– 0.008 0.022 0.078 – 0.225 0.217 0.341 0.087 0.022 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
Ho He PD CE PIC P
0.692 0.694 0.853 0.431 0.657 0.968
0.802 0.805 0.932 0.574 0.793 0.786
0.857 0.860 0.965 0.660 0.857 0.563
0.825 0.827 0.949 0.622 0.815 0.665
0.848 0.851 0.960 0.644 0.848 0.738
0.849 0.852 0.961 0.663 0.840 0.865
0.785 0.788 0.919 0.535 0.765 0.822
0.797 0.800 0.930 0.565 0.788 0.818
0.769 0.772 0.913 0.529 0.747 0.936
0.655 0.657 0.832 0.397 0.648 0.902
0.642 0.644 0.813 0.366 0.633 0.887
0.771 0.774 0.913 0.536 0.753 0.698
Ho (observed heterozigosity), He (expected heterozigosity), PD (power of discrimination), CE (a priori chance of exclusion), PIC (polymorphic information content), P (exact test of Hardy–Weinberg equilibrium).
X. Wang et al. / Forensic Science International 132 (2003) 161–163
Acknowledgements This study was supported by grants from the Japan China Medical Association—the Japan Foundation.
References [1] S.W.M. John, G. Weitzner, R. Rozen, C.R. Scriver, A rapid procedure for extracting genomic DNA from leukocytes, Nudeic Acids Res. 19 (1991) 408. [2] S.W. Guo, E.A. Thompson, Performing the exact test of Hardy–Weinberg population for multiples alleles, Biometrics 48 (1992) 361–372. [3] B.W. Grunbaum, S. Selvin, N. Pace, D.M. Black, Frequency distribution and discrimination probability of twelve protein genetic variants in human blood as functions of race, J. Forensic Sci. 23 (1978) 577–587. [4] M. Nei, A.K. Roychoudhury, Sampling variances of heterozygosity and genetic distance, Genetic 76 (1974) 379– 390.
163
[5] D. Botstein, R.L. White, M. Skolnick, R.W. Davis, Construction of a genetic linkage map in man using restriction fragment length polymorphisms, Am. J. Hum. Genet. 32 (1980) 314–331. [6] Y. Ohno, I.M. Sebetan, S. Akaishi, A simple method for calculating the probability of excluding paternity with any number of codominant alleles, Forensic Sci. Int. 19 (1982) 93–98. [7] W.K. Fung, K.L. Leong, C.L. Wong, Chinese population data in Macau at nine STR loci, Forensic Sci. Int. 126 (2002) 95–96. [8] Y.L. Ma, B.C. Gong, J.H. Xia, H.X. Deng, Q. Pan, Q. Li, H.P. Dai, S. Wen, K. Xia, Han Chinese population data for ten STR loci in Changsha, China, J. Forensic Sci. 47 (2002) 404–405. [9] L. Gusmao, M.J. Prata, P. Sanchez-Diz, M.V. Lareu, A. Carracedo, C. Alves, N. Martins, A. Amorim, Str data for AmpF‘STR profiler plus loci from Macau (China), Forensic Sci. Int. 123 (2001) 74–75. [10] Y. Hou, Y. Li, J. Wu, J. Tang, M. Prinz, Polymorphisms of 13 STR markers in population, Prog. Forensic Genet. 8 (2000) 242–244. [11] P. Lincoln, A. Carracedo, Publication of population data of human polymorphisms, Forensic Sci. Int. 110 (2000) 3–5.