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Japanese population database for nine STR loci of the AmpFℓSTR Profiler kit
Forensic Science International 132 (2003) 166–167
Announcement of population data
Japanese population database for nine STR loci of the AmpF‘STR Profiler kit Kanako Yoshida*, Natsuko Mizuno, Koji Fujii, Hiroaki Senju, Kazumasa Sekiguchi, Kentaro Kasai, Hajime Sato National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan Received 21 November 2002; received in revised form 17 December 2002; accepted 18 December 2002
Abstract Allele frequencies for nine short tandem repeats (STR) loci: D3S1358, vWA, FGA, TH01, TPOX, CSF1PO, D5S818, D13S317 and D7S820 were determined in a Japanese population using the AmpF‘STR Profiler PCR amplification kit (Applied biosystems). # 2003 Elsevier Science Ireland Ltd. All rights reserved. Keywords: Short tandem repeats; AmpF‘STR Profiler PCR amplification kit; Japanese population
Population sample: Blood samples were collected from 1200 unrelated individuals in Japan. DNA extraction: DNA was isolated from the blood sample using MagNA Pure LC (Roche Diagnostic). The extracted DNA was quantified by spectrophotometric method. PCR amplification: Multiplex PCR was performed according to manufacture’s recommendation (AmpF‘STR Profiler PCR amplification kit: Applied biosystems) using 0.5–2 ng of template DNA. The samples were amplified using GeneAmp PCR System 9700 thermal cycler (Applied biosystems). Electrophoresis and typing: Amplified products were electrophoresed on an ABI PRISM 310 capillary electrophoresis and were analyzed using Gene Scan analysis software (version 3.1) and genotyper software (version 2.5). Alleles were designated by comparison with the allelic
ladder marker contained in the kit according to the AmpF‘STR Use’s Manual. Result: See Table 1. Analysis of data: Statistical test for fit to Hardy–Weinberg equilibrium expectations was performed using the computer program GENEPOP software (version 3.3) [1]. Power of discrimination was calculated following Fisher’s method [2]. Other remarks: Another information on Japanese population samples, which were collected from 206 Japanese, can be found in the previous report [3]. From 1200 samples analyzed in this study, we can find many alleles, which were not reported in the previous report of 206 Japanese population samples [3] (Table 1). This paper follows the guidelines for publication of population data by the journal [4].
* Corresponding author. Tel.: þ81-4-7135-8001; fax: þ81-4-7133-9159. E-mail address: [email protected] (K. Yoshida).
0379-0738/03/$ – see front matter # 2003 Elsevier Science Ireland Ltd. All rights reserved. doi:10.1016/S0379-0738(03)00008-2
K. Yoshida et al. / Forensic Science International 132 (2003) 166–167
167
Table 1 The distribution of allele frequencies at nine STR loci in a Japanese population (n ¼ 1200) D3S1358
vWA
FGA
TH01
TPOX
CSF1PO
D5S818
D13S317
D7S820
5 6 7 8 9 9.1 9.3 10 10.1 10.3 11 12 13 14 15 16 17 18 19 20 21 22 22.2 23 23.2 24 24.2 25 25.2 26 27 28
– – – – – – – – – – – 0.0016a 0.0004a 0.0300 0.3996 0.3046 0.1992 0.0600 0.0036 0.0004a 0.0004a – – – – – – – – – – –
– – – – – – – – – – – – 0.0004 0.1908 0.0258 0.1854 0.2802 0.2350 0.0658 0.0100 0.0021a 0.0004a – – – – – – – – – –
– – – – – – – – – – – – – – – 0.0004a 0.0042 0.0263 0.0646 0.0913 0.1304 0.2038 0.0021 0.2083 0.0042a 0.1492 0.0004 0.0725 0.0021 0.0317 0.0067 0.0021a
0.0008 0.2167 0.2654 0.0633 0.4079 – 0.0354 0.0104 – – – – – – – – – – – – – – – – – – – – – – – –
– – – 0.4558 0.1104 – – 0.0308 – – 0.3629 0.0379 0.0012 0.0008 – – – – – – – – – – – – – – – – – –
– – 0.0104 0.0013a 0.0446 – – 0.2158 – – 0.2138 0.4179 0.0721 0.0179 0.0068 0.0004a – – – – – – – – – – – – – – – –
– – 0.0025 0.0071 0.0871 – – 0.1992 – – 0.2900 0.2371 0.1677 0.0092 0.0013 – – – – – – – – – – – – – – – – –
– – 0.0008a 0.2571 0.1258 – – 0.1200 – – 0.2313 0.2029 0.0483 0.0129 0.0008a – – – – – – – – – – – – – – – – –
– – 0.0033 0.1225 0.0446 0.0004a – 0.2175 0.0004a 0.0004a 0.3317 0.2379 0.0338 0.0071a 0.0004a – – – – – – – – – – – – – – – – –
Ob. H Ex. H PD P
0.736 0.704 0.852 0.343
0.784 0.788 0.921 0.570
0.857 0.857 0.962 0.165
0.707 0.711 0.876 0.240
0.628 0.646 0.814 0.079
0.728 0.726 0.886 0.686
0.778 0.785 0.919 0.330
0.812 0.807 0.934 0.922
0.784 0.768 0.908 0.964
Ob. H: observed heterozygosity, Ex. H: expected heterozygosity, PD: power of discrimination, P: Hardy–Weinberg equilibrium, exact test based on 100 batches. a These alleles were not found in previous survey of Japanese population [3].
References [1] M. Raymond, F. Rousset, GENEPOP (version 1.2): population genetics software for exact tests and ecumenicist, J. Heredity 86 (1995) 248–249. [2] R.A. Fisher, Standard calculation for evaluating a blood-group system, Heredity 5 (1951) 95–102.
[3] T. Yamamoto, R. Uchihi, H. Nozawa, X.L. Huang, Y.K. Leong, M. Tanaka, M. Mizutani, K. Tamaki, Y. Katsumata, Allele distribution at nine STR loci-D3S1358, vWA, FGA, TH01, TPOX, CSF1PO, D5S818, D13S317 and D7S820—in the Japanese population by multiplex PCR and capillary electrophoresis, J. Foren. Sci. 44 (1999) 167–170. [4] P. Lincoln, A. Carracedo, Publication of population data of human polymorphisms, Foren. Sci. Int. 110 (2000) 3–5.
Announcement of population data
Japanese population database for nine STR loci of the AmpF‘STR Profiler kit Kanako Yoshida*, Natsuko Mizuno, Koji Fujii, Hiroaki Senju, Kazumasa Sekiguchi, Kentaro Kasai, Hajime Sato National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan Received 21 November 2002; received in revised form 17 December 2002; accepted 18 December 2002
Abstract Allele frequencies for nine short tandem repeats (STR) loci: D3S1358, vWA, FGA, TH01, TPOX, CSF1PO, D5S818, D13S317 and D7S820 were determined in a Japanese population using the AmpF‘STR Profiler PCR amplification kit (Applied biosystems). # 2003 Elsevier Science Ireland Ltd. All rights reserved. Keywords: Short tandem repeats; AmpF‘STR Profiler PCR amplification kit; Japanese population
Population sample: Blood samples were collected from 1200 unrelated individuals in Japan. DNA extraction: DNA was isolated from the blood sample using MagNA Pure LC (Roche Diagnostic). The extracted DNA was quantified by spectrophotometric method. PCR amplification: Multiplex PCR was performed according to manufacture’s recommendation (AmpF‘STR Profiler PCR amplification kit: Applied biosystems) using 0.5–2 ng of template DNA. The samples were amplified using GeneAmp PCR System 9700 thermal cycler (Applied biosystems). Electrophoresis and typing: Amplified products were electrophoresed on an ABI PRISM 310 capillary electrophoresis and were analyzed using Gene Scan analysis software (version 3.1) and genotyper software (version 2.5). Alleles were designated by comparison with the allelic
ladder marker contained in the kit according to the AmpF‘STR Use’s Manual. Result: See Table 1. Analysis of data: Statistical test for fit to Hardy–Weinberg equilibrium expectations was performed using the computer program GENEPOP software (version 3.3) [1]. Power of discrimination was calculated following Fisher’s method [2]. Other remarks: Another information on Japanese population samples, which were collected from 206 Japanese, can be found in the previous report [3]. From 1200 samples analyzed in this study, we can find many alleles, which were not reported in the previous report of 206 Japanese population samples [3] (Table 1). This paper follows the guidelines for publication of population data by the journal [4].
* Corresponding author. Tel.: þ81-4-7135-8001; fax: þ81-4-7133-9159. E-mail address: [email protected] (K. Yoshida).
0379-0738/03/$ – see front matter # 2003 Elsevier Science Ireland Ltd. All rights reserved. doi:10.1016/S0379-0738(03)00008-2
K. Yoshida et al. / Forensic Science International 132 (2003) 166–167
167
Table 1 The distribution of allele frequencies at nine STR loci in a Japanese population (n ¼ 1200) D3S1358
vWA
FGA
TH01
TPOX
CSF1PO
D5S818
D13S317
D7S820
5 6 7 8 9 9.1 9.3 10 10.1 10.3 11 12 13 14 15 16 17 18 19 20 21 22 22.2 23 23.2 24 24.2 25 25.2 26 27 28
– – – – – – – – – – – 0.0016a 0.0004a 0.0300 0.3996 0.3046 0.1992 0.0600 0.0036 0.0004a 0.0004a – – – – – – – – – – –
– – – – – – – – – – – – 0.0004 0.1908 0.0258 0.1854 0.2802 0.2350 0.0658 0.0100 0.0021a 0.0004a – – – – – – – – – –
– – – – – – – – – – – – – – – 0.0004a 0.0042 0.0263 0.0646 0.0913 0.1304 0.2038 0.0021 0.2083 0.0042a 0.1492 0.0004 0.0725 0.0021 0.0317 0.0067 0.0021a
0.0008 0.2167 0.2654 0.0633 0.4079 – 0.0354 0.0104 – – – – – – – – – – – – – – – – – – – – – – – –
– – – 0.4558 0.1104 – – 0.0308 – – 0.3629 0.0379 0.0012 0.0008 – – – – – – – – – – – – – – – – – –
– – 0.0104 0.0013a 0.0446 – – 0.2158 – – 0.2138 0.4179 0.0721 0.0179 0.0068 0.0004a – – – – – – – – – – – – – – – –
– – 0.0025 0.0071 0.0871 – – 0.1992 – – 0.2900 0.2371 0.1677 0.0092 0.0013 – – – – – – – – – – – – – – – – –
– – 0.0008a 0.2571 0.1258 – – 0.1200 – – 0.2313 0.2029 0.0483 0.0129 0.0008a – – – – – – – – – – – – – – – – –
– – 0.0033 0.1225 0.0446 0.0004a – 0.2175 0.0004a 0.0004a 0.3317 0.2379 0.0338 0.0071a 0.0004a – – – – – – – – – – – – – – – – –
Ob. H Ex. H PD P
0.736 0.704 0.852 0.343
0.784 0.788 0.921 0.570
0.857 0.857 0.962 0.165
0.707 0.711 0.876 0.240
0.628 0.646 0.814 0.079
0.728 0.726 0.886 0.686
0.778 0.785 0.919 0.330
0.812 0.807 0.934 0.922
0.784 0.768 0.908 0.964
Ob. H: observed heterozygosity, Ex. H: expected heterozygosity, PD: power of discrimination, P: Hardy–Weinberg equilibrium, exact test based on 100 batches. a These alleles were not found in previous survey of Japanese population [3].
References [1] M. Raymond, F. Rousset, GENEPOP (version 1.2): population genetics software for exact tests and ecumenicist, J. Heredity 86 (1995) 248–249. [2] R.A. Fisher, Standard calculation for evaluating a blood-group system, Heredity 5 (1951) 95–102.
[3] T. Yamamoto, R. Uchihi, H. Nozawa, X.L. Huang, Y.K. Leong, M. Tanaka, M. Mizutani, K. Tamaki, Y. Katsumata, Allele distribution at nine STR loci-D3S1358, vWA, FGA, TH01, TPOX, CSF1PO, D5S818, D13S317 and D7S820—in the Japanese population by multiplex PCR and capillary electrophoresis, J. Foren. Sci. 44 (1999) 167–170. [4] P. Lincoln, A. Carracedo, Publication of population data of human polymorphisms, Foren. Sci. Int. 110 (2000) 3–5.