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Allele frequencies of 10 STR loci in Koreans
Forensic Science International 140 (2004) 133–135
Announcement of population data
Allele frequencies of 10 STR loci in Koreans Chang Ho Shin, Philip Jang, Kyeong Man Hong, Moon Kee Paik* Department of Biochemistry, Wonkwang University College of Medicine, 344-2 Shinyong-Dong, Iksan 570-749, South Korea Received 15 April 2003; received in revised form 3 October 2003; accepted 28 November 2003
Abstract Allele frequencies for the 10 STR loci, D6S1043, D9S925, D7S821, D4S2368, D21S2055, GATA193A07, D12S391, D10S2326, D15S822 and D18S51 were obtained from a sample of 217–310 unrelated Koreans. In this study, 2 out of the 10 loci did not meet Hardy–Weinberg expectation. The combined probability of identity for 10 loci tested was 4:93 1014 . # 2003 Elsevier Ireland Ltd. All rights reserved. Keywords: Short tandem repeat (STR); Population data; Korean
1. Population
polyacrylamide gel. Allele assignment was performed after sequencing of the alleles.
Unrelated healthy volunteer donors born in Korea. 5. Results 2. DNA extraction See Tables 1 and 2. Genomic DNA was isolated from blood samples by Chelex extraction method [1]. 6. Analysis data 3. DNA amplification PCR amplifications were performed by modified primer sequences according GeneBank information (http:// www.gdb.org) using a GeneAmp PCR System 2400 (Applied Biosystems, Foster City, CA, USA).
Statistical parameters were evaluated with the genetic data analysis (GDA, http://lewis.eeb.uconn.edu/lewishome/ software.html) [2] and PowerStats software packages (http:// www.promega.com/geneticidtools/default.htm) [3].
7. Other remarks 4. Typing STR analysis was performed on ABI Prism 3100 Genetic Analyzer (Applied Biosystems, Foster City, CA, USA) using Genotyper software, and silver staining with denaturing * Corresponding author. Tel.: þ82-63-850-6795; fax: þ82-63-854-1459. E-mail address: [email protected] (M.K. Paik).
As shown Table 2, two loci, D15S822 and D12S391 were not met Hardy–Weinberg expectations based on the Fisher’s exact test. The observed heterozygosity showed >70% in all loci tested, and it showed the value of 0.99995 for combined exclusion power and the value of 2:01 104 for typical paternity index. Also, the calculated probability of identity was 4:93 1014 . In Table 3, statistical values of Korean for D12S391 and D18S51 locus showed the very similar to Japanese and Chinese data in other ethnic groups. The
0379-0738/$ – see front matter # 2003 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.forsciint.2003.11.027
134
C.H. Shin et al. / Forensic Science International 140 (2004) 133–135
Table 1 Parameters and repeat sequence structure of 10 STR loci Fragment length
Repeat size
D4S2368
307–331
4
D7S821
218–254
D9S925
Number of detected allele
Repeat sequence
Primers of forward and reverse
7
CTAT
4
9
TGTC/TATC
172–204
4
9
ATAG/GTAG
D6S1043
102–149
4
13
AGAT/ACAT
D21S2055
96–180
4
21
AGAT
D12S391
199–271
4
14
AGAT/AGAC
GATA193A07
295–347
4
11
AGAT
D10S2326
103–187
4
16
AGAT/AG/AGAT
D15S822
221–293
4
18
AGAC
D18S51
319–349
4
18
AGAA
F: 50 -GAGCCAGACCTTGTCTCAAA-30 R: 50 -AAGGGATTTTAGGAACTGATACG-30 F: 50 -ACAAAACCCCAAGTACGTGA-30 R: 50 -TATGACAGGCATCTGGGAGT-30 F: 50 -TGTGAGCCAAGGCCTTATAG-30 R: 50 -GTCTGGGTTCTCCAAAGAAA-30 F: 50 -CAAGGATGGGTGGATCAATA-30 R: 50 -TTGTATGAGCCACTTCCCAT-30 F: 50 -CACAACCAATTGGCTATCTTCG-30 R: 50 -TGCTAAATCACTTGGATCAGAT-30 F: 50 -TGGATCAATCGATGCATTGC-30 R: 50 -AGGCTTTTACACCTGCACTG-30 F: 50 -TCCCTGTGGAATCTTGTATC-30 R: 50 -GTCCTGCCTCATAGTCTTAC-30 F: 50 -TGCTTATATATCCAGCTAATATAAATC-30 R: 50 -GCATGAGGATTATTTTCCCC-30 F: 50 -ATTCTCACCTCTGCTTCTCG-30 R: 50 -AGAGATTATCCACTCTCAGG-3’ F: 50 -GAAACCCGAGTACCAGCATG-30 R: 50 -CAGCCATGTTGATGCCACAG-30
Table 2 Allele frequencies of 10 STR loci in Koreans Allele
D4S2368 (n ¼ 310)
8 9 10 11 12 13 14 15 16 17 18 19 20 21 21.3 22 23 24 25 26 27 28 29 30 31 32 33 34
0.010 0.048 0.181 0.377 0.323 0.56 0.005
D9S925 (n ¼ 310)
0.006 0.010 0.140 0.202 0.334 0.218 0.085 0.003 0.002
D7S821 (n ¼ 310)
0.011 0.100 0.079 0.189 0.277 0.224 0.094 0.024 0.002
D6S1043 (n ¼ 310)
0.024 0.097 0.115 0.145 0.145 0.018 0.002 0.052 0.158 0.179 0.052 0.008 0.006
D10S2326 D15S822 (n ¼ 217) (n ¼ 217)
0.002 0.007 0.014 0.050 0.141 0.170 0.164 0.159 0.095 0.064 0.064 0.020 0.020 0.016
0.016 0.016 0.143 0.220 0.084 0.020
0.002 0.036 0.150 0.118 0.043 0.036 0.023 0.059 0.030 0.002
D18S51 (n ¼ 217)
0.002 0.005 0.020 0.095 0.166 0.184 0.148 0.050 0.045 0.080 0.052
0.007 0.002 0.002 0.002
D21S2055 D12S391 (n ¼ 217) (n ¼ 217)
GATA193A07 (n ¼ 217)
0.014 0.105 0.014 0.005 0.002 0.011 0.005 0.025 0.168 0.214 0.041 0.039 0.036 0.023 0.027 0.039 0.048 0.077 0.068 0.025 0.016
0.018 0.002 0.091 0.268 0.170 0.132 0.120 0.070 0.066 0.025 0.020 0.009 0.005
0.016 0.280 0.295 0.218 0.064 0.034 0.043 0.023 0.020 0.005
0.002 0.002
C.H. Shin et al. / Forensic Science International 140 (2004) 133–135
135
Table 2 (Continued ) Allele 35 36 37 38 39 40 41 Het PD PIC PE PI P
D4S2368 (n ¼ 310)
0.700 0.871 0.666 0.428 1.667 0.305
D9S925 (n ¼ 310)
0.755 0.915 0.739 0.518 2.039 0.820
D7S821 (n ¼ 310)
0.806 0.940 0.876 0.611 2.583 0.651
D6S1043 (n ¼ 310)
0.881 0.966 0.858 0.756 4.189 0.052
D10S2326 D15S822 (n ¼ 217) (n ¼ 217)
0.866 0.970 0.867 0.727 3.741 0.167
0.043 0.039 0.032 0.009 0.009 0.011 0.009 0.820 0.971 0.878 0.637 2.782 0.000
D18S51 (n ¼ 217)
D21S2055 D12S391 (n ¼ 217) (n ¼ 217)
GATA193A07 (n ¼ 217)
0.848 0.970 0.866 0.691 3.288 0.175
0.848 0.976 0.884 0.691 3.288 0.116
0.777 0.920 0.748 0.504 1.973 0.078
0.797 0.956 0.832 0.594 2.466 0.003
Het: observed heterozygosity, PD: power of discrimination, PIC: polymorphism information content, PE: power of exclusion PI: paternity index, P: HWE, exact test based on 10000 shufflings.
Table 3 Comparison of the polymorphic information content, power of exclusion and typical paternity index values for D12S391 and D18S51 locus in the various ethnic groups D12S391 locus
PIC
PE
PI
This work German Puna Thai Chinese Japanese Vietnamese General Asian
0.83 0.87 0.69 0.84 0.81 0.81
0.594 0.786 0.489 0.722 0.689 0.695
2.47 4.77 1.91 3.67 3.26 3.33
distribution patterns of alleles in the D12S391 and D18S51 loci were very similar to other Asian data, especially Japanese [4–9]. This paper follows the guidelines for publication of population data requested by the journal [10]. Acknowledgements This work was supported by a grant from the Wonkwang University in 2002. References [1] P.S. Walsh, D.A. Metzger, R. Higuchi, Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material, Biotechniques 10 (1991) 506–518. [2] P.O. Lewis, D.Zaykin, Genetic Data Analysis, version 1.0. [3] Promega Corporation, PowerStats version 1.2.
D18S51 locus
PIC
PE
PI
0.87
0.691
3.29
0.85 0.83 0.82 0.86
0.742 0.707 0.599 0.844
3.96 3.47 2.50 6.53
[4] W. Waiyawuth, L. Zhang, C. Rittner, P.M. Peter, M. Schneider, Genetic analysis of the short tandem repeat system D12S391 in the German and three Asian populations, Forensic Sci. Int. 94 (1998) 25–31. [5] W.K. Fung, J. Ye, L. Hu, X. Zhao, B. Liu, D.M. Wong, M.Y. Law, Allele frequencies for nine STR loci in Beijing, Chinese, Forensic Sci. Int. 121 (2001) 207–209. [6] K.B. Lim, N.H. Jeevan, P. Jaya, M.I. Othman, Y.H. Lee, STR data for the AmpFlSTR Profiler loci from the three main ethnic population groups (Malay, Chinese and Indian) in Malaysia, Forensic Sci. Int. 119 (2001) :109–112. [7] B. Budowle, B. Shea, S. Niezgoda, R. Chakraborty, CODIS STR loci data from 41 sample populations, J. Forensic Sci. 46 (2001) :453–89. [8] M. Hashiyada, Y. Itakura, T. Nagashima, M. Nata, M. Funayama, Polymorphism of 17 STRs by multiplex analysis in Japanese population, Forensic Sci. Int. 133 (2003) 250–253. [9] X. Wang, T. Sawaguchi, A. Sawagushi, Analysis of STR polymorphisms in the northeast Chinese population, Forensic Sci. Int. 132 (2003) 161–163. [10] P. Lincoln, A. Carracedo, Publication data of human polymorphisms, Forensic Sci. Int. 110 (2000) 3–5.
Announcement of population data
Allele frequencies of 10 STR loci in Koreans Chang Ho Shin, Philip Jang, Kyeong Man Hong, Moon Kee Paik* Department of Biochemistry, Wonkwang University College of Medicine, 344-2 Shinyong-Dong, Iksan 570-749, South Korea Received 15 April 2003; received in revised form 3 October 2003; accepted 28 November 2003
Abstract Allele frequencies for the 10 STR loci, D6S1043, D9S925, D7S821, D4S2368, D21S2055, GATA193A07, D12S391, D10S2326, D15S822 and D18S51 were obtained from a sample of 217–310 unrelated Koreans. In this study, 2 out of the 10 loci did not meet Hardy–Weinberg expectation. The combined probability of identity for 10 loci tested was 4:93 1014 . # 2003 Elsevier Ireland Ltd. All rights reserved. Keywords: Short tandem repeat (STR); Population data; Korean
1. Population
polyacrylamide gel. Allele assignment was performed after sequencing of the alleles.
Unrelated healthy volunteer donors born in Korea. 5. Results 2. DNA extraction See Tables 1 and 2. Genomic DNA was isolated from blood samples by Chelex extraction method [1]. 6. Analysis data 3. DNA amplification PCR amplifications were performed by modified primer sequences according GeneBank information (http:// www.gdb.org) using a GeneAmp PCR System 2400 (Applied Biosystems, Foster City, CA, USA).
Statistical parameters were evaluated with the genetic data analysis (GDA, http://lewis.eeb.uconn.edu/lewishome/ software.html) [2] and PowerStats software packages (http:// www.promega.com/geneticidtools/default.htm) [3].
7. Other remarks 4. Typing STR analysis was performed on ABI Prism 3100 Genetic Analyzer (Applied Biosystems, Foster City, CA, USA) using Genotyper software, and silver staining with denaturing * Corresponding author. Tel.: þ82-63-850-6795; fax: þ82-63-854-1459. E-mail address: [email protected] (M.K. Paik).
As shown Table 2, two loci, D15S822 and D12S391 were not met Hardy–Weinberg expectations based on the Fisher’s exact test. The observed heterozygosity showed >70% in all loci tested, and it showed the value of 0.99995 for combined exclusion power and the value of 2:01 104 for typical paternity index. Also, the calculated probability of identity was 4:93 1014 . In Table 3, statistical values of Korean for D12S391 and D18S51 locus showed the very similar to Japanese and Chinese data in other ethnic groups. The
0379-0738/$ – see front matter # 2003 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.forsciint.2003.11.027
134
C.H. Shin et al. / Forensic Science International 140 (2004) 133–135
Table 1 Parameters and repeat sequence structure of 10 STR loci Fragment length
Repeat size
D4S2368
307–331
4
D7S821
218–254
D9S925
Number of detected allele
Repeat sequence
Primers of forward and reverse
7
CTAT
4
9
TGTC/TATC
172–204
4
9
ATAG/GTAG
D6S1043
102–149
4
13
AGAT/ACAT
D21S2055
96–180
4
21
AGAT
D12S391
199–271
4
14
AGAT/AGAC
GATA193A07
295–347
4
11
AGAT
D10S2326
103–187
4
16
AGAT/AG/AGAT
D15S822
221–293
4
18
AGAC
D18S51
319–349
4
18
AGAA
F: 50 -GAGCCAGACCTTGTCTCAAA-30 R: 50 -AAGGGATTTTAGGAACTGATACG-30 F: 50 -ACAAAACCCCAAGTACGTGA-30 R: 50 -TATGACAGGCATCTGGGAGT-30 F: 50 -TGTGAGCCAAGGCCTTATAG-30 R: 50 -GTCTGGGTTCTCCAAAGAAA-30 F: 50 -CAAGGATGGGTGGATCAATA-30 R: 50 -TTGTATGAGCCACTTCCCAT-30 F: 50 -CACAACCAATTGGCTATCTTCG-30 R: 50 -TGCTAAATCACTTGGATCAGAT-30 F: 50 -TGGATCAATCGATGCATTGC-30 R: 50 -AGGCTTTTACACCTGCACTG-30 F: 50 -TCCCTGTGGAATCTTGTATC-30 R: 50 -GTCCTGCCTCATAGTCTTAC-30 F: 50 -TGCTTATATATCCAGCTAATATAAATC-30 R: 50 -GCATGAGGATTATTTTCCCC-30 F: 50 -ATTCTCACCTCTGCTTCTCG-30 R: 50 -AGAGATTATCCACTCTCAGG-3’ F: 50 -GAAACCCGAGTACCAGCATG-30 R: 50 -CAGCCATGTTGATGCCACAG-30
Table 2 Allele frequencies of 10 STR loci in Koreans Allele
D4S2368 (n ¼ 310)
8 9 10 11 12 13 14 15 16 17 18 19 20 21 21.3 22 23 24 25 26 27 28 29 30 31 32 33 34
0.010 0.048 0.181 0.377 0.323 0.56 0.005
D9S925 (n ¼ 310)
0.006 0.010 0.140 0.202 0.334 0.218 0.085 0.003 0.002
D7S821 (n ¼ 310)
0.011 0.100 0.079 0.189 0.277 0.224 0.094 0.024 0.002
D6S1043 (n ¼ 310)
0.024 0.097 0.115 0.145 0.145 0.018 0.002 0.052 0.158 0.179 0.052 0.008 0.006
D10S2326 D15S822 (n ¼ 217) (n ¼ 217)
0.002 0.007 0.014 0.050 0.141 0.170 0.164 0.159 0.095 0.064 0.064 0.020 0.020 0.016
0.016 0.016 0.143 0.220 0.084 0.020
0.002 0.036 0.150 0.118 0.043 0.036 0.023 0.059 0.030 0.002
D18S51 (n ¼ 217)
0.002 0.005 0.020 0.095 0.166 0.184 0.148 0.050 0.045 0.080 0.052
0.007 0.002 0.002 0.002
D21S2055 D12S391 (n ¼ 217) (n ¼ 217)
GATA193A07 (n ¼ 217)
0.014 0.105 0.014 0.005 0.002 0.011 0.005 0.025 0.168 0.214 0.041 0.039 0.036 0.023 0.027 0.039 0.048 0.077 0.068 0.025 0.016
0.018 0.002 0.091 0.268 0.170 0.132 0.120 0.070 0.066 0.025 0.020 0.009 0.005
0.016 0.280 0.295 0.218 0.064 0.034 0.043 0.023 0.020 0.005
0.002 0.002
C.H. Shin et al. / Forensic Science International 140 (2004) 133–135
135
Table 2 (Continued ) Allele 35 36 37 38 39 40 41 Het PD PIC PE PI P
D4S2368 (n ¼ 310)
0.700 0.871 0.666 0.428 1.667 0.305
D9S925 (n ¼ 310)
0.755 0.915 0.739 0.518 2.039 0.820
D7S821 (n ¼ 310)
0.806 0.940 0.876 0.611 2.583 0.651
D6S1043 (n ¼ 310)
0.881 0.966 0.858 0.756 4.189 0.052
D10S2326 D15S822 (n ¼ 217) (n ¼ 217)
0.866 0.970 0.867 0.727 3.741 0.167
0.043 0.039 0.032 0.009 0.009 0.011 0.009 0.820 0.971 0.878 0.637 2.782 0.000
D18S51 (n ¼ 217)
D21S2055 D12S391 (n ¼ 217) (n ¼ 217)
GATA193A07 (n ¼ 217)
0.848 0.970 0.866 0.691 3.288 0.175
0.848 0.976 0.884 0.691 3.288 0.116
0.777 0.920 0.748 0.504 1.973 0.078
0.797 0.956 0.832 0.594 2.466 0.003
Het: observed heterozygosity, PD: power of discrimination, PIC: polymorphism information content, PE: power of exclusion PI: paternity index, P: HWE, exact test based on 10000 shufflings.
Table 3 Comparison of the polymorphic information content, power of exclusion and typical paternity index values for D12S391 and D18S51 locus in the various ethnic groups D12S391 locus
PIC
PE
PI
This work German Puna Thai Chinese Japanese Vietnamese General Asian
0.83 0.87 0.69 0.84 0.81 0.81
0.594 0.786 0.489 0.722 0.689 0.695
2.47 4.77 1.91 3.67 3.26 3.33
distribution patterns of alleles in the D12S391 and D18S51 loci were very similar to other Asian data, especially Japanese [4–9]. This paper follows the guidelines for publication of population data requested by the journal [10]. Acknowledgements This work was supported by a grant from the Wonkwang University in 2002. References [1] P.S. Walsh, D.A. Metzger, R. Higuchi, Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material, Biotechniques 10 (1991) 506–518. [2] P.O. Lewis, D.Zaykin, Genetic Data Analysis, version 1.0. [3] Promega Corporation, PowerStats version 1.2.
D18S51 locus
PIC
PE
PI
0.87
0.691
3.29
0.85 0.83 0.82 0.86
0.742 0.707 0.599 0.844
3.96 3.47 2.50 6.53
[4] W. Waiyawuth, L. Zhang, C. Rittner, P.M. Peter, M. Schneider, Genetic analysis of the short tandem repeat system D12S391 in the German and three Asian populations, Forensic Sci. Int. 94 (1998) 25–31. [5] W.K. Fung, J. Ye, L. Hu, X. Zhao, B. Liu, D.M. Wong, M.Y. Law, Allele frequencies for nine STR loci in Beijing, Chinese, Forensic Sci. Int. 121 (2001) 207–209. [6] K.B. Lim, N.H. Jeevan, P. Jaya, M.I. Othman, Y.H. Lee, STR data for the AmpFlSTR Profiler loci from the three main ethnic population groups (Malay, Chinese and Indian) in Malaysia, Forensic Sci. Int. 119 (2001) :109–112. [7] B. Budowle, B. Shea, S. Niezgoda, R. Chakraborty, CODIS STR loci data from 41 sample populations, J. Forensic Sci. 46 (2001) :453–89. [8] M. Hashiyada, Y. Itakura, T. Nagashima, M. Nata, M. Funayama, Polymorphism of 17 STRs by multiplex analysis in Japanese population, Forensic Sci. Int. 133 (2003) 250–253. [9] X. Wang, T. Sawaguchi, A. Sawagushi, Analysis of STR polymorphisms in the northeast Chinese population, Forensic Sci. Int. 132 (2003) 161–163. [10] P. Lincoln, A. Carracedo, Publication data of human polymorphisms, Forensic Sci. Int. 110 (2000) 3–5.