- Email: [email protected]
Population database on nine STR loci of the AmpFℓSTR Profiler kit in Koreans
Legal Medicine 8 (2006) 55–57 www.elsevier.com/locate/legalmed
Announcement of Population Data
Population database on nine STR loci of the AmpF[STR Profiler kit in Koreans Nam Soo Choa,*, Gu-Hyun Kanga, Sang-Yong Leea, Il-Hyun Parkb, Joong-Seok Seoa a
Department of Forensic Medicine, Central District Office, National Institute of Scientific Investigation, Daejeon 305-348, South Korea b Department of Biochemistry, Chungnam National University, Daejeon 305-764, South Korea Received 14 May 2005; received in revised form 4 August 2005; accepted 19 August 2005 Available online 6 October 2005
Abstract Allele frequencies for nine STR loci included in the AmpF[STR Profiler Kit (D3S1358, vWA, FGA, TH01, TPOX, CSF1PO, D5S818, D13S317 and D7S820), were obtained from a sample of 1206 unrelated individuals living in the central region of Korea. q 2005 Elsevier Ireland Ltd. All rights reserved. Keywords: Short tandem repeats (STRs); Allele frequency; AmpF[STR Profiler; Korean
1. Population DNA samples were obtained from 1206 unrelated, randomly selected individuals from criminal cases in the central region of Korea.
2. DNA Extraction Genomic DNA was isolated by the standard method of Phenol–chloroform procedure. The extracted DNA was quantified fluorimetrically or using the QuantiBlot kit (PE, Foster City, Calif.) with chemilumiescence detection.
The PCR products were injected for 5 s, and electrophoresis was performed at 15 kV using Performance Optimized Polymer (POPe4, Applied Biosystems) at 60 8C in a 47 cm capillary. GeneScan collection and analysis software packages were utilized for data collection and size estimation of the fluorescent labeled DNA fragments. Genotyper software (version 3.7) was used for automated genotyping of the samples.
4. Results See Table 1.
5. Analysis of data 3. PCR and typing Approximately 1–2 ng target DNA was amplified with the AmpF[STR Profiler Amplification kit (Applied Biosystems, Foster City, USA) according to the manufacturer’s instructions. Amplified products of PCR were subjected to capillary electrophoresis on an ABI PRISM 310 Genetic Analyzer instrument (Applied Biosystems, Foster City, CA).
Statistical analysis was performed using the Genetic Data Analysis Software, version 1.0 d16c (http://lewis.eeb. uconn.edu/lewishome/gda.html) [1]. Results were considered to be significant at P! 0.05. Power of discrimination was calculated following Fisher’s method [2].
6. Other remarks * Corresponding author. Tel.: C82 042 862 8072; fax: C82 042 862 8074. E-mail address: [email protected] (N.S. Cho).
1344-6223/$ - see front matter q 2005 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.legalmed.2005.08.004
The observed heterozygosity (OH) ranges from 0.6302 (TPOX) to 0.8599 (FGA). All loci were found to be no
56
N.S. Cho et al. / Legal Medicine 8 (2006) 55–57
Table 1 The distribution of allele frequencies at nine STR loci in a Korean population (nZ1206) Allele
D3S1358
vWA
FGA
TH01
TPOX
CSF1PO
D5S818
D13S317
D7S820
6 7 8 8.1 9 9.1 9.3 10 10.1 11 11.1 12 12.3 13 14 15 16 17 18 19 20 20.2 21 21.2 22 22.2 23 23.2 24 24.2 25 25.2 26 26.2 27 28 Hob Hex PD PI *P **P
0.0050 0.0004 0.0481 0.3947 0.2832 0.2011 0.0647 0.0025 0.0004 0.7181 0.7174 0.8685 0.1315 0.1372 0.0737
– – – – – – – – – – – 0.0004 – 0.0012 0.2123 0.0299 0.1878 0.2865 0.1866 0.0767 0.0166
– – – – – – – – – – – – – – – – – 0.0041 0.0240 0.0576 0.0614 0.0004 0.1119 0.0025 0.1799 0.0037 0.2301 0.0066 0.1596 0.0046 0.1003 0.0008 0.0427 0.0004 0.0079 0.0012 0.8599 0.8573 0.9639 0.0361 0.8992 0.9599
0.1592 0.2500 0.0448 – 0.4938 – 0.0390 0.0120 – 0.0012 – – – – – – – – – – – – – – – – – – – – – – – – – – 0.6418 0.6649 0.8430 0.1570 0.6542 0.6155
– 0.0004a 0.4726 – 0.1169 – – 0.0269 – 0.3570 – 0.0224 – 0.0033 0.0004a – – – – – – – – – – – – – – – – – – – – – 0.6302 0.6345 0.7973 0.2027 0.4723 0.3816
– 0.0025 0.0012 – 0.0456 – – 0.2533 – 0.2421 – 0.3653 0.0004a 0.0763 0.0124 0.0008 – – – – – – – – – – – – – – – – – – – – 0.7330 0.7360 0.8867 0.1133 0.7026 0.8694
– 0.0120 0.0079 – 0.0949 – – 0.2044 – 0.3093 – 0.2090 – 0.1517 0.0095 0.0012 – – – – – – – – – – – – – – – – – – – – 0.8035 0.7869 0.9207 0.0793 0.5653 0.7192
0.0004 0.0012 0.2658 – 0.1410 – – 0.1405 – 0.2334 – 0.1741 – 0.0340 0.0079 0.0017 – – – – – – – – – – – – – – – – – – – – 0.7877 0.8041 0.9334 0.0666 0.1089 0.5088
– 0.0050 0.1352 0.0008a 0.0585 0.0008a – 0.1721 0.0012a 0.3677 0.0004a 0.2214 – 0.0340 0.0025 0.0004 – – – – – – – – – – – – – – – – – – – – 0.7769 0.7636 0.9081 0.0919 0.2771 0.7444
0.0017 0.0004a
0.7985 0.7961 0.9275 0.0725 0.7326 0.8976
Hob, observed heterozygosity; Hex, expected heterozygosity; PD, power of discrimination; PI, power of Identity; *P, Hardy–Weinberg equilibrium, c2 test; **P, Hardy-Weinberg equilibrium, exact test based on 10,000 shufflings. a These alleles were not found in previous survey of Korean population [3–7].
deviations from Hardy-Weinberg expectations (PO0.05). For forensic testing, the power of discrimination (PD) index ranged from 0.7973 at TPOX to 0.9639 at FGA and the combined power of discrimination of the nineplex was 0.999999999399. The combination of these nine STR systems is a powerful tool for forensic identification and paternity resting. By comparison of the allele frequencies with other Korean population studies, no significant differences were found. But at the CSF1PO locus, one 12.3 allele and at the D7S820 locus, two 8.1 allele, two 9.1 allele, three 10.1 allele and one 11.1 allele were observed that have not yet been
reported in other Korean population studies [3–7]. In other Asian populations, 9.1, 9.2, 9.3, 10.1, 10.3 alleles have been detected [8,9]. Recent developments in fluorescent dyes and capillary electrophoresis technology made it possible to determine the size of STR alleles accurately [10,11]. For accurate analysis, we performed re-extraction and reamplification procedure on nine samples additionally. Most of the commercially available PCR kits for STR typing contain allelic ladders. However, the high sequence variability of STR loci can occur but may not be detected easily. So determination and identification of allele may be
N.S. Cho et al. / Legal Medicine 8 (2006) 55–57
more difficult especially when the possibility of variants is not considered.
References [1] Lewis PO, Zaykin DD. Genetic data analysis: computer program for the analysis of allelic data, Version 1.0(d16c). [2] Fisher RA. Standard calculations for evaluating a blood group system. Heredity 1951;5:95–102. [3] Han GR, Lee YW, Lee HL, Kim SM, Ku TW, Kang IH, et al. A Korean population study of the nine STR loci FGA, VWA, D3S1358, D18S51, D21S11, D8S1179, D7S820, D13S317 and D5S818. Int J Legal Med 2000;114(1–2):41–4. [4] Han MS, Kang PW, Choi DH, Lee YH, Choi SK, Yoon SR, et al. Korean population genetic data for eleven STR loci. Forensic Sci Int 2001;123(2–3):230–1. [5] Han MS, Hong SB, Choi SK, Cho YH, Jin HJ, Kwak KD, et al. Population genetics data on thirteen CODIS short tandem repeat loci in Koreans. Kor J Genetics 2002;24:83–7.
57
[6] Kim YL, Hwang JY, Kim YJ, Lee S, Chung NG, Goh HG. Allele frequencies of 15 STR loci using AmpF/STR identifiler kit in a Korean population. Forensic Sci Int 2003;136(1–3): 92–5. [7] Cho NS, Hwang JH, Lee YA, Park IH. Population genetics of nine STR loci: TH01, TPOX, CSF1PO, vWA, FESFPS, F13A01, D13S317, D7S820 and D16S539 in a Korean population. Forensic Sci Int 2003;137(1):97–9. [8] Yoshida K, Mizuno N, Fujii K, Senju H, Sekiguchi K, Kasai K, et al. Japanese population database for nine STR loci of the AmpFlSTR profiler kit. Forensic Sci Int 2003;132:166–7. [9] Hu SP, Yu XJ, Liu JW, Cai KL. Analysis of STR polymorphisms in the Chao Shan population in South China. Forensic Sci Int 2005;147: 93–5. [10] Yamamoto T, Kojima T, Nozawa H, Huang XL, Ohtaki H, Uchihi R, et al. A rapid typing system at three STR loci from bloodstains using a simple DNA extraction kit and capillary electrophoresis. Jpn J Leg Med 1997;51:396–400. [11] Wenz H, Robertson JM, Menchen S, Oaks F, Demorest DM, Scheibler D, et al. High-precision genotyping by denaturing capillary electrophoresis. Genome Res 1998;8:69–80.
Announcement of Population Data
Population database on nine STR loci of the AmpF[STR Profiler kit in Koreans Nam Soo Choa,*, Gu-Hyun Kanga, Sang-Yong Leea, Il-Hyun Parkb, Joong-Seok Seoa a
Department of Forensic Medicine, Central District Office, National Institute of Scientific Investigation, Daejeon 305-348, South Korea b Department of Biochemistry, Chungnam National University, Daejeon 305-764, South Korea Received 14 May 2005; received in revised form 4 August 2005; accepted 19 August 2005 Available online 6 October 2005
Abstract Allele frequencies for nine STR loci included in the AmpF[STR Profiler Kit (D3S1358, vWA, FGA, TH01, TPOX, CSF1PO, D5S818, D13S317 and D7S820), were obtained from a sample of 1206 unrelated individuals living in the central region of Korea. q 2005 Elsevier Ireland Ltd. All rights reserved. Keywords: Short tandem repeats (STRs); Allele frequency; AmpF[STR Profiler; Korean
1. Population DNA samples were obtained from 1206 unrelated, randomly selected individuals from criminal cases in the central region of Korea.
2. DNA Extraction Genomic DNA was isolated by the standard method of Phenol–chloroform procedure. The extracted DNA was quantified fluorimetrically or using the QuantiBlot kit (PE, Foster City, Calif.) with chemilumiescence detection.
The PCR products were injected for 5 s, and electrophoresis was performed at 15 kV using Performance Optimized Polymer (POPe4, Applied Biosystems) at 60 8C in a 47 cm capillary. GeneScan collection and analysis software packages were utilized for data collection and size estimation of the fluorescent labeled DNA fragments. Genotyper software (version 3.7) was used for automated genotyping of the samples.
4. Results See Table 1.
5. Analysis of data 3. PCR and typing Approximately 1–2 ng target DNA was amplified with the AmpF[STR Profiler Amplification kit (Applied Biosystems, Foster City, USA) according to the manufacturer’s instructions. Amplified products of PCR were subjected to capillary electrophoresis on an ABI PRISM 310 Genetic Analyzer instrument (Applied Biosystems, Foster City, CA).
Statistical analysis was performed using the Genetic Data Analysis Software, version 1.0 d16c (http://lewis.eeb. uconn.edu/lewishome/gda.html) [1]. Results were considered to be significant at P! 0.05. Power of discrimination was calculated following Fisher’s method [2].
6. Other remarks * Corresponding author. Tel.: C82 042 862 8072; fax: C82 042 862 8074. E-mail address: [email protected] (N.S. Cho).
1344-6223/$ - see front matter q 2005 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.legalmed.2005.08.004
The observed heterozygosity (OH) ranges from 0.6302 (TPOX) to 0.8599 (FGA). All loci were found to be no
56
N.S. Cho et al. / Legal Medicine 8 (2006) 55–57
Table 1 The distribution of allele frequencies at nine STR loci in a Korean population (nZ1206) Allele
D3S1358
vWA
FGA
TH01
TPOX
CSF1PO
D5S818
D13S317
D7S820
6 7 8 8.1 9 9.1 9.3 10 10.1 11 11.1 12 12.3 13 14 15 16 17 18 19 20 20.2 21 21.2 22 22.2 23 23.2 24 24.2 25 25.2 26 26.2 27 28 Hob Hex PD PI *P **P
0.0050 0.0004 0.0481 0.3947 0.2832 0.2011 0.0647 0.0025 0.0004 0.7181 0.7174 0.8685 0.1315 0.1372 0.0737
– – – – – – – – – – – 0.0004 – 0.0012 0.2123 0.0299 0.1878 0.2865 0.1866 0.0767 0.0166
– – – – – – – – – – – – – – – – – 0.0041 0.0240 0.0576 0.0614 0.0004 0.1119 0.0025 0.1799 0.0037 0.2301 0.0066 0.1596 0.0046 0.1003 0.0008 0.0427 0.0004 0.0079 0.0012 0.8599 0.8573 0.9639 0.0361 0.8992 0.9599
0.1592 0.2500 0.0448 – 0.4938 – 0.0390 0.0120 – 0.0012 – – – – – – – – – – – – – – – – – – – – – – – – – – 0.6418 0.6649 0.8430 0.1570 0.6542 0.6155
– 0.0004a 0.4726 – 0.1169 – – 0.0269 – 0.3570 – 0.0224 – 0.0033 0.0004a – – – – – – – – – – – – – – – – – – – – – 0.6302 0.6345 0.7973 0.2027 0.4723 0.3816
– 0.0025 0.0012 – 0.0456 – – 0.2533 – 0.2421 – 0.3653 0.0004a 0.0763 0.0124 0.0008 – – – – – – – – – – – – – – – – – – – – 0.7330 0.7360 0.8867 0.1133 0.7026 0.8694
– 0.0120 0.0079 – 0.0949 – – 0.2044 – 0.3093 – 0.2090 – 0.1517 0.0095 0.0012 – – – – – – – – – – – – – – – – – – – – 0.8035 0.7869 0.9207 0.0793 0.5653 0.7192
0.0004 0.0012 0.2658 – 0.1410 – – 0.1405 – 0.2334 – 0.1741 – 0.0340 0.0079 0.0017 – – – – – – – – – – – – – – – – – – – – 0.7877 0.8041 0.9334 0.0666 0.1089 0.5088
– 0.0050 0.1352 0.0008a 0.0585 0.0008a – 0.1721 0.0012a 0.3677 0.0004a 0.2214 – 0.0340 0.0025 0.0004 – – – – – – – – – – – – – – – – – – – – 0.7769 0.7636 0.9081 0.0919 0.2771 0.7444
0.0017 0.0004a
0.7985 0.7961 0.9275 0.0725 0.7326 0.8976
Hob, observed heterozygosity; Hex, expected heterozygosity; PD, power of discrimination; PI, power of Identity; *P, Hardy–Weinberg equilibrium, c2 test; **P, Hardy-Weinberg equilibrium, exact test based on 10,000 shufflings. a These alleles were not found in previous survey of Korean population [3–7].
deviations from Hardy-Weinberg expectations (PO0.05). For forensic testing, the power of discrimination (PD) index ranged from 0.7973 at TPOX to 0.9639 at FGA and the combined power of discrimination of the nineplex was 0.999999999399. The combination of these nine STR systems is a powerful tool for forensic identification and paternity resting. By comparison of the allele frequencies with other Korean population studies, no significant differences were found. But at the CSF1PO locus, one 12.3 allele and at the D7S820 locus, two 8.1 allele, two 9.1 allele, three 10.1 allele and one 11.1 allele were observed that have not yet been
reported in other Korean population studies [3–7]. In other Asian populations, 9.1, 9.2, 9.3, 10.1, 10.3 alleles have been detected [8,9]. Recent developments in fluorescent dyes and capillary electrophoresis technology made it possible to determine the size of STR alleles accurately [10,11]. For accurate analysis, we performed re-extraction and reamplification procedure on nine samples additionally. Most of the commercially available PCR kits for STR typing contain allelic ladders. However, the high sequence variability of STR loci can occur but may not be detected easily. So determination and identification of allele may be
N.S. Cho et al. / Legal Medicine 8 (2006) 55–57
more difficult especially when the possibility of variants is not considered.
References [1] Lewis PO, Zaykin DD. Genetic data analysis: computer program for the analysis of allelic data, Version 1.0(d16c). [2] Fisher RA. Standard calculations for evaluating a blood group system. Heredity 1951;5:95–102. [3] Han GR, Lee YW, Lee HL, Kim SM, Ku TW, Kang IH, et al. A Korean population study of the nine STR loci FGA, VWA, D3S1358, D18S51, D21S11, D8S1179, D7S820, D13S317 and D5S818. Int J Legal Med 2000;114(1–2):41–4. [4] Han MS, Kang PW, Choi DH, Lee YH, Choi SK, Yoon SR, et al. Korean population genetic data for eleven STR loci. Forensic Sci Int 2001;123(2–3):230–1. [5] Han MS, Hong SB, Choi SK, Cho YH, Jin HJ, Kwak KD, et al. Population genetics data on thirteen CODIS short tandem repeat loci in Koreans. Kor J Genetics 2002;24:83–7.
57
[6] Kim YL, Hwang JY, Kim YJ, Lee S, Chung NG, Goh HG. Allele frequencies of 15 STR loci using AmpF/STR identifiler kit in a Korean population. Forensic Sci Int 2003;136(1–3): 92–5. [7] Cho NS, Hwang JH, Lee YA, Park IH. Population genetics of nine STR loci: TH01, TPOX, CSF1PO, vWA, FESFPS, F13A01, D13S317, D7S820 and D16S539 in a Korean population. Forensic Sci Int 2003;137(1):97–9. [8] Yoshida K, Mizuno N, Fujii K, Senju H, Sekiguchi K, Kasai K, et al. Japanese population database for nine STR loci of the AmpFlSTR profiler kit. Forensic Sci Int 2003;132:166–7. [9] Hu SP, Yu XJ, Liu JW, Cai KL. Analysis of STR polymorphisms in the Chao Shan population in South China. Forensic Sci Int 2005;147: 93–5. [10] Yamamoto T, Kojima T, Nozawa H, Huang XL, Ohtaki H, Uchihi R, et al. A rapid typing system at three STR loci from bloodstains using a simple DNA extraction kit and capillary electrophoresis. Jpn J Leg Med 1997;51:396–400. [11] Wenz H, Robertson JM, Menchen S, Oaks F, Demorest DM, Scheibler D, et al. High-precision genotyping by denaturing capillary electrophoresis. Genome Res 1998;8:69–80.