- Email: [email protected]
STR Identifiler kit in a Korean population
Forensic Science International 136 (2003) 92–95
Announcement of population data
Allele frequencies of 15 STR loci using AmpF/STR Identifiler kit in a Korean population Yoo-Li Kim, Ji-Yeon Hwang, Yoo-Jin Kim, Seok Lee, Nak-Gyun Chung, Hyun-Gyung Goh, Chun-Choo Kim, Dong-Wook Kim* Molecular Hematology Laboratory, Catholic Hematopoietic Stem Cell Transplantation Center, The Catholic University of Korea, 62 Youido-Dong, Youngdeungpo-Gu, Seoul 150-713, South Korea Received 21 May 2003; received in revised form 26 May 2003; accepted 27 May 2003
Abstract The genetic variations for 15 short tandem repeat (STR) loci D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA were performed on 231 unrelated Korean population using commercially available AmpF/STR Identifiler kit. # 2003 Elsevier Ireland Ltd. All rights reserved. Keywords: Short tandem repeat; AmpF/STR Identifiler; Korean population
Population: Two hundred thirty-one unrelated individuals living in Korea. Extraction: Genomic DNA was extracted using the High Pure PCR Template Preparation Kit (Roche, Mannheim, Germany). PCR: Multiplex PCR using 1–2 ng target DNA was performed with the AmpF/STR Identifiler PCR Amplification kit (PE Applied Biosystems, Foster City, CA, USA) according to the manufacturer’s instructions. Typing: ABI Prism 310 Genetic Analyzer (PE Applied Biosystems). Results: See Table 1. Quality control: Kit controls. Analysis of data: The allele frequencies and statistical analysis were performed on PowerStats program (http:// www.promega.com/geneticidtools/Default.htm) and P value of exact test for Hardy–Weinberg equilibrium and expected heterozygosity were calculated by TFPGA (http://bioweb. usu.edu/mpmbio/index.htm) program. Other remarks: The combined PD and PE for the 15 STR loci in a Korean population were 2:85 1017 and * Corresponding author. Tel.: þ82-2-3779-1001; fax: þ82-2-785-1340. E-mail address: [email protected] (D.-W. Kim).
0.9999968, respectively. When we compared the data with the value from other populations supplied by PE Applied Biosystems (Table 2). It showed that this AmpF/STR multiplex system in Korean has lower forensic capacity than Caucasian and African. However, it has similar forensic capacity with Native American. Even though the TPOX locus showed significant deviation (P < 0:05) with lower PD, PIC and PE in a Korean population, 14 of 15 STR loci except TPOX exhibited no significant deviation from Hardy–Weinberg equilibrium. In recent years, the genetic data for STR loci in a Korean population have been reported but they had a limited number of STR loci [1–5]. This is the first study of allele frequency distribution of D19S433 and D2S1338 in a Korean population. More STR loci will be needed to successfully identify individuals in various situations such as forensic identification, paternity testing, and engraftment assessment after hematopoietic stem cell transplantation. In conclusion, we could obtain the potentially useful data using AmpF/STR Identifiler kit for individual identification in a Korean population and establish that the use of AmpF/STR Identifiler PCR Amplification system offers a highly polymorphic tool for genetic variation analysis. This paper follows the guidelines for publication of population data requested by [6].
0379-0738/$ – see front matter # 2003 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/S0379-0738(03)00255-X
Table 1 Allele frequencies and statistical parameters for 15 STR loci in the Korean population Allele
D21S11
D7S820
CSF1PO
0.2
0.2 11.9 3.7
4.8
15.2 8.4
15.2 40
24.2 23.6
18
21.9
38.1
21.9
6.5
7.4
16
0.6
0.9
14.1
D19S433
vWA
TPOX
D18S51
D3S1358
0.4
0.6
0.2 0.2 2.8 0.4 32.7 2.6 26.8 10.2 5.4 15.2
4.5
20.6 2.2
47.8 12.8
0.2
3.7 32.9
0.2 1.5
2.6
5
0.2
18.4 25.1 18
0.2
3.5 35.1
TH01
D13S317
D16S539
D2S1338
17.3 24.7 3.7 48.9 5.4
0.2 22.3 16.5
30.1
1.3 1.1 11.5
14.1 23.6
17.7 27.3
17.7 29.4
19.9
17.1
25.3
2.2
7.6
12.1
1.3
D5S818
FGA
1.5 0.2
18.2
8.7
33.1
0.6
30.3
6.7
18.4
10.2
0.4
18.2 8.9
4.5 5.4
8.9 0.9
3.5 6.9
1.7
2.8
14.7 18.2 0.2 11.3
2.6 0.4 0.4
1.9 2.8 17.5
3.2 1.7 0.2
13.4 6.9
4.5 0.2 14.1 16.9 22.5 0.2 18 9.5
Y.-L. Kim et al. / Forensic Science International 136 (2003) 92–95
0.2 1.5 0.4 3.7 0.9 25.1 37.4 0.4 9.7 7.1
3
0.2
93
6 7 8 9 9.3 10 11 11.2 12 12.2 13 13.2 14 14.2 15 15.2 16 16.2 17 17.2 18 19 19.2 20 20.2 21 22 23 23.2 24 25 25.2 26 27 28 28.2 29 30 30.2 31 31.2
D8S1179
94
Table 1 (Continued ) D8S1179
32 32.2 33 33.2 34 34.2 35 Mpa PDb PICc PEd TPIe Hobsf Hexpg Ph a
D21S11
D7S820
CSF1PO
D19S433
vWA
TPOX
D18S51
D3S1358
TH01
D13S317
D16S539
D2S1338
D5S818
FGA
0.097 0.903 0.71 0.472 1.83 72.7 75.1 0.802
0.114 0.886 0.69 0.486 1.89 73.6 73.4 0.848
0.084 0.916 0.75 0.577 2.36 78.8 78.4 0.658
0.075 0.925 0.76 0.561 2.26 77.9 79.3 0.547
0.182 0.818 0.58 0.298 1.27 60.6 64.6 0.032
0.043 0.957 0.83 0.744 3.98 87.4 85.2 0.661
0.123 0.877 0.68 0.424 1.65 69.7 72.6 0.059
0.164 0.836 0.62 0.385 1.52 67.1 66.9 0.204
0.066 0.934 0.78 0.577 2.36 78.8 80.9 0.600
0.091 0.909 0.73 0.523 2.06 75.8 77.1 0.963
0.035 0.965 0.85 0.7 3.4 85.3 86.9 0.572
0.077 0.923 0.76 0.585 2.41 79.2 79.1 0.908
0.042 0.958 0.83 0.658 2.96 83.1 85.4 0.345
2.4 7.6 0.6 4.1 0.2 0.4 0.2 0.046 0.954 0.82 0.675 3.12 84 84 0.959
0.083 0.917 0.74 0.641 2.82 82.3 77.5 0.623
Matching probability (MP). Power of discrimination (PD). c Polymorphism information content (PIC). d Power of exclusion (PE). e Typical paternity index (TPI). f Observed heterozygosity (Hobs). g Expected heterozygosity (Hexp). h Exact test for HWE (P). b
Y.-L. Kim et al. / Forensic Science International 136 (2003) 92–95
Allele
Y.-L. Kim et al. / Forensic Science International 136 (2003) 92–95
95
Table 2 Comparison of the probability of identity and paternity exclusion values for the 15 STR loci in the various ethnic populations Locus
African-American
US Caucasian (PD/PE)
US Hispanic
Native American
This study (Korean)
CSF1PO D2S1338 D3S1358 D5S818 D7S820 D8S1179 D13S317 D16S539 D18S51 D19S433 D21S11 FGA TH01 TPOX vWA
0.079/0.545 0.023/0.748 0.097/0.591 0.104/0.506 0.085/0.591 0.074/0.580 0.132/0.383 0.077/0.649 0.033/0.760 0.042/0.601 0.037/0.737 0.034/0.760 0.109/0.492 0.089/0.521 0.066/0.709
0.132/0.496 0.027/0.725 0.076/0.630 0.147/0.440 0.063/0.582 0.064/0.680 0.079/0.487 0.097/0.566 0.031/0.731 0.087/0.531 0.044/0.708 0.035/0.766 0.079/0.566 0.188/0.329 0.066/0.625
0.141/0.450 0.038/0.671 0.112/0.495 0.115/0.525 0.083/0.574 0.089/0.599 0.056/0.638 0.090/0.567 0.031/0.767 0.049/0.678 0.047/0.586 0.032/0.739 0.097/0.618 0.168/0.392 0.080/0.555
0.123/0.409 0.043/0.399 0.158/0.510 0.110/0.601 0.081/0.492 0.104/0.601 0.056/0.370 0.082/0.428 0.046/0.329 0.044/0.360 0.074/0.399 0.031/0.309 0.134/0.646 0.159/0.687 0.103/0.528
0.108/0.675 0.036/0.641 0.134/0.472 0.082/0.486 0.108/0.577 0.048/0.561 0.069/0.298 0.091/0.744 0.041/0.424 0.086/0.385 0.076/0.577 0.043/0.523 0.163/0.700 0.189/0.585 0.079/0.658
Combined
1.31 1018/0.9999996
5.01 1018/0.9999992
7.65 1018/0.9999990
3.62 1017/0.999952
2.85 1017/0.9999968
Acknowledgements This work was supported by grant no. R21-2002-00000010-0 (2002) from the Basic Research Program of the Korea Science and Engineering Foundation.
[3]
[4]
References [1] M.R. Choi, J.H. Kim, D.H. Lee, S.H. Lee, H.M. Rho, Frequency data on four tetrameric STR loci D18S1270, D14S608, D16S3253 and D21S1437 in a Korean population, Int. J. Legal Med. 113 (2000) 179–180. [2] G.R. Han, Y.W. Lee, H.L. Lee, S.M. Kim, T.W. Ku, I.H. Kang, H.S. Lee, J.J. Hwang, A Korean population study of the nine
[5]
[6]
STR loci FGA, vWA, D3S1358, D18S51, D21S11, D8S1179, D7S820, D13S317 and D5S818, Int. J. Legal Med. 114 (2000) 41–44. M.S. Han, P.W. Kang, D.H. Choi, Y.H. Lee, S.K. Choi, W. Kim, Genetic variation at eight STR loci in the Korean population, Forensic Sci. Int. 116 (2001) 35–36. M.S. Han, P.W. Kang, D.H. Choi, Y.H. Lee, S.K. Choi, S.R. Yoon, D.J. Shin, J.M. Kim, H.J. Jin, K.D. Kwak, W. Kim, Korean population genetic data for eleven STR loci, Forensic Sci. Int. 123 (2001) 230–231. D.H. Lee, J.S. Han, W.G. Lee, S.W. Lee, H.M. Rho, Quadruplex amplification of polymorphic STR loci in a Korean population, Int. J. Legal Med. 111 (1998) 320–322. P. Lincoln, A. Carracedo, Publication of population data of human polymorphism, Forensic Sci. Int. 110 (2000) 3–5.
Announcement of population data
Allele frequencies of 15 STR loci using AmpF/STR Identifiler kit in a Korean population Yoo-Li Kim, Ji-Yeon Hwang, Yoo-Jin Kim, Seok Lee, Nak-Gyun Chung, Hyun-Gyung Goh, Chun-Choo Kim, Dong-Wook Kim* Molecular Hematology Laboratory, Catholic Hematopoietic Stem Cell Transplantation Center, The Catholic University of Korea, 62 Youido-Dong, Youngdeungpo-Gu, Seoul 150-713, South Korea Received 21 May 2003; received in revised form 26 May 2003; accepted 27 May 2003
Abstract The genetic variations for 15 short tandem repeat (STR) loci D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA were performed on 231 unrelated Korean population using commercially available AmpF/STR Identifiler kit. # 2003 Elsevier Ireland Ltd. All rights reserved. Keywords: Short tandem repeat; AmpF/STR Identifiler; Korean population
Population: Two hundred thirty-one unrelated individuals living in Korea. Extraction: Genomic DNA was extracted using the High Pure PCR Template Preparation Kit (Roche, Mannheim, Germany). PCR: Multiplex PCR using 1–2 ng target DNA was performed with the AmpF/STR Identifiler PCR Amplification kit (PE Applied Biosystems, Foster City, CA, USA) according to the manufacturer’s instructions. Typing: ABI Prism 310 Genetic Analyzer (PE Applied Biosystems). Results: See Table 1. Quality control: Kit controls. Analysis of data: The allele frequencies and statistical analysis were performed on PowerStats program (http:// www.promega.com/geneticidtools/Default.htm) and P value of exact test for Hardy–Weinberg equilibrium and expected heterozygosity were calculated by TFPGA (http://bioweb. usu.edu/mpmbio/index.htm) program. Other remarks: The combined PD and PE for the 15 STR loci in a Korean population were 2:85 1017 and * Corresponding author. Tel.: þ82-2-3779-1001; fax: þ82-2-785-1340. E-mail address: [email protected] (D.-W. Kim).
0.9999968, respectively. When we compared the data with the value from other populations supplied by PE Applied Biosystems (Table 2). It showed that this AmpF/STR multiplex system in Korean has lower forensic capacity than Caucasian and African. However, it has similar forensic capacity with Native American. Even though the TPOX locus showed significant deviation (P < 0:05) with lower PD, PIC and PE in a Korean population, 14 of 15 STR loci except TPOX exhibited no significant deviation from Hardy–Weinberg equilibrium. In recent years, the genetic data for STR loci in a Korean population have been reported but they had a limited number of STR loci [1–5]. This is the first study of allele frequency distribution of D19S433 and D2S1338 in a Korean population. More STR loci will be needed to successfully identify individuals in various situations such as forensic identification, paternity testing, and engraftment assessment after hematopoietic stem cell transplantation. In conclusion, we could obtain the potentially useful data using AmpF/STR Identifiler kit for individual identification in a Korean population and establish that the use of AmpF/STR Identifiler PCR Amplification system offers a highly polymorphic tool for genetic variation analysis. This paper follows the guidelines for publication of population data requested by [6].
0379-0738/$ – see front matter # 2003 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/S0379-0738(03)00255-X
Table 1 Allele frequencies and statistical parameters for 15 STR loci in the Korean population Allele
D21S11
D7S820
CSF1PO
0.2
0.2 11.9 3.7
4.8
15.2 8.4
15.2 40
24.2 23.6
18
21.9
38.1
21.9
6.5
7.4
16
0.6
0.9
14.1
D19S433
vWA
TPOX
D18S51
D3S1358
0.4
0.6
0.2 0.2 2.8 0.4 32.7 2.6 26.8 10.2 5.4 15.2
4.5
20.6 2.2
47.8 12.8
0.2
3.7 32.9
0.2 1.5
2.6
5
0.2
18.4 25.1 18
0.2
3.5 35.1
TH01
D13S317
D16S539
D2S1338
17.3 24.7 3.7 48.9 5.4
0.2 22.3 16.5
30.1
1.3 1.1 11.5
14.1 23.6
17.7 27.3
17.7 29.4
19.9
17.1
25.3
2.2
7.6
12.1
1.3
D5S818
FGA
1.5 0.2
18.2
8.7
33.1
0.6
30.3
6.7
18.4
10.2
0.4
18.2 8.9
4.5 5.4
8.9 0.9
3.5 6.9
1.7
2.8
14.7 18.2 0.2 11.3
2.6 0.4 0.4
1.9 2.8 17.5
3.2 1.7 0.2
13.4 6.9
4.5 0.2 14.1 16.9 22.5 0.2 18 9.5
Y.-L. Kim et al. / Forensic Science International 136 (2003) 92–95
0.2 1.5 0.4 3.7 0.9 25.1 37.4 0.4 9.7 7.1
3
0.2
93
6 7 8 9 9.3 10 11 11.2 12 12.2 13 13.2 14 14.2 15 15.2 16 16.2 17 17.2 18 19 19.2 20 20.2 21 22 23 23.2 24 25 25.2 26 27 28 28.2 29 30 30.2 31 31.2
D8S1179
94
Table 1 (Continued ) D8S1179
32 32.2 33 33.2 34 34.2 35 Mpa PDb PICc PEd TPIe Hobsf Hexpg Ph a
D21S11
D7S820
CSF1PO
D19S433
vWA
TPOX
D18S51
D3S1358
TH01
D13S317
D16S539
D2S1338
D5S818
FGA
0.097 0.903 0.71 0.472 1.83 72.7 75.1 0.802
0.114 0.886 0.69 0.486 1.89 73.6 73.4 0.848
0.084 0.916 0.75 0.577 2.36 78.8 78.4 0.658
0.075 0.925 0.76 0.561 2.26 77.9 79.3 0.547
0.182 0.818 0.58 0.298 1.27 60.6 64.6 0.032
0.043 0.957 0.83 0.744 3.98 87.4 85.2 0.661
0.123 0.877 0.68 0.424 1.65 69.7 72.6 0.059
0.164 0.836 0.62 0.385 1.52 67.1 66.9 0.204
0.066 0.934 0.78 0.577 2.36 78.8 80.9 0.600
0.091 0.909 0.73 0.523 2.06 75.8 77.1 0.963
0.035 0.965 0.85 0.7 3.4 85.3 86.9 0.572
0.077 0.923 0.76 0.585 2.41 79.2 79.1 0.908
0.042 0.958 0.83 0.658 2.96 83.1 85.4 0.345
2.4 7.6 0.6 4.1 0.2 0.4 0.2 0.046 0.954 0.82 0.675 3.12 84 84 0.959
0.083 0.917 0.74 0.641 2.82 82.3 77.5 0.623
Matching probability (MP). Power of discrimination (PD). c Polymorphism information content (PIC). d Power of exclusion (PE). e Typical paternity index (TPI). f Observed heterozygosity (Hobs). g Expected heterozygosity (Hexp). h Exact test for HWE (P). b
Y.-L. Kim et al. / Forensic Science International 136 (2003) 92–95
Allele
Y.-L. Kim et al. / Forensic Science International 136 (2003) 92–95
95
Table 2 Comparison of the probability of identity and paternity exclusion values for the 15 STR loci in the various ethnic populations Locus
African-American
US Caucasian (PD/PE)
US Hispanic
Native American
This study (Korean)
CSF1PO D2S1338 D3S1358 D5S818 D7S820 D8S1179 D13S317 D16S539 D18S51 D19S433 D21S11 FGA TH01 TPOX vWA
0.079/0.545 0.023/0.748 0.097/0.591 0.104/0.506 0.085/0.591 0.074/0.580 0.132/0.383 0.077/0.649 0.033/0.760 0.042/0.601 0.037/0.737 0.034/0.760 0.109/0.492 0.089/0.521 0.066/0.709
0.132/0.496 0.027/0.725 0.076/0.630 0.147/0.440 0.063/0.582 0.064/0.680 0.079/0.487 0.097/0.566 0.031/0.731 0.087/0.531 0.044/0.708 0.035/0.766 0.079/0.566 0.188/0.329 0.066/0.625
0.141/0.450 0.038/0.671 0.112/0.495 0.115/0.525 0.083/0.574 0.089/0.599 0.056/0.638 0.090/0.567 0.031/0.767 0.049/0.678 0.047/0.586 0.032/0.739 0.097/0.618 0.168/0.392 0.080/0.555
0.123/0.409 0.043/0.399 0.158/0.510 0.110/0.601 0.081/0.492 0.104/0.601 0.056/0.370 0.082/0.428 0.046/0.329 0.044/0.360 0.074/0.399 0.031/0.309 0.134/0.646 0.159/0.687 0.103/0.528
0.108/0.675 0.036/0.641 0.134/0.472 0.082/0.486 0.108/0.577 0.048/0.561 0.069/0.298 0.091/0.744 0.041/0.424 0.086/0.385 0.076/0.577 0.043/0.523 0.163/0.700 0.189/0.585 0.079/0.658
Combined
1.31 1018/0.9999996
5.01 1018/0.9999992
7.65 1018/0.9999990
3.62 1017/0.999952
2.85 1017/0.9999968
Acknowledgements This work was supported by grant no. R21-2002-00000010-0 (2002) from the Basic Research Program of the Korea Science and Engineering Foundation.
[3]
[4]
References [1] M.R. Choi, J.H. Kim, D.H. Lee, S.H. Lee, H.M. Rho, Frequency data on four tetrameric STR loci D18S1270, D14S608, D16S3253 and D21S1437 in a Korean population, Int. J. Legal Med. 113 (2000) 179–180. [2] G.R. Han, Y.W. Lee, H.L. Lee, S.M. Kim, T.W. Ku, I.H. Kang, H.S. Lee, J.J. Hwang, A Korean population study of the nine
[5]
[6]
STR loci FGA, vWA, D3S1358, D18S51, D21S11, D8S1179, D7S820, D13S317 and D5S818, Int. J. Legal Med. 114 (2000) 41–44. M.S. Han, P.W. Kang, D.H. Choi, Y.H. Lee, S.K. Choi, W. Kim, Genetic variation at eight STR loci in the Korean population, Forensic Sci. Int. 116 (2001) 35–36. M.S. Han, P.W. Kang, D.H. Choi, Y.H. Lee, S.K. Choi, S.R. Yoon, D.J. Shin, J.M. Kim, H.J. Jin, K.D. Kwak, W. Kim, Korean population genetic data for eleven STR loci, Forensic Sci. Int. 123 (2001) 230–231. D.H. Lee, J.S. Han, W.G. Lee, S.W. Lee, H.M. Rho, Quadruplex amplification of polymorphic STR loci in a Korean population, Int. J. Legal Med. 111 (1998) 320–322. P. Lincoln, A. Carracedo, Publication of population data of human polymorphism, Forensic Sci. Int. 110 (2000) 3–5.