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Genetic variation in a Japanese population, using the multiplex 24 STRs analysis system
Forensic Science International: Genetics Supplement Series 4 (2013) e41–e42
Contents lists available at ScienceDirect
Forensic Science International: Genetics Supplement Series journal homepage: www.elsevier.com/locate/FSIGSS
Genetic variation in a Japanese population, using the multiplex 24 STRs analysis system Masaki Hashiayda *, Kiyotaka Usui, Tsukasa Ohuchi, Yoshie Hashizaki, Tadashi Hosoya, Yui Igari, Tomoya Ikeda, Tomomi Aramaki, Jun Sakai, Masato Funayama Division of Forensic Medicine, Department of Public Health and Forensic Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
A R T I C L E I N F O
A B S T R A C T
Article history: Received 30 August 2013 Accepted 2 October 2013
Allele frequency distributions for 24 short tandem repeat (STR) loci were determined using the PowerPlexR Fusion System (Promega) in 407 Japanese samples. The most informative locus among the 22 STR loci, excluding Amelogenin and DYS391, was Penta E (power of discrimination (PD) = 0.98), while the least informative was TPOX(PD = 0.831). The 22 loci combined matching probability (MP) was calculated to be 4.13 10 26. These parameters indicated the usefulness of this 24 STR analysis in forensic personal identification and parentage testing among Japanese population. ß 2013 Elsevier Ireland Ltd. All rights reserved.
Keywords: STR Japanese PowerPlexR Fusion System
1. Introduction
2. Materials and methods
Recently, more STR loci have been required to confirm positive human identification by many domestic and international forensic agencies [1,2]. As the world becomes increasingly connected, authorities have begun to see the benefit of a larger combined panel of loci for sharing across borders and improved discrimination. The 24 STR loci included in the PowerPlexR Fusion System (Promega) [3] meet both the current 13 core CODIS(US) and 12 core European Standard Set requirements and added some loci such as Penta E, Penta D and DYS391. This study revealed the allele frequency distribution of 24 STR and forensic parameters in Japanese population.
Genomic DNA extracted from blood was amplified by the PowerPlexR Fusion System (Promega) which contains 24 STRs, that is D3S1358, D1S1656, D2S441, D10S1248, D13S317, Penta E, D16S539, D18S51, D2S1338, CSF1PO, Penta D, TH01, vWA, D21S11, D7S820, D5S818, TPOX, D8S1179, D12S391, D19S433, FGA and D22S1045, as well as Amelogenin and DYS391 for gender determination. PCR was performed according to manufactures’ protocol. Electrophoresis and allele typing were carried on Applied Biosystems 3500 Genetic Analyzer and GeneMapper ID-X ver.1.2 software (Lifetechnologies). In addition, this population study was
Table 1 Allele frequencies and forensic parameters in Japanese population (n = 407).
Hetero MP PIC
AL
D31358
AL
D10S1248
AL
D13S317
AL
D5S818
AL
TPOX
AL
D22S1045
AL
TH01
AL
vWA
12 14 15 16 17 18 19
0.0049 0.0283 0.3931 0.2752 0.1953 0.0995 0.0037
11 12 13 14 15 16 17 18
0.0012 0.0934 0.3145 0.2899 0.2138 0.0700 0.0160 0.0012
7 8 9 10 11 12 13 14
0.0012 0.2924 0.1290 0.1069 0.2027 0.2150 0.0467 0.0061
6 8 9 10 11 12 13 14
0.0012 0.0074 0.1020 0.2064 0.2764 0.2383 0.1548 0.0135
8 9 10 11 12 13 14
0.4435 0.1167 0.0418 0.3526 0.0418 0.0012 0.0025
17 18 19 20 21 22 22
0.2015 0.2899 0.2383 0.2273 0.0369 0.0049 0.0012
3 5 6 7 8 9 9.3 10
0.0012 0.0012 0.2432 0.2494 0.0590 0.4091 0.0319 0.0049
14 15 16 17 18 19 20 21
0.2052 0.0209 0.1892 0.2727 0.2236 0.0737 0.0135 0.0012
0.720 0.124 0.674
0.737 0.100 0.718
0.803 0.074 0.767
0.789 0.078 0.757
* Corresponding author. Tel.: +81 22 717 8110; fax: +81 22 717 8112. E-mail addresses: [email protected], [email protected] (M. Hashiayda). 1875-1768/$ – see front matter ß 2013 Elsevier Ireland Ltd. All rights reserved. http://dx.doi.org/10.1016/j.fsigss.2013.10.021
0.634 0.169 0.602
0.767 0.096 0.725
0.722 0.138 0.656
0.794 0.076 0.759
approved by the ethical committee of Tohoku University School of Medicine (Table 1).
M. Hashiayda et al. / Forensic Science International: Genetics Supplement Series 4 (2013) e41–e42
e42 Table 1 (Continued ) AL
AL
D10S1248
0.460 1.79
PE TPI
AL
0.488 1.90
D13S317
AL
0.605 2.54
D5S818
AL
0.578 2.37
TPOX
AL
0.334 1.37
D22S1045
AL
TH01
0.539 2.14
AL
0.464 1.80
vWA 0.587 2.42
AL
D7S820
AL
D16S539
AL
D8S1179
AL
Penta D
AL
CSF1PO
AL
D1S1656
AL
D2S441
7 8 9 9.3 10 11 12 13 14
0.0037 0.1339 0.0430 0.0012 0.2027 0.3661 0.2015 0.0442 0.0037
7 9 10 11 12 13 14
0.0037 0.3182 0.1855 0.2260 0.1794 0.0774 0.0098
9 10 11 12 12 13 14 15 16 17
0.0025 0.1167 0.1155 0.1155 0.0025 0.2383 0.2113 0.1400 0.0553 0.0025
7 8 9 10 11 12 13 14 15 16
0.0049 0.0283 0.2875 0.2285 0.1929 0.1278 0.1007 0.0233 0.0049 0.0012
7 9 10 11 12 13 14 15
0.0049 0.0405 0.2052 0.2150 0.4287 0.0835 0.0197 0.0025
11 12 13 14 15 15 16 16 17 17 18 18 19 19 20
0.0319 0.0418 0.1044 0.0577 0.2543 0.0012 0.2346 0.0197 0.1069 0.0774 0.0184 0.0467 0.0012 0.0025 0.0012
8 8.1 9 9.1 10 10 11 11 12 12 12 13 13 14 15
0.0037 0.0012 0.0012 0.0295 0.2641 0.0012 0.3096 0.0246 0.1990 0.0012 0.0012 0.0491 0.0012 0.1069 0.0061
Hetero MP PIC PE TPI
Hetero MP PIC PE TPI
D31358
0.769 0.094 0.728 0.543 2.16
0.771 0.087 0.739 0.547 2.19
0.823 0.050 0.815 0.643 2.83
0.794 0.071 0.771 0.587 2.42
0.725 0.120 0.678 0.468 1.82
0.838 0.044 0.826 0.671 3.08
0.791 0.086 0.747 0.583 2.39
AL
D12S391
AL
D19S433
AL
FGA
AL
D21S11
AL
PentaE
AL
D18S51
AL
D2S1338
15 16 17 17 18 18 19 19 20 20 21 22 23 24 25 26 27
0.0295 0.0209 0.0762 0.0012 0.2506 0.0012 0.1916 0.0012 0.1609 0.0037 0.1179 0.0516 0.0381 0.0283 0.0160 0.0098 0.0012
10 10 11 12 12 13 13 14 14 14 15 15 16 16 17 28
0.0012 0.0012 0.0037 0.0369 0.0098 0.3059 0.0246 0.3366 0.0025 0.0651 0.0455 0.1302 0.0061 0.0270 0.0025 0.0012
17 18 19 20 21 22 22 23 23 24 24 25 25 25 26 27 28
0.0037 0.0209 0.0786 0.0946 0.1265 0.1855 0.0074 0.2346 0.0037 0.1474 0.0012 0.0639 0.0012 0.0025 0.0209 0.0049 0.0025
26 27 28 28.2 29 29.1 29.2 30 30.2 30.3 31 31.2 32 32.2 33 33.1 33.2 34.2
0.0012 0.0012 0.0442 0.0074 0.2764 0.0025 0.0025 0.3170 0.0037 0.0012 0.0983 0.0455 0.0270 0.1462 0.0012 0.0012 0.0221 0.0012
5 8 9 10 11 12 13 14 15 16 17 18 18 19 19 20 21 22 23 24 25 26
0.0921 0.0147 0.0086 0.0430 0.1450 0.1388 0.0258 0.0467 0.1032 0.0946 0.1020 0.0627 0.0012 0.0393 0.0037 0.0295 0.0209 0.0184 0.0061 0.0012 0.0012 0.0012
11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 27
0.0111 0.0442 0.1953 0.2015 0.2101 0.1437 0.0627 0.0405 0.0332 0.0184 0.0135 0.0123 0.0025 0.0049 0.0049 0.0012
15 16 17 18 19 20 21 22 23 24 25 26 27
0.0012 0.0111 0.0971 0.1486 0.2260 0.1229 0.0111 0.0455 0.1364 0.0946 0.0663 0.0319 0.0074
0.835 0.041 0.831 0.666 3.04
0.762 0.083 0.735 0.530 2.10
0.840 0.040 0.836 0.676 3.13
0.791 0.075 0.758 0.583 2.39
0.894 0.017 0.902 0.784 4.73
0.862 0.045 0.829 0.719 3.63
0.860 0.032 0.853 0.715 3.57
MP: matching probability, PD: power of discrimination, PE: power of exclusion, TPI: typical paternity index.
3. Results and discussion Forensic statistics parameters, such as the observed heterozygosity, matching probability (MP), polymorphism information content (PIC) and probability values of the Hardy–Weinberg equilibrium were calculated by PopwerStats spreadsheet (Promega) and Arlequin ver3.5. The result revealed the most highly polymorphic locus was Penta E (MP:0.017 and PIC:0.902), and TPOX showed the lowest value (0.169 and 0.602). The combined matching probability value for 22 loci excluding the Amelogenin and DYS391 was 4.13 10 26. Furthermore, no significant deviation from Hardy–Weinberg Equilibrium was detected. We concluded that these 24 STRs analysis offer high effectiveness for forensic and genetic application.
Conflict of interest None.
References [1] J. Ge, A. Eisenberg, B. Budowle, Developing criteria and data to determine best options for expanding the core CODIS loci, Investigative Genetics 3 (2012) http:// www.investigativegenetics.com/content/3/1/1. [2] W.A. Welch, P. Gill, C. Phillips, R. Ansell, N. Morling, W. Person, J.U. Palo, I. Bastisch, European Network of Forensic Science Institutes (ENFSI): evaluation of new commercial STR multiplexes that include the European Standard Set (ESS) of markers, Forensic Science International: Genetics 6 (2012) 819–826. [3] Technical Manual PowerPlex Fusion System (Promega) http://www.promega.com/ resources/protocols/technical-manuals/101/powerplex-fusion-system-protocol/.
Contents lists available at ScienceDirect
Forensic Science International: Genetics Supplement Series journal homepage: www.elsevier.com/locate/FSIGSS
Genetic variation in a Japanese population, using the multiplex 24 STRs analysis system Masaki Hashiayda *, Kiyotaka Usui, Tsukasa Ohuchi, Yoshie Hashizaki, Tadashi Hosoya, Yui Igari, Tomoya Ikeda, Tomomi Aramaki, Jun Sakai, Masato Funayama Division of Forensic Medicine, Department of Public Health and Forensic Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
A R T I C L E I N F O
A B S T R A C T
Article history: Received 30 August 2013 Accepted 2 October 2013
Allele frequency distributions for 24 short tandem repeat (STR) loci were determined using the PowerPlexR Fusion System (Promega) in 407 Japanese samples. The most informative locus among the 22 STR loci, excluding Amelogenin and DYS391, was Penta E (power of discrimination (PD) = 0.98), while the least informative was TPOX(PD = 0.831). The 22 loci combined matching probability (MP) was calculated to be 4.13 10 26. These parameters indicated the usefulness of this 24 STR analysis in forensic personal identification and parentage testing among Japanese population. ß 2013 Elsevier Ireland Ltd. All rights reserved.
Keywords: STR Japanese PowerPlexR Fusion System
1. Introduction
2. Materials and methods
Recently, more STR loci have been required to confirm positive human identification by many domestic and international forensic agencies [1,2]. As the world becomes increasingly connected, authorities have begun to see the benefit of a larger combined panel of loci for sharing across borders and improved discrimination. The 24 STR loci included in the PowerPlexR Fusion System (Promega) [3] meet both the current 13 core CODIS(US) and 12 core European Standard Set requirements and added some loci such as Penta E, Penta D and DYS391. This study revealed the allele frequency distribution of 24 STR and forensic parameters in Japanese population.
Genomic DNA extracted from blood was amplified by the PowerPlexR Fusion System (Promega) which contains 24 STRs, that is D3S1358, D1S1656, D2S441, D10S1248, D13S317, Penta E, D16S539, D18S51, D2S1338, CSF1PO, Penta D, TH01, vWA, D21S11, D7S820, D5S818, TPOX, D8S1179, D12S391, D19S433, FGA and D22S1045, as well as Amelogenin and DYS391 for gender determination. PCR was performed according to manufactures’ protocol. Electrophoresis and allele typing were carried on Applied Biosystems 3500 Genetic Analyzer and GeneMapper ID-X ver.1.2 software (Lifetechnologies). In addition, this population study was
Table 1 Allele frequencies and forensic parameters in Japanese population (n = 407).
Hetero MP PIC
AL
D31358
AL
D10S1248
AL
D13S317
AL
D5S818
AL
TPOX
AL
D22S1045
AL
TH01
AL
vWA
12 14 15 16 17 18 19
0.0049 0.0283 0.3931 0.2752 0.1953 0.0995 0.0037
11 12 13 14 15 16 17 18
0.0012 0.0934 0.3145 0.2899 0.2138 0.0700 0.0160 0.0012
7 8 9 10 11 12 13 14
0.0012 0.2924 0.1290 0.1069 0.2027 0.2150 0.0467 0.0061
6 8 9 10 11 12 13 14
0.0012 0.0074 0.1020 0.2064 0.2764 0.2383 0.1548 0.0135
8 9 10 11 12 13 14
0.4435 0.1167 0.0418 0.3526 0.0418 0.0012 0.0025
17 18 19 20 21 22 22
0.2015 0.2899 0.2383 0.2273 0.0369 0.0049 0.0012
3 5 6 7 8 9 9.3 10
0.0012 0.0012 0.2432 0.2494 0.0590 0.4091 0.0319 0.0049
14 15 16 17 18 19 20 21
0.2052 0.0209 0.1892 0.2727 0.2236 0.0737 0.0135 0.0012
0.720 0.124 0.674
0.737 0.100 0.718
0.803 0.074 0.767
0.789 0.078 0.757
* Corresponding author. Tel.: +81 22 717 8110; fax: +81 22 717 8112. E-mail addresses: [email protected], [email protected] (M. Hashiayda). 1875-1768/$ – see front matter ß 2013 Elsevier Ireland Ltd. All rights reserved. http://dx.doi.org/10.1016/j.fsigss.2013.10.021
0.634 0.169 0.602
0.767 0.096 0.725
0.722 0.138 0.656
0.794 0.076 0.759
approved by the ethical committee of Tohoku University School of Medicine (Table 1).
M. Hashiayda et al. / Forensic Science International: Genetics Supplement Series 4 (2013) e41–e42
e42 Table 1 (Continued ) AL
AL
D10S1248
0.460 1.79
PE TPI
AL
0.488 1.90
D13S317
AL
0.605 2.54
D5S818
AL
0.578 2.37
TPOX
AL
0.334 1.37
D22S1045
AL
TH01
0.539 2.14
AL
0.464 1.80
vWA 0.587 2.42
AL
D7S820
AL
D16S539
AL
D8S1179
AL
Penta D
AL
CSF1PO
AL
D1S1656
AL
D2S441
7 8 9 9.3 10 11 12 13 14
0.0037 0.1339 0.0430 0.0012 0.2027 0.3661 0.2015 0.0442 0.0037
7 9 10 11 12 13 14
0.0037 0.3182 0.1855 0.2260 0.1794 0.0774 0.0098
9 10 11 12 12 13 14 15 16 17
0.0025 0.1167 0.1155 0.1155 0.0025 0.2383 0.2113 0.1400 0.0553 0.0025
7 8 9 10 11 12 13 14 15 16
0.0049 0.0283 0.2875 0.2285 0.1929 0.1278 0.1007 0.0233 0.0049 0.0012
7 9 10 11 12 13 14 15
0.0049 0.0405 0.2052 0.2150 0.4287 0.0835 0.0197 0.0025
11 12 13 14 15 15 16 16 17 17 18 18 19 19 20
0.0319 0.0418 0.1044 0.0577 0.2543 0.0012 0.2346 0.0197 0.1069 0.0774 0.0184 0.0467 0.0012 0.0025 0.0012
8 8.1 9 9.1 10 10 11 11 12 12 12 13 13 14 15
0.0037 0.0012 0.0012 0.0295 0.2641 0.0012 0.3096 0.0246 0.1990 0.0012 0.0012 0.0491 0.0012 0.1069 0.0061
Hetero MP PIC PE TPI
Hetero MP PIC PE TPI
D31358
0.769 0.094 0.728 0.543 2.16
0.771 0.087 0.739 0.547 2.19
0.823 0.050 0.815 0.643 2.83
0.794 0.071 0.771 0.587 2.42
0.725 0.120 0.678 0.468 1.82
0.838 0.044 0.826 0.671 3.08
0.791 0.086 0.747 0.583 2.39
AL
D12S391
AL
D19S433
AL
FGA
AL
D21S11
AL
PentaE
AL
D18S51
AL
D2S1338
15 16 17 17 18 18 19 19 20 20 21 22 23 24 25 26 27
0.0295 0.0209 0.0762 0.0012 0.2506 0.0012 0.1916 0.0012 0.1609 0.0037 0.1179 0.0516 0.0381 0.0283 0.0160 0.0098 0.0012
10 10 11 12 12 13 13 14 14 14 15 15 16 16 17 28
0.0012 0.0012 0.0037 0.0369 0.0098 0.3059 0.0246 0.3366 0.0025 0.0651 0.0455 0.1302 0.0061 0.0270 0.0025 0.0012
17 18 19 20 21 22 22 23 23 24 24 25 25 25 26 27 28
0.0037 0.0209 0.0786 0.0946 0.1265 0.1855 0.0074 0.2346 0.0037 0.1474 0.0012 0.0639 0.0012 0.0025 0.0209 0.0049 0.0025
26 27 28 28.2 29 29.1 29.2 30 30.2 30.3 31 31.2 32 32.2 33 33.1 33.2 34.2
0.0012 0.0012 0.0442 0.0074 0.2764 0.0025 0.0025 0.3170 0.0037 0.0012 0.0983 0.0455 0.0270 0.1462 0.0012 0.0012 0.0221 0.0012
5 8 9 10 11 12 13 14 15 16 17 18 18 19 19 20 21 22 23 24 25 26
0.0921 0.0147 0.0086 0.0430 0.1450 0.1388 0.0258 0.0467 0.1032 0.0946 0.1020 0.0627 0.0012 0.0393 0.0037 0.0295 0.0209 0.0184 0.0061 0.0012 0.0012 0.0012
11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 27
0.0111 0.0442 0.1953 0.2015 0.2101 0.1437 0.0627 0.0405 0.0332 0.0184 0.0135 0.0123 0.0025 0.0049 0.0049 0.0012
15 16 17 18 19 20 21 22 23 24 25 26 27
0.0012 0.0111 0.0971 0.1486 0.2260 0.1229 0.0111 0.0455 0.1364 0.0946 0.0663 0.0319 0.0074
0.835 0.041 0.831 0.666 3.04
0.762 0.083 0.735 0.530 2.10
0.840 0.040 0.836 0.676 3.13
0.791 0.075 0.758 0.583 2.39
0.894 0.017 0.902 0.784 4.73
0.862 0.045 0.829 0.719 3.63
0.860 0.032 0.853 0.715 3.57
MP: matching probability, PD: power of discrimination, PE: power of exclusion, TPI: typical paternity index.
3. Results and discussion Forensic statistics parameters, such as the observed heterozygosity, matching probability (MP), polymorphism information content (PIC) and probability values of the Hardy–Weinberg equilibrium were calculated by PopwerStats spreadsheet (Promega) and Arlequin ver3.5. The result revealed the most highly polymorphic locus was Penta E (MP:0.017 and PIC:0.902), and TPOX showed the lowest value (0.169 and 0.602). The combined matching probability value for 22 loci excluding the Amelogenin and DYS391 was 4.13 10 26. Furthermore, no significant deviation from Hardy–Weinberg Equilibrium was detected. We concluded that these 24 STRs analysis offer high effectiveness for forensic and genetic application.
Conflict of interest None.
References [1] J. Ge, A. Eisenberg, B. Budowle, Developing criteria and data to determine best options for expanding the core CODIS loci, Investigative Genetics 3 (2012) http:// www.investigativegenetics.com/content/3/1/1. [2] W.A. Welch, P. Gill, C. Phillips, R. Ansell, N. Morling, W. Person, J.U. Palo, I. Bastisch, European Network of Forensic Science Institutes (ENFSI): evaluation of new commercial STR multiplexes that include the European Standard Set (ESS) of markers, Forensic Science International: Genetics 6 (2012) 819–826. [3] Technical Manual PowerPlex Fusion System (Promega) http://www.promega.com/ resources/protocols/technical-manuals/101/powerplex-fusion-system-protocol/.