- Email: [email protected]
PowerPlex® Fusion kit: A 23 plex autosomal STR kit for human identity testing
Forensic Science International: Genetics Supplement Series 4 (2013) e344–e345
Contents lists available at ScienceDirect
Forensic Science International: Genetics Supplement Series journal homepage: www.elsevier.com/locate/FSIGSS
PowerPlex1 Fusion kit: A 23 plex autosomal STR kit for human identity testing A. Verzeletti a,*, V. Cortellini a, N. Cerri a, A. Bosetti b, S. Pretto a, F. De Ferrari a a b
Department of Forensic Medicine, University of Brescia, Brescia, Italy Promega Italia Srl, Milano, Italy
A R T I C L E I N F O
A B S T R A C T
Article history: Received 19 August 2013 Received in revised form 4 October 2013 Accepted 5 October 2013
In case of deficient paternity or maternity investigations with short tandem repeat (STR) analysis, sometimes common STRs cannot provide good results. Thus, it is recommended that additional STRs are used to complement conventional analysis for more reliable forensic information. We analyzed variation of 22 STRs contained in the new PowerPlex1 Fusion kit (Promega) in 52 unrelated individuals, living in Northern Italy, involved in paternity testing casework, to contribute to create an Italian database. ß 2013 Elsevier Ireland Ltd. All rights reserved.
Keywords: STR, PowerPlex1 Fusion kit, Database
information [1]. The PowerPlex1 Fusion System (Promega) is a 24-locus multiplex for human identification applications including forensic analysis, relationship testing and research use, which allows co-amplification of the 13 core CODIS loci, the 12 core ESS loci and Amelogenin. In addition, the male-specific DYS391 locus, Penta D, Penta E, D2S1338 and D19S433 loci are included. This extended panel of STR markers is intended to satisfy both CODIS
1. Introduction In case of paternity or maternity investigations with STR analysis, deficient cases, missing persons, or mutations are encountered and sometimes common STRs cannot provide good results. Thus, it is recommended that additional STR are used to complement conventional analysis for more reliable forensic Table 1 Allele frequencies and forensic parameters in a population sample from Brescia. Alleli 5 6 7 8 9 9.3 10 11 11.3 12 13 14 14.2 15 15.2 15.3 16 16.2 16.3 17 17.3 18 18.3 19 19.3 20 20.3 21 21.2 22 23 23.2 24 25
D3S1358
D1S1656
D2S441
D10S1248
D13S317
PENTA E
D16S539
D18S51
D2S1338
CSF1P0
PENTA D
0.0385
0.0385 0.1538
0.0481 0.202 0.1154 0.0962
0.0192
0.0192 0.0577
0.0288
0.0288 0.2692
0.1058 0.0865
0.0577 0.375
0.0096
0.2692 0.2885
0.0962 0.1538
0.0385 0.2692 0.3558
0.2981 0.1346 0.0577
0.1731 0.1058 0.0769
0.3077 0.1635 0.0192
0.1731 0.1827 0.1731
0.2788 0.1058 0.0192
0.1538 0.2597 0.0769
0.0769
0.0962 0.0865 0.0962
0.1827 0.327 0.0481 0.0288 0.0673 0.3077
0.2404
0.1923
0.0288
0.1634
0.0192
0.1442
0.25
0.0577 0.1346
0.0096
0.0962
0.0865
0.0962
0.0769
0.0481
0.0096
0.0673
0.25
0.0385
0.0577
0.0577
0.0288
0.0577
0.1154
0.0096
0.1154
0.0288
0.0288
0.0769
0.3077 0.1058
0.0865 0.0385 0.1058 0.0096 0.0192
0.0192
* Corresponding author at: Piazzale Spedali Civili 1, 25123 Brescia, Italy. Tel.: +39 033995480; fax: +39 030 3995839. E-mail address: [email protected] (A. Verzeletti). 1875-1768/$ – see front matter ß 2013 Elsevier Ireland Ltd. All rights reserved. http://dx.doi.org/10.1016/j.fsigss.2013.10.175
0.0673
0.0192 0.1731 0.0962 0.0673
A. Verzeletti et al. / Forensic Science International: Genetics Supplement Series 4 (2013) e344–e345
e345
Table 1 (Continued ) Alleli
D3S1358
D1S1656
D2S441
D10S1248
D13S317
PENTA E
D16S539
D18S51
D2S1338
CSF1P0
PENTA D
PIC PE PD PI Hoss Hatt Estd HWE
0.7299 0.5485 0.8783 0.1217 0.8462 0.775 5.8575 10 0.1921
0.8789 0.7761 0.9564 4.3650 10 0.9615 0.8977 0.0435 0.3989
0.7186 0.5394 0.875 0.125 0.8462 0.7422 0.0595 0.0681
0.725 0.5486 0.8735 0.1265 0.8269 0.7677 5.9195 10 0.023
0.7651 0.6013 0.9223 0.0776 0.8462 0.8015 5.6102 10 0.7735
0.8692 0.672 0.9608 3.9221 10 0.9039 0.8891 4.4981 10 0.6871
0.6874 0.5007 0.8372 0.1628 0.8654 0.7388 6.1525 10 0.0941
0.8495 0.6436 0.9556 4.4429 10 0.9039 0.8729 4.7471 10 0.969
0.8414 0.7162 0.9504 4.9589 10 0.9039 0.8643 4.8592 10 0.6431
0.7111 0.5225 0.8957 0.1043 0.75 0.76 5.9763 10 0.9923
0.8213 0.6828 0.9386 6.1432 10 0.8654 0.8486 5.0786 10 0.3669
Alleli
TH01
D21S11
D7S820
D5S818
TPOX
D8S1179
0.0288 0.1731 0.1346
0.0096
0.0096 0.5865 0.0673
0.0096 0.0288
0.25 0.2309
0.0385 0.3654
0.0769 0.2309
0.0673 0.0577
0.1634 0.0192
0.3654 0.2115 0.0096
0.0288
0.1058 0.4231 0.1731
5 6 7 8 9 9.3 10 11 11.3 12 13 14 14.2 15 15.2 15.3 16 16.2 16.3 17 17.3 18 18.3 19 19.3 20 20.3 21 21.2 22 23 23.2 24 25 26 27 28 29 30 30.2 31 31.2 32.2 33.2 PIC PE PD PI Hoss Hatt Estd HWE
2
2
vWA
0.2885 0.1058 0.1635 0.0865 0.3461 0.0096
2
0.0865
2
2
2
2
2
2
D12S391
0.1731
0.0962
0.0673
0.2597
0.0288
0.0385
0.3173
0.0096
0.0865
0.1442
2
2
D19S433
FGA
0.0096
0.125
0.1154 0.2404 0.2692 0.0192 0.1828 0.0865
0.0096
0.0481 0.0192
0.2981
0.0577 0.4327
0.0673
0.0865
0.1346 0.0096 0.1827 0.2404 0.0096 0.1154 0.0577 0.0385 0.0096
0.0577 0.0673 0.125 0.2597 0.2597 0.0192 0.0096 0.0769 0.1634 0.0192
2
0.7382 0.5605 0.8942 0.1058 0.8077 0.7944 5.8049 10 0.0059
2
0.7861 0.6306 0.9114 8.8545 10 0.8846 0.8295 5.4236 10 0.0013
2
2
0.7801 0.6173 0.9305 6.9535 10 0.7885 0.8161 5.4598 10 0.9481
2
2
0.626 0.4194 0.8394 0.1605 0.6346 0.6932 0.0643 0.4215
0.5455 0.3592 0.7667 0.233 0.5385 0.6004 6.8171 10 0.0703
2
0.7369 0.576 0.8979 0.1021 0.7115 0.7683 5.9152 10 0.1509
2
0.8776 0.7743 0.9557 4.4337 10 0.9039 0.8966 4.3747 10 0.0997
0.0096
0.1154
0.125 0.0865
0.7119 0.5276 0.8817 0.1183 0.8077 0.7588 5.9929 10 0.5114
2
D22S1045
0.0192
0.1924 0.0192 0.0673 0.0096 0.1442 0.0096 0.0962
0.0096
2
2
2
2
0.7867 0.6316 0.9378 6.2154 10 0.7692 0.82 5.4170 10 0.5069
2
2
0.8347 0.7042 0.9519 4.8111 10 0.8846 0.8602 4.9311 10 0.976
2
2
0.6536 0.4634 0.8239 0.1761 0.7885 0.7071 0.0635 0.18
Hobs, observed heterozygosity; Hexp, expected heterozygosity; SE, standard error; PIC, polymorphism information content; PD, power of discrimination; PE, power of exclusion; PI, power of inclusion; HWE, p-value from exact test for Hardy-Weinberg equilibrium.
and ESS recommendations [2]. In this study we analyzed variation of 22 autosomal STRs contained in the new PowerPlex1 Fusion kit to contribute to create an Italian database. Allele frequencies and forensic parameters were used to evaluate suitability and robustness of the new kit for forensic genetic analysis as well as in concordance studies with other kit (AmpFlTR 1IdentifilerTM and NGMTM). Data regarding the allelic frequencies for STRs in these populations would be highly welcomed to be used in forensic genetics for identification and paternity testing. 2. Materials and methods The study was conducted on a sample of 52 unrelated, living in Northern Italy. DNA was extracted from buccal swabs or blood using Chelex1 100 procedure. PCR amplifications were performed in a GeneAmp1 PCR System 9700 Gold Plate using the commercial kit PowerPlex Fusion. Typing was performed by capillary electrophoresis on a ABI Prism1 310 Genetic Analyzer; allele calling was performed with the software GeneMapperID V3.2.
Bonferroni correction for multiple testing (p 0.002). Larger samples sizes are necessary to understand the cause of deviation from equilibrium model at the locus surveyed. There are two explanations for these so-called ‘‘spurious’’ associations: the excess of homozygotes observed in the three markers, due to population substructure and high inbreeding due to widespread endogamy. Designed to meet CODIS and European standards, the PowerPlex1 Fusion System kit enables laboratories to: achieve the most inter database compatibility and highest discrimination of any autosomal STR kit; obtain a higher success rate with difficult casework samples due to robustness and sensitivity; simplify validation and QC efforts by using one kit for both casework and databasing sections. Role of funding None. Conflict of interest None.
3. Results and discussion References Allele frequencies and statistical parameters of forensic importance were estimated; ARLEQUIN software Ver. 3.11 was used to assess departures Hardy-Weinberg equilibrium (Table 1). Deviation has been detected for D21S11 (p = 0.0013) locus, even after a
[1] J.M. Butler, C.R. Hill, Biology and genetics of new autosomal STR loci useful for forensic DNA analysis, Forensic Sci. Rev. 24 (1) (2012) 5–26. [2] S.H. Katsanis, J.K. Wagner, Characterization of the standard and recommended CODIS markers, J. Forensic Sci. 58 (Suppl. 1) (2013) S169–S172.
Contents lists available at ScienceDirect
Forensic Science International: Genetics Supplement Series journal homepage: www.elsevier.com/locate/FSIGSS
PowerPlex1 Fusion kit: A 23 plex autosomal STR kit for human identity testing A. Verzeletti a,*, V. Cortellini a, N. Cerri a, A. Bosetti b, S. Pretto a, F. De Ferrari a a b
Department of Forensic Medicine, University of Brescia, Brescia, Italy Promega Italia Srl, Milano, Italy
A R T I C L E I N F O
A B S T R A C T
Article history: Received 19 August 2013 Received in revised form 4 October 2013 Accepted 5 October 2013
In case of deficient paternity or maternity investigations with short tandem repeat (STR) analysis, sometimes common STRs cannot provide good results. Thus, it is recommended that additional STRs are used to complement conventional analysis for more reliable forensic information. We analyzed variation of 22 STRs contained in the new PowerPlex1 Fusion kit (Promega) in 52 unrelated individuals, living in Northern Italy, involved in paternity testing casework, to contribute to create an Italian database. ß 2013 Elsevier Ireland Ltd. All rights reserved.
Keywords: STR, PowerPlex1 Fusion kit, Database
information [1]. The PowerPlex1 Fusion System (Promega) is a 24-locus multiplex for human identification applications including forensic analysis, relationship testing and research use, which allows co-amplification of the 13 core CODIS loci, the 12 core ESS loci and Amelogenin. In addition, the male-specific DYS391 locus, Penta D, Penta E, D2S1338 and D19S433 loci are included. This extended panel of STR markers is intended to satisfy both CODIS
1. Introduction In case of paternity or maternity investigations with STR analysis, deficient cases, missing persons, or mutations are encountered and sometimes common STRs cannot provide good results. Thus, it is recommended that additional STR are used to complement conventional analysis for more reliable forensic Table 1 Allele frequencies and forensic parameters in a population sample from Brescia. Alleli 5 6 7 8 9 9.3 10 11 11.3 12 13 14 14.2 15 15.2 15.3 16 16.2 16.3 17 17.3 18 18.3 19 19.3 20 20.3 21 21.2 22 23 23.2 24 25
D3S1358
D1S1656
D2S441
D10S1248
D13S317
PENTA E
D16S539
D18S51
D2S1338
CSF1P0
PENTA D
0.0385
0.0385 0.1538
0.0481 0.202 0.1154 0.0962
0.0192
0.0192 0.0577
0.0288
0.0288 0.2692
0.1058 0.0865
0.0577 0.375
0.0096
0.2692 0.2885
0.0962 0.1538
0.0385 0.2692 0.3558
0.2981 0.1346 0.0577
0.1731 0.1058 0.0769
0.3077 0.1635 0.0192
0.1731 0.1827 0.1731
0.2788 0.1058 0.0192
0.1538 0.2597 0.0769
0.0769
0.0962 0.0865 0.0962
0.1827 0.327 0.0481 0.0288 0.0673 0.3077
0.2404
0.1923
0.0288
0.1634
0.0192
0.1442
0.25
0.0577 0.1346
0.0096
0.0962
0.0865
0.0962
0.0769
0.0481
0.0096
0.0673
0.25
0.0385
0.0577
0.0577
0.0288
0.0577
0.1154
0.0096
0.1154
0.0288
0.0288
0.0769
0.3077 0.1058
0.0865 0.0385 0.1058 0.0096 0.0192
0.0192
* Corresponding author at: Piazzale Spedali Civili 1, 25123 Brescia, Italy. Tel.: +39 033995480; fax: +39 030 3995839. E-mail address: [email protected] (A. Verzeletti). 1875-1768/$ – see front matter ß 2013 Elsevier Ireland Ltd. All rights reserved. http://dx.doi.org/10.1016/j.fsigss.2013.10.175
0.0673
0.0192 0.1731 0.0962 0.0673
A. Verzeletti et al. / Forensic Science International: Genetics Supplement Series 4 (2013) e344–e345
e345
Table 1 (Continued ) Alleli
D3S1358
D1S1656
D2S441
D10S1248
D13S317
PENTA E
D16S539
D18S51
D2S1338
CSF1P0
PENTA D
PIC PE PD PI Hoss Hatt Estd HWE
0.7299 0.5485 0.8783 0.1217 0.8462 0.775 5.8575 10 0.1921
0.8789 0.7761 0.9564 4.3650 10 0.9615 0.8977 0.0435 0.3989
0.7186 0.5394 0.875 0.125 0.8462 0.7422 0.0595 0.0681
0.725 0.5486 0.8735 0.1265 0.8269 0.7677 5.9195 10 0.023
0.7651 0.6013 0.9223 0.0776 0.8462 0.8015 5.6102 10 0.7735
0.8692 0.672 0.9608 3.9221 10 0.9039 0.8891 4.4981 10 0.6871
0.6874 0.5007 0.8372 0.1628 0.8654 0.7388 6.1525 10 0.0941
0.8495 0.6436 0.9556 4.4429 10 0.9039 0.8729 4.7471 10 0.969
0.8414 0.7162 0.9504 4.9589 10 0.9039 0.8643 4.8592 10 0.6431
0.7111 0.5225 0.8957 0.1043 0.75 0.76 5.9763 10 0.9923
0.8213 0.6828 0.9386 6.1432 10 0.8654 0.8486 5.0786 10 0.3669
Alleli
TH01
D21S11
D7S820
D5S818
TPOX
D8S1179
0.0288 0.1731 0.1346
0.0096
0.0096 0.5865 0.0673
0.0096 0.0288
0.25 0.2309
0.0385 0.3654
0.0769 0.2309
0.0673 0.0577
0.1634 0.0192
0.3654 0.2115 0.0096
0.0288
0.1058 0.4231 0.1731
5 6 7 8 9 9.3 10 11 11.3 12 13 14 14.2 15 15.2 15.3 16 16.2 16.3 17 17.3 18 18.3 19 19.3 20 20.3 21 21.2 22 23 23.2 24 25 26 27 28 29 30 30.2 31 31.2 32.2 33.2 PIC PE PD PI Hoss Hatt Estd HWE
2
2
vWA
0.2885 0.1058 0.1635 0.0865 0.3461 0.0096
2
0.0865
2
2
2
2
2
2
D12S391
0.1731
0.0962
0.0673
0.2597
0.0288
0.0385
0.3173
0.0096
0.0865
0.1442
2
2
D19S433
FGA
0.0096
0.125
0.1154 0.2404 0.2692 0.0192 0.1828 0.0865
0.0096
0.0481 0.0192
0.2981
0.0577 0.4327
0.0673
0.0865
0.1346 0.0096 0.1827 0.2404 0.0096 0.1154 0.0577 0.0385 0.0096
0.0577 0.0673 0.125 0.2597 0.2597 0.0192 0.0096 0.0769 0.1634 0.0192
2
0.7382 0.5605 0.8942 0.1058 0.8077 0.7944 5.8049 10 0.0059
2
0.7861 0.6306 0.9114 8.8545 10 0.8846 0.8295 5.4236 10 0.0013
2
2
0.7801 0.6173 0.9305 6.9535 10 0.7885 0.8161 5.4598 10 0.9481
2
2
0.626 0.4194 0.8394 0.1605 0.6346 0.6932 0.0643 0.4215
0.5455 0.3592 0.7667 0.233 0.5385 0.6004 6.8171 10 0.0703
2
0.7369 0.576 0.8979 0.1021 0.7115 0.7683 5.9152 10 0.1509
2
0.8776 0.7743 0.9557 4.4337 10 0.9039 0.8966 4.3747 10 0.0997
0.0096
0.1154
0.125 0.0865
0.7119 0.5276 0.8817 0.1183 0.8077 0.7588 5.9929 10 0.5114
2
D22S1045
0.0192
0.1924 0.0192 0.0673 0.0096 0.1442 0.0096 0.0962
0.0096
2
2
2
2
0.7867 0.6316 0.9378 6.2154 10 0.7692 0.82 5.4170 10 0.5069
2
2
0.8347 0.7042 0.9519 4.8111 10 0.8846 0.8602 4.9311 10 0.976
2
2
0.6536 0.4634 0.8239 0.1761 0.7885 0.7071 0.0635 0.18
Hobs, observed heterozygosity; Hexp, expected heterozygosity; SE, standard error; PIC, polymorphism information content; PD, power of discrimination; PE, power of exclusion; PI, power of inclusion; HWE, p-value from exact test for Hardy-Weinberg equilibrium.
and ESS recommendations [2]. In this study we analyzed variation of 22 autosomal STRs contained in the new PowerPlex1 Fusion kit to contribute to create an Italian database. Allele frequencies and forensic parameters were used to evaluate suitability and robustness of the new kit for forensic genetic analysis as well as in concordance studies with other kit (AmpFlTR 1IdentifilerTM and NGMTM). Data regarding the allelic frequencies for STRs in these populations would be highly welcomed to be used in forensic genetics for identification and paternity testing. 2. Materials and methods The study was conducted on a sample of 52 unrelated, living in Northern Italy. DNA was extracted from buccal swabs or blood using Chelex1 100 procedure. PCR amplifications were performed in a GeneAmp1 PCR System 9700 Gold Plate using the commercial kit PowerPlex Fusion. Typing was performed by capillary electrophoresis on a ABI Prism1 310 Genetic Analyzer; allele calling was performed with the software GeneMapperID V3.2.
Bonferroni correction for multiple testing (p 0.002). Larger samples sizes are necessary to understand the cause of deviation from equilibrium model at the locus surveyed. There are two explanations for these so-called ‘‘spurious’’ associations: the excess of homozygotes observed in the three markers, due to population substructure and high inbreeding due to widespread endogamy. Designed to meet CODIS and European standards, the PowerPlex1 Fusion System kit enables laboratories to: achieve the most inter database compatibility and highest discrimination of any autosomal STR kit; obtain a higher success rate with difficult casework samples due to robustness and sensitivity; simplify validation and QC efforts by using one kit for both casework and databasing sections. Role of funding None. Conflict of interest None.
3. Results and discussion References Allele frequencies and statistical parameters of forensic importance were estimated; ARLEQUIN software Ver. 3.11 was used to assess departures Hardy-Weinberg equilibrium (Table 1). Deviation has been detected for D21S11 (p = 0.0013) locus, even after a
[1] J.M. Butler, C.R. Hill, Biology and genetics of new autosomal STR loci useful for forensic DNA analysis, Forensic Sci. Rev. 24 (1) (2012) 5–26. [2] S.H. Katsanis, J.K. Wagner, Characterization of the standard and recommended CODIS markers, J. Forensic Sci. 58 (Suppl. 1) (2013) S169–S172.