- Email: [email protected]
Population data for Central Portugal population with NGM amplification kit
Forensic Science International: Genetics Supplement Series 4 (2013) e152–e153
Contents lists available at ScienceDirect
Forensic Science International: Genetics Supplement Series journal homepage: www.elsevier.com/locate/FSIGSS
Population data for Central Portugal population with NGM amplification kit A.M. Bento a,b,*, A. Semo a, V. Lopes a,b, V. Bogas a,b, P. Brito a,b, A. Serra a,b, L. Andrade a,b, L. Souto b,c, F. Corte-Real b,d, M.J. Anjos a,b a
Forensics Genetic Service, Central Delegation, National Institute of Legal Medicine and Forensic Sciences, I.P., Coimbra, Portugal Cencifor, Forensic Science Centre, Portugal Department of Biology, University of Aveiro, Portugal d National Institute of Legal Medicine and Forensic Sciences, I.P., Portugal b c
A R T I C L E I N F O
A B S T R A C T
Article history: Received 4 September 2013 Accepted 2 October 2013
The purpose of this work was to establish frequencies and population statistic parameters for Central Portugal population using NGM amplification kit as well as carry out a comparative study with other population groups. ß 2013 Elsevier Ireland Ltd. All rights reserved.
Keywords: Central Portugal ESS markers NGM Population data
1. Introduction The AmpF‘STR1 NGMTM PCR Amplification Kit simultaneously amplifies the 10 SGM Plus1 Kit loci together with the 5 recommended loci (D10S1248, D22S1045, D2S441, D1S1656 and D12S391). The purpose of this work was to establish frequencies and population statistic parameters for Central Portugal population using NGM amplification kit as well as carry out a comparative study with other population groups.
Arlequin software v3.0 [2] was used to calculate allele frequencies as well as to assess departures from Hardy–Weinberg equilibrium. Other relevant forensic parameters were determined using PowerStat v1.2 [3]. Genetic distances between central Portugal and populations from Spain [4], Austria [5], Galicia (Spain) [6], Turkey [7], Southern Italy [8], Poland [9] and North Portugal [10] were calculated with PHYLIP [11] and p-values from locus to locus comparations with GENEPOP [12]. 3. Results and discussion
2. Materials and methods DNA was extracted from buccal swabs by Chelex 100 method [1] from 150 healthy unrelated individuals from Central Portugal, involved in paternity testing after consent. PCR amplifications were performed using the AmpFlSTR NGM Amplification kit according to manufacturer’s instructions. The electrophoresis was carried out on ABI PRISMTM 3130 Genetic Analyser and data analysis and allele calling was done using GeneMapper V3.2 analysis software.
* Corresponding author at: Forensics Genetic Service, Central Delegation, National Institute of Legal Medicine and Forensic Sciences, I.P., Coimbra, Portugal. Tel.: +351 239 854 220; fax: +351 239 826 132. E-mail address: [email protected] (A.M. Bento). 1875-1768/$ – see front matter ß 2013 Elsevier Ireland Ltd. All rights reserved. http://dx.doi.org/10.1016/j.fsigss.2013.10.079
Table 1 contains allelic frequencies and forensic parameters for all studied markers. No significant deviations from Hardy– Weinberg equilibrium were observed (p < 0.05), except for D2S441. For the 15 loci, the combined power of discrimination was higher than 0.999999 and the combined probability of exclusion was 0.9999995. The high values reflect the forensic value of the used markers. The p-values from locus to locus comparations between Central Portugal population and the other populations highlight the significant differences in one of the 15 loci (vWA) in the Spanish population, in two of the 15 loci (D21D11 and vWA) in the Austrian population, in three of the 15 loci (D3S1358, D19S433 and vWA) in the Galicia population, in eight of the 15 loci (TH01, D16S539, D19S433, D18S51, FGA, D1S1656, D22S1045 and D2S441) in the Turkey population, in five of the 15 loci (TH01, D18S51, D1S1656, D12S391 and D2S441) in the Italy population, in eight of the 15 loci
A.M. Bento et al. / Forensic Science International: Genetics Supplement Series 4 (2013) e152–e153
e153
Table 1 Allele frequencies and forensic parameters of 15 STR loci in Central Portuguese population. D10S1248 vWA 11 12 13 14 15 16 17
P MP PD PE Ho
0.0067 0.0533 0.3 0.2967 0.1967 0.1233 0.0233
0.0790 0.0938 0.9062 0.4079 0.3133
13 14 15 16 17 18 19 20 21
0.01 0.09 0.12 0.22 0.28 0.2 0.04 0.0367 0.0033
0.8901 0.0638 0.9362 0.6240 0.1867
D16S539
D2S1338
D8S1179
D21S11
D18S51
D22S1045 D19S433
8 9 10 11 12 13 14 15
16 17 18 19 20 21 22 23 24 25 26 27
8 9 10 11 12 13 14 15 16 17
20 21.2 27 28 29 30 30.2 31 31.2 32.2 33.2 35 35.2
10 11 12 13 14 15 16 16.2 17 18 19 20 21 22 26
11 12 13 14 15 16 17 18
0.0133 0.0767 0.07 0.2833 0.3267 0.1767 0.0467 0.0067
0.8132 0.0903 0.9097 0.5505 0.2267
0.0467 0.2467 0.1033 0.1067 0.1467 0.02 0.0333 0.11 0.0967 0.0733 0.0133 0.0033
0.9440 0.0343 0.9657 0.7413 0.1267
0.0167 0.0233 0.0533 0.08 0.1133 0.3067 0.25 0.12 0.0267 0.01
0.0642 0.0697 0.9303 0.5745 0.2133
0.0067 0.0033 0.02 0.1567 0.22 0.2667 0.02 0.0367 0.1 0.12 0.0433 0.0033 0.0033
0.2785 0.0520 0.9480 0.5990 0.2000
0.0267 0.0133 0.1767 0.14 0.1167 0.1233 0.18 0.0033 0.0867 0.0667 0.0367 0.0133 0.0067 0.0067 0.0033
0.5740 0.0358 0.9642 0.7413 0.1267
0.1067 0.0033 0.0033 0.03 0.3667 0.3567 0.1233 0.01
0.5337 0.1337 0.8663 0.4707 0.2733
11 12 13 13.2 14 14.2 15 15.2 16 16.2 17 17.2
TH01
0.0033 6 0.12 7 0.2833 8 0.02 8.3 0.28 9 0.02 9.3 0.18 10 0.03 0.0333 0.02 0.0067 0.0033
0.2032 0.0715 0.9284 0.4928 0.2600
FGA 0.2133 0.17 0.1233 0.0033 0.19 0.28 0.02
0.5429 0.0780 0.9220 0.5990 0.2000
17 18 19 20 21 21.2 22 23 23.2 24 25 26 27
0.0067 0.0167 0.0667 0.1633 0.1733 0.0067 0.19 0.1533 0.0033 0.1267 0.0533 0.0333 0.0067
0.3988 0.0446 0.9554 0.7280 0.1333
D2S441
D3S1358
D1S1656
D12S391
10 11 11.3 12 13 13.3 14 15 16
14 15 16 17 18 19
10 11 12 13 14 14.3 15 15.3 16 16.3 17 17.3 18.3 19.3 20.3 22
15 16 17 17.3 18 18.3 19 19.3 20 20.3 21 22 23 24 25 26
0.18 0.3267 0.0767 0.0233 0.0567 0.0067 0.2933 0.03 0.0067
0.0012 0.0998 0.9006 0.5155 0.2467
0.0767 0.22 0.2867 0.25 0.1533 0.0133
0.7694 0.0876 0.9124 0.5387 0.2333
0.01 0.0467 0.1333 0.0733 0.12 0.0033 0.1533 0.0667 0.08 0.04 0.0567 0.1533 0.0433 0.0133 0.0033 0.0033
0.1111 0.0264 0.9736 0.8091 0.0933
0.0267 0.0267 0.1167 0.0233 0.2367 0.03 0.12 0.0233 0.0867 0.0033 0.08 0.0833 0.1 0.0233 0.0167 0.0033
0.1902 0.0303 0.9697 0.6494 0.1733
P: Hardy–Weinberg equilibrium; MP: matching probability; PD: power of discrimination; PE: probability of exclusion; Ho: observed homozigoty.
(D21S11, D3S1358, TH01, D19S433, D18S51, D1S1656, D10S1248 and D2S441) in the Polish population and in four of the 15 loci (D8S1179, D21S11, D3S1358 and D16S539) in the North Portugal population. According to genetic differences between all population pairs Turkish and Polish population groups are more distant from Central Portuguese population than the other population compared in this study. This study reveals the usefulness of NGM STR markers, which can be seen in the high values obtained for the forensic parameters, namely the combined power of discrimination and combined probability of exclusion, making this set of markers a powerful tool for forensic analysis. The Central Portuguese population is similar to other European populations compared. Funding No funding. Conflict of interest None.
References [1] P.S. Walsh, D.A. Metzger, R. Higuchi, Chelex 100 as a medium for simple extraction of DNA for PCR-based typing for forensic material, Biotechniques 10 (1991) 506–513. [2] L. Excoffier, G. Laval, S. Schneider, Arlequin ver. 3.0: an integrated software package for population genetic data analysis, Evol. Bioinform. Online 1 (2005) 47–50. [3] A. Tereba, Tools for analysis of population statistics, Profile DNA (1999) 14–16. [4] O. Garcı´a, J. Alonso, J.A. Cano, et al., Population genetic data and concordance study for the kits Identifiler, NGM, PowerPlex ESX 17 System and Investigator ESSplex in Spain, Forensic Sci. Int. Genet. 6 (2012) e78–e79. [5] P. Hatzer-Grubwieser, B. Berger, D. Niederwieser, M. Steinlechner, Allele frequencies and concordance study of 16 STR loci – including the new European Standard Set (ESS) loci – in anna Austrian population sample, Forensic Sci. Int. Genet. 6 (2012) e50–e51. [6] L. Fernandez-Formoso, C. Phillips, A. Rodriguez, et al., Allele frequencies of 20 STRs from Northwest Spain (Galicia), Forensic Sci. Int. Genet. 6 (2012) e149–e150. [7] O. Bulbul, L. Fernandez-Formoso, H. Altuncul, et al., Allele frequencies of the five new European Standard Set (ESS) STRs and 15 establish STRs in a Turkish population, Forensic Sci. Int. Genet. (2013), http://dx.doi.org/10.1016/j.fsigen.2013.05.006. [8] A. Barbaro, C. Phillips, L.F. Formoso, et al., Distribution of allele frequencies of 20 STRs loci in a population sample from Calabria, Southern Italy, Forensic Sci. Int. Genet. 6 (2012) e137–e138. [9] M. Jedrzejczyk, R. Jacewicz, S. Szram, et al., Genetic population studies on 15 NGMTM STR loci in central Poland population, Forensic Sci. Int. Genet. 6 (2012) e119–e120. [10] M.L. Pontes, M.F. Pinheiro, Population data of the AmpF‘STR1 NGMTM STr loci in a North of Portugal sample, Forensic Sci. Int. Genet. 6 (2012) e127–e128. [11] J. Felsenstein, PHYLIP (Version 3.573c), University of Washington, 1993. [12] M. Raymond, F. Rousset, GENEPOP (version 3.4), 2003.
Contents lists available at ScienceDirect
Forensic Science International: Genetics Supplement Series journal homepage: www.elsevier.com/locate/FSIGSS
Population data for Central Portugal population with NGM amplification kit A.M. Bento a,b,*, A. Semo a, V. Lopes a,b, V. Bogas a,b, P. Brito a,b, A. Serra a,b, L. Andrade a,b, L. Souto b,c, F. Corte-Real b,d, M.J. Anjos a,b a
Forensics Genetic Service, Central Delegation, National Institute of Legal Medicine and Forensic Sciences, I.P., Coimbra, Portugal Cencifor, Forensic Science Centre, Portugal Department of Biology, University of Aveiro, Portugal d National Institute of Legal Medicine and Forensic Sciences, I.P., Portugal b c
A R T I C L E I N F O
A B S T R A C T
Article history: Received 4 September 2013 Accepted 2 October 2013
The purpose of this work was to establish frequencies and population statistic parameters for Central Portugal population using NGM amplification kit as well as carry out a comparative study with other population groups. ß 2013 Elsevier Ireland Ltd. All rights reserved.
Keywords: Central Portugal ESS markers NGM Population data
1. Introduction The AmpF‘STR1 NGMTM PCR Amplification Kit simultaneously amplifies the 10 SGM Plus1 Kit loci together with the 5 recommended loci (D10S1248, D22S1045, D2S441, D1S1656 and D12S391). The purpose of this work was to establish frequencies and population statistic parameters for Central Portugal population using NGM amplification kit as well as carry out a comparative study with other population groups.
Arlequin software v3.0 [2] was used to calculate allele frequencies as well as to assess departures from Hardy–Weinberg equilibrium. Other relevant forensic parameters were determined using PowerStat v1.2 [3]. Genetic distances between central Portugal and populations from Spain [4], Austria [5], Galicia (Spain) [6], Turkey [7], Southern Italy [8], Poland [9] and North Portugal [10] were calculated with PHYLIP [11] and p-values from locus to locus comparations with GENEPOP [12]. 3. Results and discussion
2. Materials and methods DNA was extracted from buccal swabs by Chelex 100 method [1] from 150 healthy unrelated individuals from Central Portugal, involved in paternity testing after consent. PCR amplifications were performed using the AmpFlSTR NGM Amplification kit according to manufacturer’s instructions. The electrophoresis was carried out on ABI PRISMTM 3130 Genetic Analyser and data analysis and allele calling was done using GeneMapper V3.2 analysis software.
* Corresponding author at: Forensics Genetic Service, Central Delegation, National Institute of Legal Medicine and Forensic Sciences, I.P., Coimbra, Portugal. Tel.: +351 239 854 220; fax: +351 239 826 132. E-mail address: [email protected] (A.M. Bento). 1875-1768/$ – see front matter ß 2013 Elsevier Ireland Ltd. All rights reserved. http://dx.doi.org/10.1016/j.fsigss.2013.10.079
Table 1 contains allelic frequencies and forensic parameters for all studied markers. No significant deviations from Hardy– Weinberg equilibrium were observed (p < 0.05), except for D2S441. For the 15 loci, the combined power of discrimination was higher than 0.999999 and the combined probability of exclusion was 0.9999995. The high values reflect the forensic value of the used markers. The p-values from locus to locus comparations between Central Portugal population and the other populations highlight the significant differences in one of the 15 loci (vWA) in the Spanish population, in two of the 15 loci (D21D11 and vWA) in the Austrian population, in three of the 15 loci (D3S1358, D19S433 and vWA) in the Galicia population, in eight of the 15 loci (TH01, D16S539, D19S433, D18S51, FGA, D1S1656, D22S1045 and D2S441) in the Turkey population, in five of the 15 loci (TH01, D18S51, D1S1656, D12S391 and D2S441) in the Italy population, in eight of the 15 loci
A.M. Bento et al. / Forensic Science International: Genetics Supplement Series 4 (2013) e152–e153
e153
Table 1 Allele frequencies and forensic parameters of 15 STR loci in Central Portuguese population. D10S1248 vWA 11 12 13 14 15 16 17
P MP PD PE Ho
0.0067 0.0533 0.3 0.2967 0.1967 0.1233 0.0233
0.0790 0.0938 0.9062 0.4079 0.3133
13 14 15 16 17 18 19 20 21
0.01 0.09 0.12 0.22 0.28 0.2 0.04 0.0367 0.0033
0.8901 0.0638 0.9362 0.6240 0.1867
D16S539
D2S1338
D8S1179
D21S11
D18S51
D22S1045 D19S433
8 9 10 11 12 13 14 15
16 17 18 19 20 21 22 23 24 25 26 27
8 9 10 11 12 13 14 15 16 17
20 21.2 27 28 29 30 30.2 31 31.2 32.2 33.2 35 35.2
10 11 12 13 14 15 16 16.2 17 18 19 20 21 22 26
11 12 13 14 15 16 17 18
0.0133 0.0767 0.07 0.2833 0.3267 0.1767 0.0467 0.0067
0.8132 0.0903 0.9097 0.5505 0.2267
0.0467 0.2467 0.1033 0.1067 0.1467 0.02 0.0333 0.11 0.0967 0.0733 0.0133 0.0033
0.9440 0.0343 0.9657 0.7413 0.1267
0.0167 0.0233 0.0533 0.08 0.1133 0.3067 0.25 0.12 0.0267 0.01
0.0642 0.0697 0.9303 0.5745 0.2133
0.0067 0.0033 0.02 0.1567 0.22 0.2667 0.02 0.0367 0.1 0.12 0.0433 0.0033 0.0033
0.2785 0.0520 0.9480 0.5990 0.2000
0.0267 0.0133 0.1767 0.14 0.1167 0.1233 0.18 0.0033 0.0867 0.0667 0.0367 0.0133 0.0067 0.0067 0.0033
0.5740 0.0358 0.9642 0.7413 0.1267
0.1067 0.0033 0.0033 0.03 0.3667 0.3567 0.1233 0.01
0.5337 0.1337 0.8663 0.4707 0.2733
11 12 13 13.2 14 14.2 15 15.2 16 16.2 17 17.2
TH01
0.0033 6 0.12 7 0.2833 8 0.02 8.3 0.28 9 0.02 9.3 0.18 10 0.03 0.0333 0.02 0.0067 0.0033
0.2032 0.0715 0.9284 0.4928 0.2600
FGA 0.2133 0.17 0.1233 0.0033 0.19 0.28 0.02
0.5429 0.0780 0.9220 0.5990 0.2000
17 18 19 20 21 21.2 22 23 23.2 24 25 26 27
0.0067 0.0167 0.0667 0.1633 0.1733 0.0067 0.19 0.1533 0.0033 0.1267 0.0533 0.0333 0.0067
0.3988 0.0446 0.9554 0.7280 0.1333
D2S441
D3S1358
D1S1656
D12S391
10 11 11.3 12 13 13.3 14 15 16
14 15 16 17 18 19
10 11 12 13 14 14.3 15 15.3 16 16.3 17 17.3 18.3 19.3 20.3 22
15 16 17 17.3 18 18.3 19 19.3 20 20.3 21 22 23 24 25 26
0.18 0.3267 0.0767 0.0233 0.0567 0.0067 0.2933 0.03 0.0067
0.0012 0.0998 0.9006 0.5155 0.2467
0.0767 0.22 0.2867 0.25 0.1533 0.0133
0.7694 0.0876 0.9124 0.5387 0.2333
0.01 0.0467 0.1333 0.0733 0.12 0.0033 0.1533 0.0667 0.08 0.04 0.0567 0.1533 0.0433 0.0133 0.0033 0.0033
0.1111 0.0264 0.9736 0.8091 0.0933
0.0267 0.0267 0.1167 0.0233 0.2367 0.03 0.12 0.0233 0.0867 0.0033 0.08 0.0833 0.1 0.0233 0.0167 0.0033
0.1902 0.0303 0.9697 0.6494 0.1733
P: Hardy–Weinberg equilibrium; MP: matching probability; PD: power of discrimination; PE: probability of exclusion; Ho: observed homozigoty.
(D21S11, D3S1358, TH01, D19S433, D18S51, D1S1656, D10S1248 and D2S441) in the Polish population and in four of the 15 loci (D8S1179, D21S11, D3S1358 and D16S539) in the North Portugal population. According to genetic differences between all population pairs Turkish and Polish population groups are more distant from Central Portuguese population than the other population compared in this study. This study reveals the usefulness of NGM STR markers, which can be seen in the high values obtained for the forensic parameters, namely the combined power of discrimination and combined probability of exclusion, making this set of markers a powerful tool for forensic analysis. The Central Portuguese population is similar to other European populations compared. Funding No funding. Conflict of interest None.
References [1] P.S. Walsh, D.A. Metzger, R. Higuchi, Chelex 100 as a medium for simple extraction of DNA for PCR-based typing for forensic material, Biotechniques 10 (1991) 506–513. [2] L. Excoffier, G. Laval, S. Schneider, Arlequin ver. 3.0: an integrated software package for population genetic data analysis, Evol. Bioinform. Online 1 (2005) 47–50. [3] A. Tereba, Tools for analysis of population statistics, Profile DNA (1999) 14–16. [4] O. Garcı´a, J. Alonso, J.A. Cano, et al., Population genetic data and concordance study for the kits Identifiler, NGM, PowerPlex ESX 17 System and Investigator ESSplex in Spain, Forensic Sci. Int. Genet. 6 (2012) e78–e79. [5] P. Hatzer-Grubwieser, B. Berger, D. Niederwieser, M. Steinlechner, Allele frequencies and concordance study of 16 STR loci – including the new European Standard Set (ESS) loci – in anna Austrian population sample, Forensic Sci. Int. Genet. 6 (2012) e50–e51. [6] L. Fernandez-Formoso, C. Phillips, A. Rodriguez, et al., Allele frequencies of 20 STRs from Northwest Spain (Galicia), Forensic Sci. Int. Genet. 6 (2012) e149–e150. [7] O. Bulbul, L. Fernandez-Formoso, H. Altuncul, et al., Allele frequencies of the five new European Standard Set (ESS) STRs and 15 establish STRs in a Turkish population, Forensic Sci. Int. Genet. (2013), http://dx.doi.org/10.1016/j.fsigen.2013.05.006. [8] A. Barbaro, C. Phillips, L.F. Formoso, et al., Distribution of allele frequencies of 20 STRs loci in a population sample from Calabria, Southern Italy, Forensic Sci. Int. Genet. 6 (2012) e137–e138. [9] M. Jedrzejczyk, R. Jacewicz, S. Szram, et al., Genetic population studies on 15 NGMTM STR loci in central Poland population, Forensic Sci. Int. Genet. 6 (2012) e119–e120. [10] M.L. Pontes, M.F. Pinheiro, Population data of the AmpF‘STR1 NGMTM STr loci in a North of Portugal sample, Forensic Sci. Int. Genet. 6 (2012) e127–e128. [11] J. Felsenstein, PHYLIP (Version 3.573c), University of Washington, 1993. [12] M. Raymond, F. Rousset, GENEPOP (version 3.4), 2003.