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STR data for the 15 AmpFlSTR® Identifiler™ loci in the Brazilian population of São Paulo State
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Forensic Science International: Genetics Supplement Series 1 (2008) 367–369 www.elsevier.com/locate/FSIGSS
Research article
STR data for the 15 AmpFlSTR1 IdentifilerTM loci in the Brazilian population of Sa˜o Paulo State M. Sa˜o-Bento a,*, M. Carvalho a, L. Andrade a, V. Lopes a, A. Serra a, J.J. Gamero b, F. Corte-Real c, M.C. Vide a, M.J. Anjos a a
Forensic Genetic Service, Central Region Department, National Institute of Legal Medicine, Portugal b Department of Legal Medicine, Faculty of Medicine, University of Ca´diz, Spain c National Institute of Legal Medicine, Portugal Received 20 August 2007; received in revised form 16 October 2007; accepted 25 October 2007
Abstract Allele frequencies and statistical parameters of forensic interest for the 15 STRs loci of the AmpFlSTR1 IdentifilerTM System were estimated in 294 healthy unrelated individuals of the Brazilian population of Sa˜o Paulo State. A phylogenetic tree was elaborated. The results are in agreement with other population studies and historical data. # 2008 Elsevier Ireland Ltd. All rights reserved. Keywords: Short tandem repeat; Identifiler; Sa˜o Paulo State; Population data
1. Introduction The settlement of Brazil began in Sa˜o Paulo State, in 1532, with the Portuguese arrival. Its ethnic variety, which characterizes this population, has an historical context related with the coming of African slaves groups and subsequent migratory waves of the Spanish, Italian, German and Japanese. A population study of the population of Sa˜o Paulo State was conducted using the Identifiler Amplification Kit [1]. STR data was compared to other population data and a phylogenetic tree was elaborated. 2. Materials and methods Genomic DNA was extracted from blood stains from 294 unrelated, healthy individuals of the population of Sa˜o Paulo State, Brazil, using Chelex method [2]. Typing was performed on a ABI PrismTM 310 Genetic Analyzer. The determination of p values of exact test for the Hardy–Weinberg equilibrium was carried out with GENEPOP software [3]. Genetic distances * Corresponding author at: Servic¸o de Gene´tica Forense, Delegac¸a˜o do Centro, Instituto Nacional de Medicina Legal, Largo da Se´ Nova, 3000-213 Coimbra, Portugal. Tel.: +351 239 854 230; fax: +351 239 820 549. E-mail address: [email protected] (M. Sa˜o-Bento). 1875-1768/$ – see front matter # 2008 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.fsigss.2007.10.005
Fig. 1. Phylogenetic tree elaborated by the neighbor-joining method.
368
Table 1 Allelic frequencies and statistical parameters of forensic interest for the 15 STRs loci included in the Identifiler1 system in Sa˜o Paulo State Population, Brazil (N = 294) Alleles
He Ho Pex PD P
D21S11
D7S820
CSF1PO
0.01190 0.01871
0.02211 0.17517 0.10884
0.00340 0.01020 0.02381
0.06293 0.07483 0.15306
0.27551 0.22109 0.16497
0.24150 0.33503 0.32143
0.29592
0.00170 0.02551
0.21259
0.00170 0.00170
0.12925
0.00170
D3S1358
TH01 0.22959 0.18537 0.12925 0.20748 0.23980 0.00850
D13S317
D16S539
D2S1338
D19S433
0.01170 0.11565 0.07313
0.02211 0.14456
0.00170
0.06293 0.31122 0.27891
0.08503 0.29932 0.25510
0.00170 0.00680 0.11395 0.00680
0.04762
0.00340
0.11395
0.17347
0.01701
0.09524
0.04082
0.02041
0.25000 0.02211 0.30442
0.26020
0.00170
0.00170
0.03061 0.14116 0.06973 0.04252 0.00680 0.00170 0.00170
VWA
TPOX
D18S51
D5S818
0.00680 0.00510 0.48980 0.10884
0.00170
0.00680 0.00680 0.03571
0.07143 0.28061 0.03741
0.01531 0.01361 0.13776
0.05952 0.35884 0.35374
0.00170
0.13605
0.15646
0.10031
0.14966
0.02041
0.12755
0.14456
0.00170
0.22959
0.15306
0.24490
0.12075
0.00340 0.01361 0.00340 0.05952 0.11735 0.15136
0.03571
0.25000
0.04252
0.00510
0.23980
0.27041
0.13435
0.07653
0.21088
0.06803
0.01531
0.13776 0.13095 0.03231
0.07143 0.01023 0.00340
0.04932
0.02211 0.01871 0.00850 0.00170 0.00510
0.10204
0.00340
FGA
0.19558 0.00680 0.13946 0.00170 0.14456
0.09014 0.00170 0.05782 0.00680 0.00170
0.01871 0.15136 0.20408 0.00170 0.27721 0.03571 0.07653 0.09864 0.00850 0.07993 0.00170 0.00170 0.03741 0.00340 0.24024 0.23600 0.64150 0.81575 0.82810
0.24438 0.24100 0.67489 0.83350 0.81451
0.23687 0.23500 0.61283 0.80432 0.14585
0.21289 0.22600 0.47581 0.72288 0.03693
0.23116 0.23400 0.57549 0.78492 0.46583
0.23430 0.22000 0.59015 0.79559 0.05033
0.23207 0.23300 0.59477 0.78801 0.67291
0.23154 0.22700 0.58302 0.78621 0.54885
0.25259 0.25000 0.72161 0.85768 0.92790
0.09014 0.04252 0.02381 0.00170 0.00510
0.23668 0.23300 0.62264 0.80368 0.94500
0.23892 0.23900 0.62493 0.81128 0.41874
0.19524 0.19100 0.42084 0.66294 0.31673
0.25775 0.24800 0.74671 0.87521 0.07547
0.21095 0.20600 0.47760 0.71629 0.45150
He: expected heterozygosity; Ho: observed heterozygosity; Pex: probability of exclusion; PD: power of discrimination; P: probability values of exact tests for Hardy–Weinberg equilibrium.
0.25633 0.25500 0.64596 0.87040 0.90359
M. Sa˜o-Bento et al. / Forensic Science International: Genetics Supplement Series 1 (2008) 367–369
6 7 8 9 9.3 10 11 12 12.2 12.3 13 13.2 14 14.1 14.2 15 15.2 16 16.2 17 17.2 18 18.2 19 20 21 21.2 22 22.2 23 23.2 24 24.2 25 26 27 28 29 29.2 30 30.2 31 31.2 32 32.2 33 33.1 33.2 34.2
D8S1179
M. Sa˜o-Bento et al. / Forensic Science International: Genetics Supplement Series 1 (2008) 367–369
between our population and other population samples [4–19] were calculated with PHYLIP software [20] according to Nei. The correspondent phylogenetic tree was obtained with TREEVIEW software [21]. 3. Results and discussion The allelic frequencies of the Brazilian sample of Sa˜o Paulo State and the forensic interest parameters are shown in Table 1. Verified the Hardy–Weinberg equilibrium, allelic frequencies were compared with other population samples (Fig. 1). 4. Conclusions With exception of the CSF1PO system ( p = 0.03693), no deviations from the Hardy–Weinberg equilibrium were found. STR loci showed a combined probability of exclusion and power of discrimination of 0.9999995 and 0.99999999997, respectively, thus providing a powerful tool for forensic individual identification, paternity investigations and population genetic studies in Sa˜o Paulo State population. This study agrees with other population studies and historical data, since it presents a higher proximity of Sa˜o Paulo State with European populations, mainly with Portugal and Spain, than the other mentioned Brazilian populations, which are closest to African populations. Conflict of interest None. References [1] AmpFISTR1 IdentifilerTM PCR Amplification Kit, Applied Biosystems, Applera, 2001. [2] P.S. Walsh, et al., Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material, Biotechniques 10 (1991) 506–513. [3] M. Raymond, F. Rousset, GENEPOP (version 3.1b): population genetics software for exact tests GENEPOP (version 3.1b), J. Heredity 83 (1995) 248–249.
369
[4] V. Lopes, et al., Frequeˆncias ale´licas dos STRs dos sistemas multiplex Identifiler e PowerPlex-16 regia˜o centro de Portugal: ana´lise da microvariac¸a˜o regional, 2004. [5] J. Garcı´a-Hirschfeld, et al., Allele distribution of 15 STRs in a population from Extremadura (Central–Western Spain), Int. Cong. Series 1239 (2003) 165–169. [6] R. Jacewi, et al., Population genetics of the Identifiler system in Poland, Int. Cong. Series 1261 (2004) 229–232. [7] Z. Szczerkowska, et al., Northern Polish population data and forensic usefulness of 15 autosomal STR loci, Forensic Sci. Int. 144 (2004) 69–71. [8] W. Pepinski, et al., Allele distribution of 15 STR loci in a population sample of Byelorussian minority residing in the north-eastern Poland, Forensic Sci. Int. 139 (2004) 265–267. [9] S. Beleza, et al., 17 STR data (AmpF/STR Identifiler and Powerplex 16 System) from Cabinda (Angola), Forensic Sci. Int. 141 (2004) 193– 196. [10] C. Alves, et al., Contribution for an African autossomic STR database (AmpF/STR Identifiler and Powerplex 16 System) and a report on genotypic variations, Forensic Sci. Int. 139 (2004) 201–205. [11] M. Hashiyada, et al., Polymorphism of 17 STRs by multiplex analysis in Japanese population, Forensic Sci. Int. 133 (2004) 250–253. [12] Y.L. Kim, et al., Allele frequencies of 15 STR loci using AmpF/STR Identifiler kit in a Korean population, Forensic Sci. Int. 136 (2003) 92–95. [13] C.W. Wang, et al., STR data for the AmpFlSTR SGM Plus and Profiler loci from Taiwan, Forensic Sci. Int. 138 (1–3) (2003) 119–122. [14] L.H. Seah, et al., STR Data for the AmpFlSTR Identifiler loci in three ethnic groups (Malay, Chinese, Indian) of the Malaysian population, Forensic Sci. Int. 138 (2003) 134–137. [15] M.A. Chiurillo, et al., Genetic profiling of a central Venezuelan population using 15 STR markers that may be of forensic importance, Forensic Sci. Int. 136 (2003) 99–101. [16] M. Santos, et al., Population genetic data for the STR loci using the AmpF1STR1 IdentifilerTM Kit in Bahia, Brazil, Int. Cong. Series 1261 (2004) 219–222. [17] P. Brito, et al., Estudo de 15 STRs autosso´micos (AmpFISTR1 IdentifilerTM) na Populac¸a˜o do Estado do Amazonas (Brasil), 2004. [18] A.C. Goes, et al., Allele frequencies data and statistic parameters for 16 STR loci in the Rio de Janeiro population, Brazil, Forensic Sci. Int. 140 (2004) 131–132. [19] J.A. Morales, et al., Population genetic data from El Salvador (Central America) using AmpF1SRT1 Identifiler1 PCR Amplification Kit, Int. Cong. Series 1261 (2004) 223–225. [20] PHYLIP (Phylogeny Inference Package Version 3.573c), Copyright by Joseph Felsenstein and University of Washington, 1995. [21] TREEVIEW (Version 1.5.2), Copyright by Roderic D.M. Page, 1998.
Forensic Science International: Genetics Supplement Series 1 (2008) 367–369 www.elsevier.com/locate/FSIGSS
Research article
STR data for the 15 AmpFlSTR1 IdentifilerTM loci in the Brazilian population of Sa˜o Paulo State M. Sa˜o-Bento a,*, M. Carvalho a, L. Andrade a, V. Lopes a, A. Serra a, J.J. Gamero b, F. Corte-Real c, M.C. Vide a, M.J. Anjos a a
Forensic Genetic Service, Central Region Department, National Institute of Legal Medicine, Portugal b Department of Legal Medicine, Faculty of Medicine, University of Ca´diz, Spain c National Institute of Legal Medicine, Portugal Received 20 August 2007; received in revised form 16 October 2007; accepted 25 October 2007
Abstract Allele frequencies and statistical parameters of forensic interest for the 15 STRs loci of the AmpFlSTR1 IdentifilerTM System were estimated in 294 healthy unrelated individuals of the Brazilian population of Sa˜o Paulo State. A phylogenetic tree was elaborated. The results are in agreement with other population studies and historical data. # 2008 Elsevier Ireland Ltd. All rights reserved. Keywords: Short tandem repeat; Identifiler; Sa˜o Paulo State; Population data
1. Introduction The settlement of Brazil began in Sa˜o Paulo State, in 1532, with the Portuguese arrival. Its ethnic variety, which characterizes this population, has an historical context related with the coming of African slaves groups and subsequent migratory waves of the Spanish, Italian, German and Japanese. A population study of the population of Sa˜o Paulo State was conducted using the Identifiler Amplification Kit [1]. STR data was compared to other population data and a phylogenetic tree was elaborated. 2. Materials and methods Genomic DNA was extracted from blood stains from 294 unrelated, healthy individuals of the population of Sa˜o Paulo State, Brazil, using Chelex method [2]. Typing was performed on a ABI PrismTM 310 Genetic Analyzer. The determination of p values of exact test for the Hardy–Weinberg equilibrium was carried out with GENEPOP software [3]. Genetic distances * Corresponding author at: Servic¸o de Gene´tica Forense, Delegac¸a˜o do Centro, Instituto Nacional de Medicina Legal, Largo da Se´ Nova, 3000-213 Coimbra, Portugal. Tel.: +351 239 854 230; fax: +351 239 820 549. E-mail address: [email protected] (M. Sa˜o-Bento). 1875-1768/$ – see front matter # 2008 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.fsigss.2007.10.005
Fig. 1. Phylogenetic tree elaborated by the neighbor-joining method.
368
Table 1 Allelic frequencies and statistical parameters of forensic interest for the 15 STRs loci included in the Identifiler1 system in Sa˜o Paulo State Population, Brazil (N = 294) Alleles
He Ho Pex PD P
D21S11
D7S820
CSF1PO
0.01190 0.01871
0.02211 0.17517 0.10884
0.00340 0.01020 0.02381
0.06293 0.07483 0.15306
0.27551 0.22109 0.16497
0.24150 0.33503 0.32143
0.29592
0.00170 0.02551
0.21259
0.00170 0.00170
0.12925
0.00170
D3S1358
TH01 0.22959 0.18537 0.12925 0.20748 0.23980 0.00850
D13S317
D16S539
D2S1338
D19S433
0.01170 0.11565 0.07313
0.02211 0.14456
0.00170
0.06293 0.31122 0.27891
0.08503 0.29932 0.25510
0.00170 0.00680 0.11395 0.00680
0.04762
0.00340
0.11395
0.17347
0.01701
0.09524
0.04082
0.02041
0.25000 0.02211 0.30442
0.26020
0.00170
0.00170
0.03061 0.14116 0.06973 0.04252 0.00680 0.00170 0.00170
VWA
TPOX
D18S51
D5S818
0.00680 0.00510 0.48980 0.10884
0.00170
0.00680 0.00680 0.03571
0.07143 0.28061 0.03741
0.01531 0.01361 0.13776
0.05952 0.35884 0.35374
0.00170
0.13605
0.15646
0.10031
0.14966
0.02041
0.12755
0.14456
0.00170
0.22959
0.15306
0.24490
0.12075
0.00340 0.01361 0.00340 0.05952 0.11735 0.15136
0.03571
0.25000
0.04252
0.00510
0.23980
0.27041
0.13435
0.07653
0.21088
0.06803
0.01531
0.13776 0.13095 0.03231
0.07143 0.01023 0.00340
0.04932
0.02211 0.01871 0.00850 0.00170 0.00510
0.10204
0.00340
FGA
0.19558 0.00680 0.13946 0.00170 0.14456
0.09014 0.00170 0.05782 0.00680 0.00170
0.01871 0.15136 0.20408 0.00170 0.27721 0.03571 0.07653 0.09864 0.00850 0.07993 0.00170 0.00170 0.03741 0.00340 0.24024 0.23600 0.64150 0.81575 0.82810
0.24438 0.24100 0.67489 0.83350 0.81451
0.23687 0.23500 0.61283 0.80432 0.14585
0.21289 0.22600 0.47581 0.72288 0.03693
0.23116 0.23400 0.57549 0.78492 0.46583
0.23430 0.22000 0.59015 0.79559 0.05033
0.23207 0.23300 0.59477 0.78801 0.67291
0.23154 0.22700 0.58302 0.78621 0.54885
0.25259 0.25000 0.72161 0.85768 0.92790
0.09014 0.04252 0.02381 0.00170 0.00510
0.23668 0.23300 0.62264 0.80368 0.94500
0.23892 0.23900 0.62493 0.81128 0.41874
0.19524 0.19100 0.42084 0.66294 0.31673
0.25775 0.24800 0.74671 0.87521 0.07547
0.21095 0.20600 0.47760 0.71629 0.45150
He: expected heterozygosity; Ho: observed heterozygosity; Pex: probability of exclusion; PD: power of discrimination; P: probability values of exact tests for Hardy–Weinberg equilibrium.
0.25633 0.25500 0.64596 0.87040 0.90359
M. Sa˜o-Bento et al. / Forensic Science International: Genetics Supplement Series 1 (2008) 367–369
6 7 8 9 9.3 10 11 12 12.2 12.3 13 13.2 14 14.1 14.2 15 15.2 16 16.2 17 17.2 18 18.2 19 20 21 21.2 22 22.2 23 23.2 24 24.2 25 26 27 28 29 29.2 30 30.2 31 31.2 32 32.2 33 33.1 33.2 34.2
D8S1179
M. Sa˜o-Bento et al. / Forensic Science International: Genetics Supplement Series 1 (2008) 367–369
between our population and other population samples [4–19] were calculated with PHYLIP software [20] according to Nei. The correspondent phylogenetic tree was obtained with TREEVIEW software [21]. 3. Results and discussion The allelic frequencies of the Brazilian sample of Sa˜o Paulo State and the forensic interest parameters are shown in Table 1. Verified the Hardy–Weinberg equilibrium, allelic frequencies were compared with other population samples (Fig. 1). 4. Conclusions With exception of the CSF1PO system ( p = 0.03693), no deviations from the Hardy–Weinberg equilibrium were found. STR loci showed a combined probability of exclusion and power of discrimination of 0.9999995 and 0.99999999997, respectively, thus providing a powerful tool for forensic individual identification, paternity investigations and population genetic studies in Sa˜o Paulo State population. This study agrees with other population studies and historical data, since it presents a higher proximity of Sa˜o Paulo State with European populations, mainly with Portugal and Spain, than the other mentioned Brazilian populations, which are closest to African populations. Conflict of interest None. References [1] AmpFISTR1 IdentifilerTM PCR Amplification Kit, Applied Biosystems, Applera, 2001. [2] P.S. Walsh, et al., Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material, Biotechniques 10 (1991) 506–513. [3] M. Raymond, F. Rousset, GENEPOP (version 3.1b): population genetics software for exact tests GENEPOP (version 3.1b), J. Heredity 83 (1995) 248–249.
369
[4] V. Lopes, et al., Frequeˆncias ale´licas dos STRs dos sistemas multiplex Identifiler e PowerPlex-16 regia˜o centro de Portugal: ana´lise da microvariac¸a˜o regional, 2004. [5] J. Garcı´a-Hirschfeld, et al., Allele distribution of 15 STRs in a population from Extremadura (Central–Western Spain), Int. Cong. Series 1239 (2003) 165–169. [6] R. Jacewi, et al., Population genetics of the Identifiler system in Poland, Int. Cong. Series 1261 (2004) 229–232. [7] Z. Szczerkowska, et al., Northern Polish population data and forensic usefulness of 15 autosomal STR loci, Forensic Sci. Int. 144 (2004) 69–71. [8] W. Pepinski, et al., Allele distribution of 15 STR loci in a population sample of Byelorussian minority residing in the north-eastern Poland, Forensic Sci. Int. 139 (2004) 265–267. [9] S. Beleza, et al., 17 STR data (AmpF/STR Identifiler and Powerplex 16 System) from Cabinda (Angola), Forensic Sci. Int. 141 (2004) 193– 196. [10] C. Alves, et al., Contribution for an African autossomic STR database (AmpF/STR Identifiler and Powerplex 16 System) and a report on genotypic variations, Forensic Sci. Int. 139 (2004) 201–205. [11] M. Hashiyada, et al., Polymorphism of 17 STRs by multiplex analysis in Japanese population, Forensic Sci. Int. 133 (2004) 250–253. [12] Y.L. Kim, et al., Allele frequencies of 15 STR loci using AmpF/STR Identifiler kit in a Korean population, Forensic Sci. Int. 136 (2003) 92–95. [13] C.W. Wang, et al., STR data for the AmpFlSTR SGM Plus and Profiler loci from Taiwan, Forensic Sci. Int. 138 (1–3) (2003) 119–122. [14] L.H. Seah, et al., STR Data for the AmpFlSTR Identifiler loci in three ethnic groups (Malay, Chinese, Indian) of the Malaysian population, Forensic Sci. Int. 138 (2003) 134–137. [15] M.A. Chiurillo, et al., Genetic profiling of a central Venezuelan population using 15 STR markers that may be of forensic importance, Forensic Sci. Int. 136 (2003) 99–101. [16] M. Santos, et al., Population genetic data for the STR loci using the AmpF1STR1 IdentifilerTM Kit in Bahia, Brazil, Int. Cong. Series 1261 (2004) 219–222. [17] P. Brito, et al., Estudo de 15 STRs autosso´micos (AmpFISTR1 IdentifilerTM) na Populac¸a˜o do Estado do Amazonas (Brasil), 2004. [18] A.C. Goes, et al., Allele frequencies data and statistic parameters for 16 STR loci in the Rio de Janeiro population, Brazil, Forensic Sci. Int. 140 (2004) 131–132. [19] J.A. Morales, et al., Population genetic data from El Salvador (Central America) using AmpF1SRT1 Identifiler1 PCR Amplification Kit, Int. Cong. Series 1261 (2004) 223–225. [20] PHYLIP (Phylogeny Inference Package Version 3.573c), Copyright by Joseph Felsenstein and University of Washington, 1995. [21] TREEVIEW (Version 1.5.2), Copyright by Roderic D.M. Page, 1998.