- Email: [email protected]
Populational genetic data for 15 STR markers in the Brazilian population of Minas Gerais
Legal Medicine 11 (2009) 45–47
Contents lists available at ScienceDirect
Legal Medicine journal homepage: www.elsevier.com/locate/legalmed
Announcement of Population Data
Populational genetic data for 15 STR markers in the Brazilian population of Minas Gerais Dora Mendez del Castillo a, Carlos Perone a,*, Allyson Rivelli de Queiroz a, Paulo Henrique Orlandi Mourão b, Leonardo de Souza Vasconcellos b, Márcia Arantes do Nascimento a, José Nélio Januario a a b
Núcleo de Ações e Pesquisa em Apoio Diagnóstico, Faculdade de Medicina, Universidade Federal de Minas Gerais (NUPAD/FM-UFMG), 30130-100 Belo Horizonte, Minas Gerais, Brazil Faculdade de Medicina, Universidade Federal de Minas Gerais, Brazil
a r t i c l e
i n f o
Article history: Received 11 March 2008 Received in revised form 4 April 2008 Accepted 22 July 2008 Available online 12 September 2008
a b s t r a c t Fifteen short tandem repeats (STR) markers were analyzed (TPOX, D2S1338, D3S1358, FGA, D5S818, CSF1PO, D7S820, D8S1179, TH01, vWA, D13S317, D16S539, D18S51, D19S433, and D21S11) in unrelated individuals undergoing paternity studies from Minas Gerais state, Brazil. Allele frequencies and statistical parameters for the 15 loci were calculated. Ó 2008 Elsevier Ireland Ltd. All rights reserved.
Keywords: Short tandem repeats (STRs) Population study Paternity Minas Gerais Brazil
Population: An average of 12,000 unrelated adults from Minas Gerais state, Brazil. All the necessary data for the statistical calculations were extracted from the paternity cases databank of the Genetic and Molecular Biology Laboratory of Núcleo de Ações e Pesquisa em Apoio Diagnóstico (NUPAD), Federal University of Minas Gerais, Brazil, between years 2000 and 2006. DNA extraction: DNA was extracted from peripheral blood samples by the Chelex-100 method [1], following the manufacturer’s recommendations. PCR and typing: The PCR were performed using AmpFlSTRÒ IdentifilerTM PCR Amplification Kit (Applied Biosystems), GenePrintÒ STR Systems (Promega Corp.), or non-commercial monoplex systems using primers according to GDB [2]. The PCRs were performed in a GeneAmpÒ PCR System 9700 thermocycler. The separation of the Identifiler PCR products was performed by capillary electrophoresis on an ABI3100-AvantÒ Genetic Analyzer, and genotyping was made by GeneScanÒ v 3.7 and GenotyperÒ v 3.7 softwares. The separation of the GenePrint and monoplex PCR products was carried out on 4% or 6% denaturing polyacrylamide gel electrophoresis and detected by silver stain. Two independent operators made genotyping manually. Results: See Table 1. Analysis of data: Allele frequencies, HWE test (Fisher exact test), observed heterozygosity, expected heterozygosity, power of * Corresponding author. Tel.: +55 31 3409 9710; fax: +55 31 3409 9724. E-mail address: [email protected] (C. Perone). 1344-6223/$ - see front matter Ó 2008 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.legalmed.2008.07.005
exclusion, power of discrimination, and polymorphism information content were calculated for all the 15 loci analyzed. Statistical calculations were performed with GenePop 3.4 [3], GDA 1.0 [4], Arlequin 3.01 [5], and Cervus 2.0 [6] population data analysis softwares. Other remarks: All loci met Hardy–Weinberg expectations based on the Fisher exact test (P > 0.05). These results shown that this panel of 15 STR loci is highly discriminative for the population of Minas Gerais, Brazil. Data comparisons (pair wise differences) with other previously published studies in Brazilian populations [7–9] showed no significant differences in the allele frequencies. Acknowledgements This study was supported by Faculdade de Medicina, Universidade Federal de Minas Gerais, Tribunal de Justiça de Minas Gerais, and Secretaria de Estado da Saúde de Minas Gerais. References [1] Walsh PS, Metzer DA, Higuchi R. Chelex-100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques 1991;10:506–13. [2] Available from: http://www.gdb.org. [3] Raymond M, Rousset F. Genepop (version 1.2): population genetics software for exact tests and ecumenicism. J Hered 1995;86:248–9. [4] Lewis PO, Zaykin D. Genetic data analysis: computer program for the analysis of allelic data, version 1.0. Distributed by the authors; 1999.
46
D.M. del Castillo et al. / Legal Medicine 11 (2009) 45–47
Table 1 Allele frequencies and statistical parameters of 15 STR loci from Minas Gerais population, Brazil Allele 4 5 6 6.3 7 7.3 8 8.3 9 9.1 9.3 10 10.2 10.3 11 11.2 12 12.2 12.3 13 13.2 14 14.2 15 15.2 16 16.2 17 17.2 18 18.2 19 19.2 20 20.2 21 21.2 22 22.2 23 23.2 24 24.2 25 25.2 26 26.2 27 28 28.2 29 29.2 30 30.2 31 31.2 32 32.2 32.3 33 33.2 34 34.2 35 35.2 36 37 38 42.2 43.2 45.2 46.2
TPOX
D2S1338
D3S1358
FGA
D5S818
CSF1PO
0.00046 0.02241
0.00011
0.00053
0.00736
0.01062
0.01883
0.44903
0.02453
0.02313
D7S820
0.00029 0.00005 0.01473 0.00003 0.17459
D8S1179
TH01
vWA
D13S317
0.00008 0.00090 0.19144
D18S51
D19S433
0.25126
0.00057 0.09454
0.02412
0.06791
0.16396
0.00113
0.00038
0.04495
0.08428
0.01195 0.00101
0.00446 0.00014
0.00433
0.30520
0.29533
0.00891
0.03071 0.00038 0.10328 0.01647
0.13809
0.00004
0.03367
0.02397
0.11798 0.00003
0.00741
0.06836
0.00008
0.06078
0.27775
0.28040
0.06117
0.21361 0.00869
0.27752
0.00080
0.31135
0.28729
0.22617
0.07639
0.00051 0.00005
0.03531
0.00370
0.35238
0.30144
0.15421
0.12375
0.00010
0.30861
0.25178
0.11770 0.00023
0.00147
0.00330
0.19180
0.05900
0.00003 0.02838
0.27633
0.00694
0.12965
0.15549
0.09448
0.01246
0.00737
0.00302
0.25791
0.08251
0.04750
0.02341
0.00223
0.00068
0.00010
0.14818
0.14952
0.00107
0.00104
0.03835
0.25265
0.20356
0.28138 0.00016 0.27430 0.00004 0.21046
0.09921 0.00056 0.12785 0.00068 0.14701 0.00011 0.15626
0.00491
0.24876
0.12480
0.07856
0.12183
0.00040
0.17139
0.08298
0.11766
0.00852
0.06688
0.06009
0.12305
0.00092
0.01412
0.03574
0.00256
0.01432 0.00034 0.00710 0.00023 0.00056
0.05229
0.06250 0.08039 0.10023 0.08911 0.07133 0.01732 0.00241 0.00023 0.00011
0.00031
0.00007
0.00087 0.00006 0.00803 0.00467 0.07385 0.00087 0.11644 0.00037 0.14626 0.00187 0.16949 0.00349 0.14776 0.00075 0.15392 0.00012 0.09882 0.00006 0.04514 0.00012 0.01588 0.00616
D21S11
0.00049 0.00011
0.16409 0.00015 0.16921
0.00126
0.00521
D16S539
0.24919 0.03375 0.27459 0.04167 0.13955 0.05311 0.03266 0.01690 0.00161 0.00085 0.00028
0.00023
0.00090 0.00240 0.00069 0.00069 0.00057
0.00023
0.00011
0.03880 0.17514 0.00011 0.21474 0.00057 0.22001 0.03011 0.06719 0.09661 0.01339 0.08494 0.00011 0.00481 0.03056 0.00389 0.00240 0.00870 0.00023 0.00286 0.00023 0.00023
0.00249 0.00006 0.00044 0.00044 0.00056 0.00006
0.00006 0.00037 0.00012 0.00006
STR
TPOX
D2S1338
D3S1358
FGA
D5S818
CSF1PO
D7S820
D8S1179
TH01
vWA
D13S317
D16S539
D18S51
D19S433
D21S11
n OH
39,396 0.69586
8720 0.87592
25,126 0.77211
16,060 0.86899
28,248 0.73421
39,510 0.74452
38,370 0.79729
9988 0.80897
38,880 0.79460
38,310 0.80574
38,418 0.77792
36,698 0.79465
8870 0.87937
21,068 0.82106
8736 0.85279
47
D.M. del Castillo et al. / Legal Medicine 11 (2009) 45–47 Table 1 (continued) STR
TPOX
D2S1338
D3S1358
FGA
D5S818
CSF1PO
D7S820
D8S1179
TH01
vWA
D13S317
D16S539
D18S51
D19S433
D21S11
EH PE PD PIC P
0.69583 0.420 0.862 0.650 0.6153
0.88703 0.769 0.977 0.877 0.1635
0.77746 0.560 0.915 0.742 0.1785
0.87319 0.741 0.970 0.860 0.2911
0.73643 0.490 0.887 0.693 0.3833
0.74447 0.500 0.890 0.700 0.2112
0.80103 0.601 0.931 0.772 0.6906
0.80878 0.620 0.938 0.783 0.8690
0.79898 0.597 0.928 0.767 0.1600
0.81102 0.620 0.938 0.785 0.4184
0.77700 0.557 0.919 0.745 0.2762
0.79011 0.581 0.925 0.759 0.6852
0.88620 0.767 0.976 0.875 0.8153
0.82412 0.644 0.948 0.803 0.0676
0.85018 0.695 0.961 0.833 0.2838
n, number of chromosomes; OH, observed heterozygosity; EH, expected heterozygosity; PE, power of exclusion; PD, power of discrimination; PIC, polymorphism information content; P, Hardy–Weinberg P-values (equilibrium test – Fisher).
[5] Excoffier L, Laval G, Schneider S. Arlequin v.3.0: an integrated software package for population genetics data analysis. Evol Bioinform 2005;1:47–50 [online]. [6] Marshall T. Cervus statistical software, v.2.0. University of Edinburgh; 1998– 2001. [7] Dellalibera E, Havro ML, Souza M, Kajihara K, Mauricio-da-Silva L, dos Santos Silva R. Genetic analysis of 13 STR loci in the population from the State of Pernambuco, northeast Brazil. Forensic Sci Int 2004;146:57–9. [8] Silva EB, Dellalibera E, Souza M, Santos RS, Silva ML. Population genetics of eight STR loci – CSF1PO, TPOX, TH01, D16S359, D7S820, D13S317, F13B and LPL – in a
Brazilian population from the State of Piaui, northeast Brazil. Forensic Sci Int 2001;126:90–2. [9] Souza Góes AC, Silva DA, Gil EHF, Silva MTD, Pereira RW, Carvalho EF. Allele frequencies data and statistic parameters for 16 STR loci – D19S433, D2S1338, CSF1PO, D16S539, D7S820, D21S11, D18S51, D13S317, D5S818, FGA, Penta E, TH01, vWa, D8S1179, TPOX, D3S1358 – in the Rio de Janeiro population, Brazil. Forensic Sci Int 2004;140:131–2.
Contents lists available at ScienceDirect
Legal Medicine journal homepage: www.elsevier.com/locate/legalmed
Announcement of Population Data
Populational genetic data for 15 STR markers in the Brazilian population of Minas Gerais Dora Mendez del Castillo a, Carlos Perone a,*, Allyson Rivelli de Queiroz a, Paulo Henrique Orlandi Mourão b, Leonardo de Souza Vasconcellos b, Márcia Arantes do Nascimento a, José Nélio Januario a a b
Núcleo de Ações e Pesquisa em Apoio Diagnóstico, Faculdade de Medicina, Universidade Federal de Minas Gerais (NUPAD/FM-UFMG), 30130-100 Belo Horizonte, Minas Gerais, Brazil Faculdade de Medicina, Universidade Federal de Minas Gerais, Brazil
a r t i c l e
i n f o
Article history: Received 11 March 2008 Received in revised form 4 April 2008 Accepted 22 July 2008 Available online 12 September 2008
a b s t r a c t Fifteen short tandem repeats (STR) markers were analyzed (TPOX, D2S1338, D3S1358, FGA, D5S818, CSF1PO, D7S820, D8S1179, TH01, vWA, D13S317, D16S539, D18S51, D19S433, and D21S11) in unrelated individuals undergoing paternity studies from Minas Gerais state, Brazil. Allele frequencies and statistical parameters for the 15 loci were calculated. Ó 2008 Elsevier Ireland Ltd. All rights reserved.
Keywords: Short tandem repeats (STRs) Population study Paternity Minas Gerais Brazil
Population: An average of 12,000 unrelated adults from Minas Gerais state, Brazil. All the necessary data for the statistical calculations were extracted from the paternity cases databank of the Genetic and Molecular Biology Laboratory of Núcleo de Ações e Pesquisa em Apoio Diagnóstico (NUPAD), Federal University of Minas Gerais, Brazil, between years 2000 and 2006. DNA extraction: DNA was extracted from peripheral blood samples by the Chelex-100 method [1], following the manufacturer’s recommendations. PCR and typing: The PCR were performed using AmpFlSTRÒ IdentifilerTM PCR Amplification Kit (Applied Biosystems), GenePrintÒ STR Systems (Promega Corp.), or non-commercial monoplex systems using primers according to GDB [2]. The PCRs were performed in a GeneAmpÒ PCR System 9700 thermocycler. The separation of the Identifiler PCR products was performed by capillary electrophoresis on an ABI3100-AvantÒ Genetic Analyzer, and genotyping was made by GeneScanÒ v 3.7 and GenotyperÒ v 3.7 softwares. The separation of the GenePrint and monoplex PCR products was carried out on 4% or 6% denaturing polyacrylamide gel electrophoresis and detected by silver stain. Two independent operators made genotyping manually. Results: See Table 1. Analysis of data: Allele frequencies, HWE test (Fisher exact test), observed heterozygosity, expected heterozygosity, power of * Corresponding author. Tel.: +55 31 3409 9710; fax: +55 31 3409 9724. E-mail address: [email protected] (C. Perone). 1344-6223/$ - see front matter Ó 2008 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.legalmed.2008.07.005
exclusion, power of discrimination, and polymorphism information content were calculated for all the 15 loci analyzed. Statistical calculations were performed with GenePop 3.4 [3], GDA 1.0 [4], Arlequin 3.01 [5], and Cervus 2.0 [6] population data analysis softwares. Other remarks: All loci met Hardy–Weinberg expectations based on the Fisher exact test (P > 0.05). These results shown that this panel of 15 STR loci is highly discriminative for the population of Minas Gerais, Brazil. Data comparisons (pair wise differences) with other previously published studies in Brazilian populations [7–9] showed no significant differences in the allele frequencies. Acknowledgements This study was supported by Faculdade de Medicina, Universidade Federal de Minas Gerais, Tribunal de Justiça de Minas Gerais, and Secretaria de Estado da Saúde de Minas Gerais. References [1] Walsh PS, Metzer DA, Higuchi R. Chelex-100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques 1991;10:506–13. [2] Available from: http://www.gdb.org. [3] Raymond M, Rousset F. Genepop (version 1.2): population genetics software for exact tests and ecumenicism. J Hered 1995;86:248–9. [4] Lewis PO, Zaykin D. Genetic data analysis: computer program for the analysis of allelic data, version 1.0. Distributed by the authors; 1999.
46
D.M. del Castillo et al. / Legal Medicine 11 (2009) 45–47
Table 1 Allele frequencies and statistical parameters of 15 STR loci from Minas Gerais population, Brazil Allele 4 5 6 6.3 7 7.3 8 8.3 9 9.1 9.3 10 10.2 10.3 11 11.2 12 12.2 12.3 13 13.2 14 14.2 15 15.2 16 16.2 17 17.2 18 18.2 19 19.2 20 20.2 21 21.2 22 22.2 23 23.2 24 24.2 25 25.2 26 26.2 27 28 28.2 29 29.2 30 30.2 31 31.2 32 32.2 32.3 33 33.2 34 34.2 35 35.2 36 37 38 42.2 43.2 45.2 46.2
TPOX
D2S1338
D3S1358
FGA
D5S818
CSF1PO
0.00046 0.02241
0.00011
0.00053
0.00736
0.01062
0.01883
0.44903
0.02453
0.02313
D7S820
0.00029 0.00005 0.01473 0.00003 0.17459
D8S1179
TH01
vWA
D13S317
0.00008 0.00090 0.19144
D18S51
D19S433
0.25126
0.00057 0.09454
0.02412
0.06791
0.16396
0.00113
0.00038
0.04495
0.08428
0.01195 0.00101
0.00446 0.00014
0.00433
0.30520
0.29533
0.00891
0.03071 0.00038 0.10328 0.01647
0.13809
0.00004
0.03367
0.02397
0.11798 0.00003
0.00741
0.06836
0.00008
0.06078
0.27775
0.28040
0.06117
0.21361 0.00869
0.27752
0.00080
0.31135
0.28729
0.22617
0.07639
0.00051 0.00005
0.03531
0.00370
0.35238
0.30144
0.15421
0.12375
0.00010
0.30861
0.25178
0.11770 0.00023
0.00147
0.00330
0.19180
0.05900
0.00003 0.02838
0.27633
0.00694
0.12965
0.15549
0.09448
0.01246
0.00737
0.00302
0.25791
0.08251
0.04750
0.02341
0.00223
0.00068
0.00010
0.14818
0.14952
0.00107
0.00104
0.03835
0.25265
0.20356
0.28138 0.00016 0.27430 0.00004 0.21046
0.09921 0.00056 0.12785 0.00068 0.14701 0.00011 0.15626
0.00491
0.24876
0.12480
0.07856
0.12183
0.00040
0.17139
0.08298
0.11766
0.00852
0.06688
0.06009
0.12305
0.00092
0.01412
0.03574
0.00256
0.01432 0.00034 0.00710 0.00023 0.00056
0.05229
0.06250 0.08039 0.10023 0.08911 0.07133 0.01732 0.00241 0.00023 0.00011
0.00031
0.00007
0.00087 0.00006 0.00803 0.00467 0.07385 0.00087 0.11644 0.00037 0.14626 0.00187 0.16949 0.00349 0.14776 0.00075 0.15392 0.00012 0.09882 0.00006 0.04514 0.00012 0.01588 0.00616
D21S11
0.00049 0.00011
0.16409 0.00015 0.16921
0.00126
0.00521
D16S539
0.24919 0.03375 0.27459 0.04167 0.13955 0.05311 0.03266 0.01690 0.00161 0.00085 0.00028
0.00023
0.00090 0.00240 0.00069 0.00069 0.00057
0.00023
0.00011
0.03880 0.17514 0.00011 0.21474 0.00057 0.22001 0.03011 0.06719 0.09661 0.01339 0.08494 0.00011 0.00481 0.03056 0.00389 0.00240 0.00870 0.00023 0.00286 0.00023 0.00023
0.00249 0.00006 0.00044 0.00044 0.00056 0.00006
0.00006 0.00037 0.00012 0.00006
STR
TPOX
D2S1338
D3S1358
FGA
D5S818
CSF1PO
D7S820
D8S1179
TH01
vWA
D13S317
D16S539
D18S51
D19S433
D21S11
n OH
39,396 0.69586
8720 0.87592
25,126 0.77211
16,060 0.86899
28,248 0.73421
39,510 0.74452
38,370 0.79729
9988 0.80897
38,880 0.79460
38,310 0.80574
38,418 0.77792
36,698 0.79465
8870 0.87937
21,068 0.82106
8736 0.85279
47
D.M. del Castillo et al. / Legal Medicine 11 (2009) 45–47 Table 1 (continued) STR
TPOX
D2S1338
D3S1358
FGA
D5S818
CSF1PO
D7S820
D8S1179
TH01
vWA
D13S317
D16S539
D18S51
D19S433
D21S11
EH PE PD PIC P
0.69583 0.420 0.862 0.650 0.6153
0.88703 0.769 0.977 0.877 0.1635
0.77746 0.560 0.915 0.742 0.1785
0.87319 0.741 0.970 0.860 0.2911
0.73643 0.490 0.887 0.693 0.3833
0.74447 0.500 0.890 0.700 0.2112
0.80103 0.601 0.931 0.772 0.6906
0.80878 0.620 0.938 0.783 0.8690
0.79898 0.597 0.928 0.767 0.1600
0.81102 0.620 0.938 0.785 0.4184
0.77700 0.557 0.919 0.745 0.2762
0.79011 0.581 0.925 0.759 0.6852
0.88620 0.767 0.976 0.875 0.8153
0.82412 0.644 0.948 0.803 0.0676
0.85018 0.695 0.961 0.833 0.2838
n, number of chromosomes; OH, observed heterozygosity; EH, expected heterozygosity; PE, power of exclusion; PD, power of discrimination; PIC, polymorphism information content; P, Hardy–Weinberg P-values (equilibrium test – Fisher).
[5] Excoffier L, Laval G, Schneider S. Arlequin v.3.0: an integrated software package for population genetics data analysis. Evol Bioinform 2005;1:47–50 [online]. [6] Marshall T. Cervus statistical software, v.2.0. University of Edinburgh; 1998– 2001. [7] Dellalibera E, Havro ML, Souza M, Kajihara K, Mauricio-da-Silva L, dos Santos Silva R. Genetic analysis of 13 STR loci in the population from the State of Pernambuco, northeast Brazil. Forensic Sci Int 2004;146:57–9. [8] Silva EB, Dellalibera E, Souza M, Santos RS, Silva ML. Population genetics of eight STR loci – CSF1PO, TPOX, TH01, D16S359, D7S820, D13S317, F13B and LPL – in a
Brazilian population from the State of Piaui, northeast Brazil. Forensic Sci Int 2001;126:90–2. [9] Souza Góes AC, Silva DA, Gil EHF, Silva MTD, Pereira RW, Carvalho EF. Allele frequencies data and statistic parameters for 16 STR loci – D19S433, D2S1338, CSF1PO, D16S539, D7S820, D21S11, D18S51, D13S317, D5S818, FGA, Penta E, TH01, vWa, D8S1179, TPOX, D3S1358 – in the Rio de Janeiro population, Brazil. Forensic Sci Int 2004;140:131–2.