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Allele frequencies of sixteen STRs in the population of Northern Portugal
Forensic Science International 148 (2005) 221–223
Announcement of population data
Allele frequencies of sixteen STRs in the population of Northern Portugal M.F. Pinheiro*, Laura Caine´, Lurdes Pontes, David Abrantes, Gabriela Lima, Maria J. Pereira, Pedro Rezende National Institute of Legal Medicine, Delegation of Porto, Portugal Received 18 March 2004; received in revised form 20 April 2004; accepted 28 April 2004 Available online 17 June 2004
Abstract Allele frequencies of sixteen autossomal short tandem repeats (STRs), D3S1358, VWA, D16S539, D8S1179, D21S11, D18S51, TH01, FGA, D5S818, D13S317, D7S820, TPOX, CSF1PO, Penta D, Penta E (included in the PowerPlex1 16 kit), and the SE33 (PowerPlex1 ES Monoplex System SE33) were determined in a sample of 200 healthy unrelated individuals from the north of Portugal. # 2004 Elsevier Ireland Ltd. All rights reserved. Keywords: Short tandem repeats; Northern Portugal; DNA typing; Population genetics
Population: A total number of 200 healthy unrelated individuals from the north of Portugal (involved in paternity testing). Extraction: Blood stains were collected and air dried. DNA was extracted using the Chelex1 resin [1]. PCR: The co-amplification of the loci D3S1358, VWA, D16S539, D8S1179, D21S11, D18S51, TH01, FGA, D5S818, D13S317, D7S820, TPOX, CSF1PO, Penta D, Penta E, Amelogenin and SE33 (ACTBP2) was performed using the PowerPlex1 16 System and PowerPlex1 ES Monoplex System SE33 (Promega). Reactions for multiplex PCR were prepared according to manufacturer’s instructions [2,3]. All loci were amplified in a thermocycler GeneAmp1 PCR System 9700 (Applied Biosystems). Typing: The amplified products were detected and separated by capillary electrophoresis using an ABI PRISM1 3100 Genetic Analyzer (Applied Biosystems). The results were analyzed with the GeneScan1 Analysis v.3.7 software and allele designations were determined automatically using the Genotyper1 v.3.7 software (Applied Biosystems) by comparison with an allelic ladder. * Corresponding author. Tel.: þ351 22 207 38 50; fax: þ351 22 332 59 31. E-mail address: [email protected] (M.F. Pinheiro).
Results: See Tables 1 and 2. Quality control: Proficiency testing of the GEP-ISFG. Analysis of data: Allele frequencies were calculated by the direct counting method (Table 1) and the Hardy–Weinberg equilibrium was tested using the exact test, involving the GENEPOP (version 3.4) software package [4]. Independence among loci was estimated by means of genotype disequilibrium testing for each pair of loci using the Fisher’s method (using the same software package). The potential usefulness of the considered loci was assessed by calculating some statistical parameters of forensic interest (Table 2). Other remarks: The results show that all but one (D5S818) loci were in Hardy–Weinberg equilibrium (Table 2). The independence of loci was also verified. The forensic parameters indicated that these sixteen loci are highly discriminating in the Portuguese population (especially the SE33 locus), for both paternity testing and routine forensic casework. The acumulated PEX is 0.999999940. The observed allele frequency distribution in the sample analysed didn’t show significant differences from other populations with similar origins like those reported for Madeira [5] and Ac¸ores Archipelagos [6]. Some alleles found in those populations were absent in our study. On the other hand in our sample other alleles were present that were not found in Madeira and Ac¸ores. In the mentioned
0379-0738/$ – see front matter # 2004 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.forsciint.2004.04.075
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M.F. Pinheiro et al. / Forensic Science International 148 (2005) 221–223
Table 1 Allele frequencies of the 16 loci in a population from the north of Portugal (n ¼ 200) Allele SE33
D3S1358 VWA
D16S539 D8S1179 D21S11 D18S51 TH01
FGA D5S818
D13S317 D7S820 TPOX CSF1PO Penta D Penta E
5 6 6.3 7 8 9 9.3 10 11 12 13 14 15 16 17 18 18.2 19 20 21 21.2 22 22.2 23 23.2 24 24.2 25 25.2 26 26.2 27 27.2 28 28.2 29 29.2 30 30.2 31 31.2 32 32.2 33 33.2 34 34.2 35
– – – – – – – – – 0.002 0.005 0.132 0.245 0.228 0.230 0.148 – 0.008 0.002 – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – 0.018 0.142 – 0.062 0.290 0.312 0.158 0.018 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – – – – – – – – – – – – 0.008 0.002 0.062 0.148 0.170 – 0.180 – 0.150 0.002 0.123 – 0.093 – 0.042 – 0.020 – – – – – – – – – – – – – – – –
– – – – 0.130 0.068 – 0.038 0.302 0.295 0.115 0.050 0.002 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – 0.002 – – – – – – 0.005 0.012 0.035 0.038 0.060 0.085 0.070 – 0.080 0.050 0.035 0.010 0.010 0.040 – 0.035 – 0.040 – 0.048 – 0.038 – 0.055 – 0.080 – 0.055 – 0.055 – 0.030 – 0.020 0.002 – 0.002 – 0.008
– – – – – – – – – – 0.002 0.088 0.128 0.248 0.277 0.205 – 0.052 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – 0.002 0.012 – 0.093 0.095 0.140 0.290 0.240 0.098 0.030 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – – – – – – – – – – – – – – – – – – – – – – – 0.002 – 0.002 – – 0.020 – 0.157 – 0.220 0.005 0.252 0.028 0.068 0.130 0.008 0.078 – 0.025 – 0.005 –
– – – – – – – 0.020 0.010 0.122 0.140 0.130 0.130 0.180 0.148 0.052 – 0.038 0.018 0.008 – – – 0.002 – – – 0.002 – – – – – – – – – – – – – – – – – – – –
– 0.202 – 0.198 0.112 0.188 0.285 0.015 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – 0.012 0.018 – 0.052 0.335 0.403 0.158 0.022 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
0.002 0.002 – 0.028 0.142 0.155 – 0.278 0.200 0.145 0.040 0.008 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – 0.528 0.102 – 0.062 0.273 0.030 0.005 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – 0.010 0.025 – 0.305 0.270 0.325 0.053 0.012 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – 0.015 0.010 0.217 – 0.060 0.190 0.175 0.235 0.065 0.025 0.008 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
0.075 – – 0.140 0.008 0.008 – 0.110 0.128 0.192 0.095 0.058 0.032 0.060 0.035 0.022 – 0.012 0.010 0.008 – 0.005 – 0.002 – – – – – – – – – – – – – – – – – – – – – – – –
Table 2 Statistical parameters of forensic interest System SE33
D3S1358 VWA
D16S539 D8S1179 D21S11 D18S51 TH01
FGA
D5S818 D13S317 D7S820 TPOX
CSF1PO Penta D Penta E
p Hobs Hesp PD PEX PIC
0.5957 0.8200 0.7979 0.9266 0.5927 0.7641
0.8844 0.8150 0.7705 0.9068 0.5549 0.7327
0.5000 0.8650 0.8669 0.9669 0.7261 0.8496
0.0284 0.7250 0.6990 0.8461 0.4494 0.6450
0.3652 0.7650 0.7266 0.8710 0.4760 0.6742
0.5131 0.9300 0.9486 0.9948 0.8909 0.9435
0.1565 0.7350 0.7950 0.9246 0.5929 0.7620
0.8283 0.8450 0.8126 0.9363 0.6309 0.7857
0.9971 0.8550 0.8358 0.9505 0.6722 0.8134
0.5396 0.8400 0.8746 0.9705 0.7416 0.8588
0.0940 0.7550 0.7927 0.9230 0.5847 0.7581
0.6804 0.7700 0.7848 0.9174 0.5849 0.7522
0.5866 0.8800 0.8172 0.9393 0.6343 0.7900
0.7714 0.6600 0.6337 0.7808 0.3869 0.5799
0.1014 0.8050 0.8240 0.9435 0.6459 0.7978
0.4561 0.8950 0.8924 0.9781 0.7798 0.8804
p: Hardy–Weinberg equilibrium exact test; Hobs: observed heterozygosity; Hexp: expected heterozygosity; PD: power of discrimination; PEX: probability of exclusion; PIC: polymorphic information content.
M.F. Pinheiro et al. / Forensic Science International 148 (2005) 221–223
populations, these referred alleles were present in low frequencies. As this is the first study that includes data from both PowerPlex1 16 System and SE33 (ACTBP2), no other comparisons were made. This paper follows the guidelines for publication data requested by the journal [7]. The complete data set is available upon request. References [1] P.S. Walsh, D.A. Metzger, R. Higuchi, CHELEX1 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material, BioTechniques 10 (4) (1991) 506– 513.
223
[2] Technical Manual, PowerPlex1 16 System, Promega Corporation. [3] Technical Manual, PowerPlex1 ES Monoplex System, Promega Corporation. [4] M. Raymond, F. Rousset, GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism, J. Hered. 86 (1995) 248–249. [5] A.T. Fernandes, A. Brehm, C. Alves, L. Gusma˜ o, A. Amorim, Genetic profile of the Madeira Archipelago population using the new PowerPlex1 16 System Kit, Forensic Sci. Int. 125 (2002) 281–283. [6] R.G. Velosa, A.T. Fernandes, A. Brehm, Genetic profile of the Ac¸ores Archipelago population using the new PowerPlex1 16 System Kit, Forensic Sci. Int. 129 (2002) 68–71. [7] P. Lincoln, A. Carracedo, Publication of data of human polymorphims, Forensic Sci. Int. 110 (2000) 3–5.
Announcement of population data
Allele frequencies of sixteen STRs in the population of Northern Portugal M.F. Pinheiro*, Laura Caine´, Lurdes Pontes, David Abrantes, Gabriela Lima, Maria J. Pereira, Pedro Rezende National Institute of Legal Medicine, Delegation of Porto, Portugal Received 18 March 2004; received in revised form 20 April 2004; accepted 28 April 2004 Available online 17 June 2004
Abstract Allele frequencies of sixteen autossomal short tandem repeats (STRs), D3S1358, VWA, D16S539, D8S1179, D21S11, D18S51, TH01, FGA, D5S818, D13S317, D7S820, TPOX, CSF1PO, Penta D, Penta E (included in the PowerPlex1 16 kit), and the SE33 (PowerPlex1 ES Monoplex System SE33) were determined in a sample of 200 healthy unrelated individuals from the north of Portugal. # 2004 Elsevier Ireland Ltd. All rights reserved. Keywords: Short tandem repeats; Northern Portugal; DNA typing; Population genetics
Population: A total number of 200 healthy unrelated individuals from the north of Portugal (involved in paternity testing). Extraction: Blood stains were collected and air dried. DNA was extracted using the Chelex1 resin [1]. PCR: The co-amplification of the loci D3S1358, VWA, D16S539, D8S1179, D21S11, D18S51, TH01, FGA, D5S818, D13S317, D7S820, TPOX, CSF1PO, Penta D, Penta E, Amelogenin and SE33 (ACTBP2) was performed using the PowerPlex1 16 System and PowerPlex1 ES Monoplex System SE33 (Promega). Reactions for multiplex PCR were prepared according to manufacturer’s instructions [2,3]. All loci were amplified in a thermocycler GeneAmp1 PCR System 9700 (Applied Biosystems). Typing: The amplified products were detected and separated by capillary electrophoresis using an ABI PRISM1 3100 Genetic Analyzer (Applied Biosystems). The results were analyzed with the GeneScan1 Analysis v.3.7 software and allele designations were determined automatically using the Genotyper1 v.3.7 software (Applied Biosystems) by comparison with an allelic ladder. * Corresponding author. Tel.: þ351 22 207 38 50; fax: þ351 22 332 59 31. E-mail address: [email protected] (M.F. Pinheiro).
Results: See Tables 1 and 2. Quality control: Proficiency testing of the GEP-ISFG. Analysis of data: Allele frequencies were calculated by the direct counting method (Table 1) and the Hardy–Weinberg equilibrium was tested using the exact test, involving the GENEPOP (version 3.4) software package [4]. Independence among loci was estimated by means of genotype disequilibrium testing for each pair of loci using the Fisher’s method (using the same software package). The potential usefulness of the considered loci was assessed by calculating some statistical parameters of forensic interest (Table 2). Other remarks: The results show that all but one (D5S818) loci were in Hardy–Weinberg equilibrium (Table 2). The independence of loci was also verified. The forensic parameters indicated that these sixteen loci are highly discriminating in the Portuguese population (especially the SE33 locus), for both paternity testing and routine forensic casework. The acumulated PEX is 0.999999940. The observed allele frequency distribution in the sample analysed didn’t show significant differences from other populations with similar origins like those reported for Madeira [5] and Ac¸ores Archipelagos [6]. Some alleles found in those populations were absent in our study. On the other hand in our sample other alleles were present that were not found in Madeira and Ac¸ores. In the mentioned
0379-0738/$ – see front matter # 2004 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.forsciint.2004.04.075
222
M.F. Pinheiro et al. / Forensic Science International 148 (2005) 221–223
Table 1 Allele frequencies of the 16 loci in a population from the north of Portugal (n ¼ 200) Allele SE33
D3S1358 VWA
D16S539 D8S1179 D21S11 D18S51 TH01
FGA D5S818
D13S317 D7S820 TPOX CSF1PO Penta D Penta E
5 6 6.3 7 8 9 9.3 10 11 12 13 14 15 16 17 18 18.2 19 20 21 21.2 22 22.2 23 23.2 24 24.2 25 25.2 26 26.2 27 27.2 28 28.2 29 29.2 30 30.2 31 31.2 32 32.2 33 33.2 34 34.2 35
– – – – – – – – – 0.002 0.005 0.132 0.245 0.228 0.230 0.148 – 0.008 0.002 – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – 0.018 0.142 – 0.062 0.290 0.312 0.158 0.018 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – – – – – – – – – – – – 0.008 0.002 0.062 0.148 0.170 – 0.180 – 0.150 0.002 0.123 – 0.093 – 0.042 – 0.020 – – – – – – – – – – – – – – – –
– – – – 0.130 0.068 – 0.038 0.302 0.295 0.115 0.050 0.002 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – 0.002 – – – – – – 0.005 0.012 0.035 0.038 0.060 0.085 0.070 – 0.080 0.050 0.035 0.010 0.010 0.040 – 0.035 – 0.040 – 0.048 – 0.038 – 0.055 – 0.080 – 0.055 – 0.055 – 0.030 – 0.020 0.002 – 0.002 – 0.008
– – – – – – – – – – 0.002 0.088 0.128 0.248 0.277 0.205 – 0.052 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – 0.002 0.012 – 0.093 0.095 0.140 0.290 0.240 0.098 0.030 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – – – – – – – – – – – – – – – – – – – – – – – 0.002 – 0.002 – – 0.020 – 0.157 – 0.220 0.005 0.252 0.028 0.068 0.130 0.008 0.078 – 0.025 – 0.005 –
– – – – – – – 0.020 0.010 0.122 0.140 0.130 0.130 0.180 0.148 0.052 – 0.038 0.018 0.008 – – – 0.002 – – – 0.002 – – – – – – – – – – – – – – – – – – – –
– 0.202 – 0.198 0.112 0.188 0.285 0.015 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – 0.012 0.018 – 0.052 0.335 0.403 0.158 0.022 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
0.002 0.002 – 0.028 0.142 0.155 – 0.278 0.200 0.145 0.040 0.008 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – 0.528 0.102 – 0.062 0.273 0.030 0.005 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – – 0.010 0.025 – 0.305 0.270 0.325 0.053 0.012 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
– – – 0.015 0.010 0.217 – 0.060 0.190 0.175 0.235 0.065 0.025 0.008 – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
0.075 – – 0.140 0.008 0.008 – 0.110 0.128 0.192 0.095 0.058 0.032 0.060 0.035 0.022 – 0.012 0.010 0.008 – 0.005 – 0.002 – – – – – – – – – – – – – – – – – – – – – – – –
Table 2 Statistical parameters of forensic interest System SE33
D3S1358 VWA
D16S539 D8S1179 D21S11 D18S51 TH01
FGA
D5S818 D13S317 D7S820 TPOX
CSF1PO Penta D Penta E
p Hobs Hesp PD PEX PIC
0.5957 0.8200 0.7979 0.9266 0.5927 0.7641
0.8844 0.8150 0.7705 0.9068 0.5549 0.7327
0.5000 0.8650 0.8669 0.9669 0.7261 0.8496
0.0284 0.7250 0.6990 0.8461 0.4494 0.6450
0.3652 0.7650 0.7266 0.8710 0.4760 0.6742
0.5131 0.9300 0.9486 0.9948 0.8909 0.9435
0.1565 0.7350 0.7950 0.9246 0.5929 0.7620
0.8283 0.8450 0.8126 0.9363 0.6309 0.7857
0.9971 0.8550 0.8358 0.9505 0.6722 0.8134
0.5396 0.8400 0.8746 0.9705 0.7416 0.8588
0.0940 0.7550 0.7927 0.9230 0.5847 0.7581
0.6804 0.7700 0.7848 0.9174 0.5849 0.7522
0.5866 0.8800 0.8172 0.9393 0.6343 0.7900
0.7714 0.6600 0.6337 0.7808 0.3869 0.5799
0.1014 0.8050 0.8240 0.9435 0.6459 0.7978
0.4561 0.8950 0.8924 0.9781 0.7798 0.8804
p: Hardy–Weinberg equilibrium exact test; Hobs: observed heterozygosity; Hexp: expected heterozygosity; PD: power of discrimination; PEX: probability of exclusion; PIC: polymorphic information content.
M.F. Pinheiro et al. / Forensic Science International 148 (2005) 221–223
populations, these referred alleles were present in low frequencies. As this is the first study that includes data from both PowerPlex1 16 System and SE33 (ACTBP2), no other comparisons were made. This paper follows the guidelines for publication data requested by the journal [7]. The complete data set is available upon request. References [1] P.S. Walsh, D.A. Metzger, R. Higuchi, CHELEX1 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material, BioTechniques 10 (4) (1991) 506– 513.
223
[2] Technical Manual, PowerPlex1 16 System, Promega Corporation. [3] Technical Manual, PowerPlex1 ES Monoplex System, Promega Corporation. [4] M. Raymond, F. Rousset, GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism, J. Hered. 86 (1995) 248–249. [5] A.T. Fernandes, A. Brehm, C. Alves, L. Gusma˜ o, A. Amorim, Genetic profile of the Madeira Archipelago population using the new PowerPlex1 16 System Kit, Forensic Sci. Int. 125 (2002) 281–283. [6] R.G. Velosa, A.T. Fernandes, A. Brehm, Genetic profile of the Ac¸ores Archipelago population using the new PowerPlex1 16 System Kit, Forensic Sci. Int. 129 (2002) 68–71. [7] P. Lincoln, A. Carracedo, Publication of data of human polymorphims, Forensic Sci. Int. 110 (2000) 3–5.