- Email: [email protected]
Genetic profile of the madeira archipelag
Forensic Science International 125 (2002) 281–283
Announcement of Population Data
Genetic profile of the Madeira Archipelago population using the new PowerPlex116 System kit Ana Teresa Fernandesa, Anto´nio Brehma,*, Cı´ntia Alvesb, Leonor Gusma˜ob, Anto´nio Amorimb,c a
Human Genetics Laboratory, Centre of Biological Sciences, University of Madeira, Campus of Penteada, 9000 Funchal, Portugal b Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal c Faculdade de Cieˆncias da Universidade do Porto, Porto, Portugal Received 6 November 2001; accepted 7 November 2001
Abstract Allele and haplotype frequencies of 17 chromosome STR loci, 15 of them included in the kit PowerPlex116 System from Promega, were determined in a sample of unrelated males from Madeira and Porto Santo Islands. PowerPlex16 includes STRs not studied before in the Madeira population. The kit includes two new allele markers (Penta D and Penta E), which proved to be extremely useful for paternity testing (PD ¼ 0:952 and 0.977, respectively). The study revealed that the Madeira population does not differ from that of the north Portugal. Nevertheless, some loci presented alleles found in sub-Saharan and North European populations which were not reported so far in Portugal. Keywords: STRs; Population data; Madeira; PowerPlex16 System; Promega
Population: A sample of 100 healthy unrelated males from Madeira and Porto Santo with known ancestors originally from the Archipelago back to at least three generations were typed for 15 STRs. Additional samples were added for estimating five STRs, two of them not included in the PowerPlex116 System (CD4 and FES), which were manually typed. The data is presented in Table 1 (12 STRs) and Table 2 (five STRs). DNA extraction: Chelex method. PCR: According to CD4 [1], FES [2], PowerPlex116 System [3]. Although, Amelogenin is included in the Promega kit, we excluded it from the analysis. Typing: By ABI Prism-310 and polyacrylamide gel electrophoresis with visualization by silver staining. Results: Tables 1 and 2. Analyses of data: GENEPOP [4], haplotype and gene diversity according to Nei [5]. Population comparisons were done using Arlequin [6].
* Corresponding author. Tel.: þ351-1291-705383; fax: þ351-1291-705399. E-mail address: [email protected] (A. Brehm).
0379-0738/02/$ – see front matter PII: S 0 3 7 9 - 0 7 3 8 ( 0 1 ) 0 0 6 2 5 - 9
Access to the data: http://www.uma.pt/ccbg/LGH/ STRMadeira. Observations: The allele frequency distributions observed in the sample studied do not show significant differences from those reported for Portuguese mainland [1,7–9]. CD4 locus had three alleles not found elsewhere in Portugal but present in African samples [10]. For all markers, the Madeira population was found to be in Hardy– Weinberg equilibrium. Penta E and Penta D, two new STRs included in the Promega kit and not used before in any of the Portuguese populations, revealed to be good markers for paternity testing (PD ¼ 0:977 and 0.952, respectively). Some features deserve to be noted. Allele 11 of D3S1358 and allele 7 of D5S818 has not been found in previous surveys of Portugal but exist in Hungary [11]. Also allele 35 of D21S11 has been reported in a North African sample and Moc¸ambique [12] but not in the population of mainland Portugal. We report the presence of allele 10.2 of D18S51 in Madeira that, otherwise, has been found in Moc¸ambique [12]. Alleles 8 and 15 of CSF1PO have been found in North Africa and Catalonia, and in the Basque country, respectively [9]. Both exist in Madeira. Finally, allele 20.2 of FGA was found in Galicia (North Iberia), but not in Portugal [13].
D3S1358 (N ¼ 100)
D21S11 (N ¼ 100)
D18S51 (N ¼ 100)
Penta E (N ¼ 100)
D5S818 (N ¼ 100)
D13S317 (N ¼ 100)
D7S820 (N ¼ 100)
D16S539 (N ¼ 100)
CSF1PO (N ¼ 100)
Penta D (N ¼ 100)
D8S1179 (N ¼ 100)
FGA (N ¼ 100)
– – – – – – 0.010 – 0.010 0.145 0.300 0.200 0.220 0.105 0.010 – – – – – – – – – – – – – – – – – – – – – 0.800 0.793 0.098 0.565 0.924
– – – – – – – – – – – – – – – – – – – – – – – – – 0.060 0.235 0.185 0.230 0.020 0.040 0.075 0.010 0.105 0.035 0.005 0.820 0.838 0.177 0.654 0.952
– – – – 0.010 0.010 0.010 0.200 0.115 0.155 0.155 0.140 0.110 0.045 0.015 0.025 – – 0.010 – – – – – – – – – – – – – – – – – 0.840 0.868 0.173 0.709 0.966
0.075 0.145 0.010 – 0.115 – 0.135 0.165 0.120 0.070 0.040 0.025 0.065 0.015 0.015 – – 0.005 – – – – – – – – – – – – – – – – – – 0.840 0.893 0.093 0.761 0.977
– 0.015 0.010 0.040 0.085 – 0.270 0.380 0.175 0.025 – – – – – – – – – – – – – – – – – – – – – – – – – – 0.720 0.746 0.480 0.501 0.894
– – 0.085 0.045 0.090 – 0.290 0.345 0.110 0.035 – – – – – – – – – – – – – – – – – – – – – – – – – – 0.800 0.770 0.836 0.544 0.912
– 0.025 0.210 0.110 0.255 – 0.225 0.145 0.030 – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.710 0.809 0.235 0.593 0.934
– – 0.065 0.125 0.030 – 0.305 0.255 0.190 0.030 – – – – – – – – – – – – – – – – – – – – – – – – – – 0.710 0.788 0.544 0.560 0.921
– – 0.005 0.010 0.295 – 0.345 0.295 0.025 0.020 0.005 – – – – – – – – – – – – – – – – – – – – – – – – – 0.690 0.709 0.973 0.424 0.856
– 0.005 0.020 0.125 0.150 – 0.115 0.220 0.200 0.150 0.015 – – – – – – – – – – – – – – – – – – – – – – – – – 0.850 0.841 0.999 0.652 0.952
– – 0.020 0.015 0.050 – 0.110 0.155 0.325 0.180 0.130 0.015 – – – – – – – – – – – – – – – – – – – – – – – – 0.800 0.810 0.477 0.606 0.938
– – – – – – – – – – – – – 0.015 0.035 0.100 0.010 0.170 0.200 0.025 0.175 0.005 0.135 0.105 0.010 0.010 0.005 – – – – – – – – – 0.820 0.863 0.312 0.699 0.964
a N is the number of samples; Ho (observed heterozygosity), He (expected heterozygosity), PD (power of discrimination and exclusion), CE (a priori chance of exclusion), P (Hardy– Weinberg equilibrium, exact test based on more than 2000 shufflings, for standard error < 0:01).
A.T. Fernandes et al. / Forensic Science International 125 (2002) 281–283
5 7 8 9 10 10.2 11 12 13 14 15 16 17 18 19 20 20.2 21 22 22.2 23 23.2 24 25 26 27 28 29 30 30.2 31 31.2 32 32.2 33.2 35 Ho He P CE PD
282
Table 1 Allele frequencies and gene diversity values at 12 STR loci, in the Madeira Archipelago populationa
A.T. Fernandes et al. / Forensic Science International 125 (2002) 281–283
283
Table 2 Allele frequencies and gene diversity values at five STR loci, in the Madeira Archipelago populationa
5 6 7 8 9 9.3 10 11 12 13 14 15 16 17 18 19 20 Ho He P CE PD
CD4 (N ¼ 210)
FES (N ¼ 204)
TH01 (N ¼ 207)
TPO (N ¼ 210)
VWA (N ¼ 209)
0.376 0.276 0.012 0.007 0.005 – 0.271 0.038 0.005 0.002 0.005 0.002 – – – – – 0.695 0.709 0.553 0.431 0.860
– – – 0.012 0.005 – 0.328 0.365 0.238 0.039 0.012 – – – – – – 0.770 0.702 0.117 0.423 0.855
0.002 0.203 0.143 0.162 0.242 0.239 0.010 – – – – – – – – – – 0.802 0.799 0.279 0.456 0.926
– 0.005 – 0.469 0.152 – 0.093 0.260 0.021 – – – – – – – – 0.729 0.682 0.114 0.420 0.849
– – – – – – – – 0.002 0.005 0.072 0.184 0.237 0.246 0.175 0.069 0.010 0.804 0.811 0.071 0.597 0.935
a
N is the number of samples; Ho (observed heterozygosity), He (expected heterozygosity), PD (power of discrimination and exclusion), CE (a priori chance of exclusion), P (Hardy–Weinberg equilibrium, exact test based on more than 2000 shufflings, for standard error < 0:01).
Overall, the data shows the presence of African markers as well as others reported in North Europe, which is concordant with the multi-origin of Madeira settlers.
[7]
Acknowledgements
[8]
This work was done under a research partnership with PROMEGA Corp. We acknowledge the long-term collaboration of the Portuguese Army Chief of Staff.
[9]
References [1] L. Gusma˜ o, M.J. Prata, A. Amorim, F. Silva, I. Bessa, Characterization of four tandem repeat loci (TH01, VWA31/ A, CD4 and TP53) in North Portugal, Hum. Biol. 69 (1997) 31–41. [2] M.H. Polymeropoulos, D.S. Rath, H. Xiao, C.R. Merril, Tetranucleotide repeat polymorphism at the human c-fes/fps proto-oncogene (FES), Nucleic Acids Res. 19 (1991) 4018. [3] PowerPlex1 16 System kit, Promega Corporation, Technical Manual. [4] M. Raymond, F. Rousset, GENEPOP (version 1.2): population genetic software for exact tests and ecumenicism, J. Hered. 86 (1995) 248–249. [5] M. Nei, Molecular Evolutionary Genetics, Columbia University Press, New York, 1987. [6] S. Schneider, J.-M. Kueffer, D. Roessli, L. Excoffier, Arlequin Version 1.1: A Software for Population Genetic
[10]
[11]
[12]
[13]
Data Analysis, Genetics and Biometry Laboratory, University of Geneva, Switzerland, 1997. L. Gusma˜ o, M.J. Prata, A. Amorim, The STR systems hTPO: population and segregation data, Int. J. Legal Med. 108 (1995) 167–169. S. Santos, B. Budowle, J.B. Smerick, K.M. Keys, T.R. Moretti, Portuguese population data on the six short tandem repeat loci-CSF1PO, TPOX, TH01, D3S1358, VWA and FGA, Forensic Sci. Int. 83 (1993) 229–235. A. Pe´ rez-Lezaun, F. Calafell, J. Clarimo´ n, E. Bosch, E. Mateu, L. Gusma˜ o, A. Amorim, N. Benchemsi, J. Bertranpetit, Allele frequencies of 13 short tandem repeats in population samples from the Iberian Peninsula and Northern Africa, Int. J. Legal Med. 113 (2000) 208–214. M.J. Prata, L. Gusma˜ o, F. Silva, I. Bessa, A. Amorim, M.J. Trovoada, M.T. Santos, Population genetics of the STRs CD4, MBP (locus B), TH01, TP53, TPO and VWA31/A in S. Tome´ e Principe, Advances in Research on DNA Polymorphisms, in: Proceedings of the ISFH Hakone Symposium on DNA Polymorphisms, Toyoshoten, Tokyo, Japan, 1997, pp. 420–423. B. Egyed, S. Furedi, M. Angyal, L. Boutrand, A. Vandenberghe, J. Woller, Z. Pa´ da´ r, Analysis of eight STR loci in two Hungarian populations, Int. J. Legal Med. 113 (2000) 272–275. A. Cı´ntia, L. Gusma˜ o, A. Amorim, STR data (AmpF/STR Profiler Plus and GenePrint CTTv) from Mozambique, Forensic Sci. Int. 119 (2001) 131–133. L. Gusma˜ o, P. Sanchez-Diz, C. Alves, M.V. Lareu, A. Carracedo, A. Amorim, Genetic diversity of nine STRs in two northwest Iberian populations: Galicia and Northern Portugal, Int. J. Legal Med. 114 (2000) 109–113.
Announcement of Population Data
Genetic profile of the Madeira Archipelago population using the new PowerPlex116 System kit Ana Teresa Fernandesa, Anto´nio Brehma,*, Cı´ntia Alvesb, Leonor Gusma˜ob, Anto´nio Amorimb,c a
Human Genetics Laboratory, Centre of Biological Sciences, University of Madeira, Campus of Penteada, 9000 Funchal, Portugal b Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal c Faculdade de Cieˆncias da Universidade do Porto, Porto, Portugal Received 6 November 2001; accepted 7 November 2001
Abstract Allele and haplotype frequencies of 17 chromosome STR loci, 15 of them included in the kit PowerPlex116 System from Promega, were determined in a sample of unrelated males from Madeira and Porto Santo Islands. PowerPlex16 includes STRs not studied before in the Madeira population. The kit includes two new allele markers (Penta D and Penta E), which proved to be extremely useful for paternity testing (PD ¼ 0:952 and 0.977, respectively). The study revealed that the Madeira population does not differ from that of the north Portugal. Nevertheless, some loci presented alleles found in sub-Saharan and North European populations which were not reported so far in Portugal. Keywords: STRs; Population data; Madeira; PowerPlex16 System; Promega
Population: A sample of 100 healthy unrelated males from Madeira and Porto Santo with known ancestors originally from the Archipelago back to at least three generations were typed for 15 STRs. Additional samples were added for estimating five STRs, two of them not included in the PowerPlex116 System (CD4 and FES), which were manually typed. The data is presented in Table 1 (12 STRs) and Table 2 (five STRs). DNA extraction: Chelex method. PCR: According to CD4 [1], FES [2], PowerPlex116 System [3]. Although, Amelogenin is included in the Promega kit, we excluded it from the analysis. Typing: By ABI Prism-310 and polyacrylamide gel electrophoresis with visualization by silver staining. Results: Tables 1 and 2. Analyses of data: GENEPOP [4], haplotype and gene diversity according to Nei [5]. Population comparisons were done using Arlequin [6].
* Corresponding author. Tel.: þ351-1291-705383; fax: þ351-1291-705399. E-mail address: [email protected] (A. Brehm).
0379-0738/02/$ – see front matter PII: S 0 3 7 9 - 0 7 3 8 ( 0 1 ) 0 0 6 2 5 - 9
Access to the data: http://www.uma.pt/ccbg/LGH/ STRMadeira. Observations: The allele frequency distributions observed in the sample studied do not show significant differences from those reported for Portuguese mainland [1,7–9]. CD4 locus had three alleles not found elsewhere in Portugal but present in African samples [10]. For all markers, the Madeira population was found to be in Hardy– Weinberg equilibrium. Penta E and Penta D, two new STRs included in the Promega kit and not used before in any of the Portuguese populations, revealed to be good markers for paternity testing (PD ¼ 0:977 and 0.952, respectively). Some features deserve to be noted. Allele 11 of D3S1358 and allele 7 of D5S818 has not been found in previous surveys of Portugal but exist in Hungary [11]. Also allele 35 of D21S11 has been reported in a North African sample and Moc¸ambique [12] but not in the population of mainland Portugal. We report the presence of allele 10.2 of D18S51 in Madeira that, otherwise, has been found in Moc¸ambique [12]. Alleles 8 and 15 of CSF1PO have been found in North Africa and Catalonia, and in the Basque country, respectively [9]. Both exist in Madeira. Finally, allele 20.2 of FGA was found in Galicia (North Iberia), but not in Portugal [13].
D3S1358 (N ¼ 100)
D21S11 (N ¼ 100)
D18S51 (N ¼ 100)
Penta E (N ¼ 100)
D5S818 (N ¼ 100)
D13S317 (N ¼ 100)
D7S820 (N ¼ 100)
D16S539 (N ¼ 100)
CSF1PO (N ¼ 100)
Penta D (N ¼ 100)
D8S1179 (N ¼ 100)
FGA (N ¼ 100)
– – – – – – 0.010 – 0.010 0.145 0.300 0.200 0.220 0.105 0.010 – – – – – – – – – – – – – – – – – – – – – 0.800 0.793 0.098 0.565 0.924
– – – – – – – – – – – – – – – – – – – – – – – – – 0.060 0.235 0.185 0.230 0.020 0.040 0.075 0.010 0.105 0.035 0.005 0.820 0.838 0.177 0.654 0.952
– – – – 0.010 0.010 0.010 0.200 0.115 0.155 0.155 0.140 0.110 0.045 0.015 0.025 – – 0.010 – – – – – – – – – – – – – – – – – 0.840 0.868 0.173 0.709 0.966
0.075 0.145 0.010 – 0.115 – 0.135 0.165 0.120 0.070 0.040 0.025 0.065 0.015 0.015 – – 0.005 – – – – – – – – – – – – – – – – – – 0.840 0.893 0.093 0.761 0.977
– 0.015 0.010 0.040 0.085 – 0.270 0.380 0.175 0.025 – – – – – – – – – – – – – – – – – – – – – – – – – – 0.720 0.746 0.480 0.501 0.894
– – 0.085 0.045 0.090 – 0.290 0.345 0.110 0.035 – – – – – – – – – – – – – – – – – – – – – – – – – – 0.800 0.770 0.836 0.544 0.912
– 0.025 0.210 0.110 0.255 – 0.225 0.145 0.030 – – – – – – – – – – – – – – – – – – – – – – – – – – – 0.710 0.809 0.235 0.593 0.934
– – 0.065 0.125 0.030 – 0.305 0.255 0.190 0.030 – – – – – – – – – – – – – – – – – – – – – – – – – – 0.710 0.788 0.544 0.560 0.921
– – 0.005 0.010 0.295 – 0.345 0.295 0.025 0.020 0.005 – – – – – – – – – – – – – – – – – – – – – – – – – 0.690 0.709 0.973 0.424 0.856
– 0.005 0.020 0.125 0.150 – 0.115 0.220 0.200 0.150 0.015 – – – – – – – – – – – – – – – – – – – – – – – – – 0.850 0.841 0.999 0.652 0.952
– – 0.020 0.015 0.050 – 0.110 0.155 0.325 0.180 0.130 0.015 – – – – – – – – – – – – – – – – – – – – – – – – 0.800 0.810 0.477 0.606 0.938
– – – – – – – – – – – – – 0.015 0.035 0.100 0.010 0.170 0.200 0.025 0.175 0.005 0.135 0.105 0.010 0.010 0.005 – – – – – – – – – 0.820 0.863 0.312 0.699 0.964
a N is the number of samples; Ho (observed heterozygosity), He (expected heterozygosity), PD (power of discrimination and exclusion), CE (a priori chance of exclusion), P (Hardy– Weinberg equilibrium, exact test based on more than 2000 shufflings, for standard error < 0:01).
A.T. Fernandes et al. / Forensic Science International 125 (2002) 281–283
5 7 8 9 10 10.2 11 12 13 14 15 16 17 18 19 20 20.2 21 22 22.2 23 23.2 24 25 26 27 28 29 30 30.2 31 31.2 32 32.2 33.2 35 Ho He P CE PD
282
Table 1 Allele frequencies and gene diversity values at 12 STR loci, in the Madeira Archipelago populationa
A.T. Fernandes et al. / Forensic Science International 125 (2002) 281–283
283
Table 2 Allele frequencies and gene diversity values at five STR loci, in the Madeira Archipelago populationa
5 6 7 8 9 9.3 10 11 12 13 14 15 16 17 18 19 20 Ho He P CE PD
CD4 (N ¼ 210)
FES (N ¼ 204)
TH01 (N ¼ 207)
TPO (N ¼ 210)
VWA (N ¼ 209)
0.376 0.276 0.012 0.007 0.005 – 0.271 0.038 0.005 0.002 0.005 0.002 – – – – – 0.695 0.709 0.553 0.431 0.860
– – – 0.012 0.005 – 0.328 0.365 0.238 0.039 0.012 – – – – – – 0.770 0.702 0.117 0.423 0.855
0.002 0.203 0.143 0.162 0.242 0.239 0.010 – – – – – – – – – – 0.802 0.799 0.279 0.456 0.926
– 0.005 – 0.469 0.152 – 0.093 0.260 0.021 – – – – – – – – 0.729 0.682 0.114 0.420 0.849
– – – – – – – – 0.002 0.005 0.072 0.184 0.237 0.246 0.175 0.069 0.010 0.804 0.811 0.071 0.597 0.935
a
N is the number of samples; Ho (observed heterozygosity), He (expected heterozygosity), PD (power of discrimination and exclusion), CE (a priori chance of exclusion), P (Hardy–Weinberg equilibrium, exact test based on more than 2000 shufflings, for standard error < 0:01).
Overall, the data shows the presence of African markers as well as others reported in North Europe, which is concordant with the multi-origin of Madeira settlers.
[7]
Acknowledgements
[8]
This work was done under a research partnership with PROMEGA Corp. We acknowledge the long-term collaboration of the Portuguese Army Chief of Staff.
[9]
References [1] L. Gusma˜ o, M.J. Prata, A. Amorim, F. Silva, I. Bessa, Characterization of four tandem repeat loci (TH01, VWA31/ A, CD4 and TP53) in North Portugal, Hum. Biol. 69 (1997) 31–41. [2] M.H. Polymeropoulos, D.S. Rath, H. Xiao, C.R. Merril, Tetranucleotide repeat polymorphism at the human c-fes/fps proto-oncogene (FES), Nucleic Acids Res. 19 (1991) 4018. [3] PowerPlex1 16 System kit, Promega Corporation, Technical Manual. [4] M. Raymond, F. Rousset, GENEPOP (version 1.2): population genetic software for exact tests and ecumenicism, J. Hered. 86 (1995) 248–249. [5] M. Nei, Molecular Evolutionary Genetics, Columbia University Press, New York, 1987. [6] S. Schneider, J.-M. Kueffer, D. Roessli, L. Excoffier, Arlequin Version 1.1: A Software for Population Genetic
[10]
[11]
[12]
[13]
Data Analysis, Genetics and Biometry Laboratory, University of Geneva, Switzerland, 1997. L. Gusma˜ o, M.J. Prata, A. Amorim, The STR systems hTPO: population and segregation data, Int. J. Legal Med. 108 (1995) 167–169. S. Santos, B. Budowle, J.B. Smerick, K.M. Keys, T.R. Moretti, Portuguese population data on the six short tandem repeat loci-CSF1PO, TPOX, TH01, D3S1358, VWA and FGA, Forensic Sci. Int. 83 (1993) 229–235. A. Pe´ rez-Lezaun, F. Calafell, J. Clarimo´ n, E. Bosch, E. Mateu, L. Gusma˜ o, A. Amorim, N. Benchemsi, J. Bertranpetit, Allele frequencies of 13 short tandem repeats in population samples from the Iberian Peninsula and Northern Africa, Int. J. Legal Med. 113 (2000) 208–214. M.J. Prata, L. Gusma˜ o, F. Silva, I. Bessa, A. Amorim, M.J. Trovoada, M.T. Santos, Population genetics of the STRs CD4, MBP (locus B), TH01, TP53, TPO and VWA31/A in S. Tome´ e Principe, Advances in Research on DNA Polymorphisms, in: Proceedings of the ISFH Hakone Symposium on DNA Polymorphisms, Toyoshoten, Tokyo, Japan, 1997, pp. 420–423. B. Egyed, S. Furedi, M. Angyal, L. Boutrand, A. Vandenberghe, J. Woller, Z. Pa´ da´ r, Analysis of eight STR loci in two Hungarian populations, Int. J. Legal Med. 113 (2000) 272–275. A. Cı´ntia, L. Gusma˜ o, A. Amorim, STR data (AmpF/STR Profiler Plus and GenePrint CTTv) from Mozambique, Forensic Sci. Int. 119 (2001) 131–133. L. Gusma˜ o, P. Sanchez-Diz, C. Alves, M.V. Lareu, A. Carracedo, A. Amorim, Genetic diversity of nine STRs in two northwest Iberian populations: Galicia and Northern Portugal, Int. J. Legal Med. 114 (2000) 109–113.