- Email: [email protected]
Data for 15 autosomal STR markers (Powerplex 16 System) from two Tunisian populations: Kesra (Berber) and Zriba (Arab)
Forensic Science International 147 (2005) 101–106
Announcement of population data
Data for 15 autosomal STR markers (Powerplex 16 System) from two Tunisian populations: Kesra (Berber) and Zriba (Arab) L. Chernia, B. Loueslati Yaaˆcoubia, L. Pereirab, C. Alvesb, H. Khodjet El Killa, A. Ben Ammar El Gaaieda, A. Amorimb,c,* a
Laboratory of Molecular Genetic Immunology and Biotechnology, Faculty of Sciences of Tunis, Tunis, Tunisia b Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), R. Dr. Roberto Frias s/n, 4200-465 Oporto, Portugal c Faculdade de Cieˆncias da Universidade do Porto, Pr. Gomes Teixeira, 4099-002 Oporto, Portugal Received 3 March 2004; received in revised form 31 March 2004; accepted 2 April 2004 Available online 28 May 2004
Abstract Allele frequencies, together with some parameters of forensic interest, for 15 STRs included in the Powerplex 16 System (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, Penta D, Penta E, TH01, TPO and VWA) were estimated from two samples of unrelated individuals from Tunisia, of different ethnicity: Kesra (Berber) and Zriba (Arab). No deviations from Hardy–Weinberg equilibrium were observed after Bonferroni’s correction for the number of loci analysed. Comparative analyses between our population data and other North African databases showed that significant differences were concentrated on loci with lowest values of diversity (mainly CSF1PO and D13S317), irrespective of ethnicity and geographic location. # 2004 Elsevier Ireland Ltd. All rights reserved. Keywords: STRs; Population data; Powerplex 16 System; Tunisia; Arab; Berber
Populations: Unrelated individuals from Kesra (n ¼ 44), a Berber community and from Zriba (n ¼ 45), an Arab community, both in Central Tunisia, and about 40 km apart. DNA extraction: Chelex method [1]. PCR: According to manufacturers (Powerplex 16 System PCR amplification kit, Promega). Typing: ABI 310 and reference sequenced ladders (Promega). Results: See Tables 1–3. Quality control: Proficiency testing of the GEP-ISFG WG. Analysis of data: Hardy–Weinberg equilibrium was assayed by an exact test [2], using GENEPOP software
* Corresponding author. Tel.: þ351-22-5570700; fax: þ351-22-5570799. E-mail address: [email protected] (A. Amorim).
[3]. Population differentiation tests were carried out with the Arlequin software ver. 2.000 [4].
1. Other remarks Population data for the 15 STRs are shown in Table 1 for Kesra and in Table 2 for Zriba. Some deviations from Hardy–Weinberg equilibrium were observed: for Kesra at D3S1358, D16S539 and FGA; while for Zriba at D3S1358, D7S820 and PE; nevertheless, none stand out after Bonferroni’s correction for the number of loci analysed. The comparison between our samples and other North African populations [5,6], showed similar observed heterozygosities, and the few significant FST P values (Table 3) corresponded to loci with the lowest diversity levels across the populations (mainly CSF1PO and D13S317, with values generally under 0.700).
0379-0738/$ – see front matter # 2004 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.forsciint.2004.04.009
102
Table 1 Population data for Powerplex 16 loci in Kesra Allele
D3S1358
D5S818
D7S820
D8S1179
D13S317
D16S539
D18S51
D21S11
FGA
Penta D
Penta E
TH01
TPO
VWA
0.024 0.012
0.023
0.233 0.279 0.372 0.070 0.023
0.011
0.148 0.205 0.273 0.227 0.125 0.011
0.034 0.034
0.205 0.011
0.023 0.398 0.250 0.182
0.352 0.295 0.068 0.068
0.080
0.058 0.081
0.023 0.186
0.143
0.171 0.098 0.024
0.071 0.071 0.155 0.250
0.070 0.337 0.407 0.035
0.035 0.291 0.209 0.198
0.143 0.167 0.155 0.345
0.037 0.195 0.159 0.159
0.190 0.179 0.083
0.012
0.058
0.012
0.037 0.073
0.190 0.167 0.060 0.190 0.214 0.048 0.071 0.036 0.012 0.012
0.024 0.012 0.060 0.036 0.179 0.214 0.190 0.131 0.048
0.036 0.012 0.238 0.167 0.024 0.083 0.119 0.167 0.060
0.083 0.060 0.036
0.012
0.012
0.119 0.226 0.167 0.262 0.143 0.083
0.023 0.477 0.193 0.159 0.136 0.011
0.083 0.250 0.190 0.226 0.155 0.095
L. Cherni et al. / Forensic Science International 147 (2005) 101–106
2.2 3.2 5 6 7 8 9 9.3 10 11 12 13 13.2 14 15 16 17 18 19 20 21 21.2 22 23 24 24.2 25 26 27 28 28.2 29 30 30.2 31 31.2 32.2 33.2
CSF1PO
34.2 35 2N 86 Ho 0.651 P-value 0.270
0.024 0.024 88 0.659 0.032a
88 0.773 0.297
88 0.773 0.781
84 0.714 0.099
86 0.674 0.691
86 0.814 0.028a
84 0.857 0.285
84 0.833 0.182
84 0.714 0.009a
84 0.810 0.136
82 0.780 0.082
84 0.833 0.833
88 84 0.795 0.786 0.773 0.845
Ho, observed heterozygosity; P, Hardy–Weinberg equilibrium, exact test based on more than 2000 shufflings, for standard error <0.01. a Bonferroni’s correction (0:05=15 ¼ 0:0033).
L. Cherni et al. / Forensic Science International 147 (2005) 101–106 103
104
Table 2 Population data for Powerplex 16 loci in Zriba Allele
D3S1358
D5S818
D7S820
D8S1179
D13S317
D16S539
D18S51
D21S11
FGA
Penta D
Penta E
TH01
TPO
VWA
0.060 0.012
0.636 0.205 0.159 0.022 0.122 0.389 0.211 0.144 0.089 0.022
0.068 0.023
0.100 0.056
0.023 0.102 0.523 0.261
0.422 0.211 0.211
0.133 0.067
0.023 0.182
0.144 0.111 0.089 0.178
0.078 0.211 0.478 0.022
0.045 0.455 0.136 0.148
0.178 0.200 0.100
0.011
0.011
0.012 0.023 0.058 0.105 0.116 0.116 0.267 0.116 0.035 0.128 0.023
0.011 0.111 0.089 0.133 0.144 0.089 0.156
0.022
0.133 0.100
0.089 0.333 0.244 0.056 0.044 0.122 0.078 0.011
0.033
0.012 0.024 0.226
0.037 0.012 0.012
0.202 0.071 0.083 0.167
0.098 0.159 0.159 0.159
0.119 0.036
0.098 0.037 0.049 0.037 0.061 0.024 0.037 0.012
0.156 0.256 0.067 0.300 0.189 0.033
0.011 0.522 0.267 0.133 0.067
0.067 0.200 0.256 0.311 0.133 0.011 0.022
L. Cherni et al. / Forensic Science International 147 (2005) 101–106
2.2 3.2 5 6 7 8 9 9.3 10 11 12 13 13.2 14 15 16 17 18 19 20 21 21.2 22 23 24 24.2 25 26 27 28 28.2 29 30 30.2 31 31.2 32.2 33.2
CSF1PO
34.2 35 2N 88 Ho 0.568 P-value 0.273
90 0.711 0.049a
88 0.705 0.801
90 0.733 0.023a
90 0.867 0.877
90 0.667 0.566
88 0.750 0.212
86 0.884 0.096
90 0.844 0.214
90 0.933 0.448
84 0.810 0.755
82 0.854 0.019a
90 0.822 0.535
90 90 0.644 0.889 0.681 0.076
Ho, observed heterozygosity; P, Hardy–Weinberg equilibrium, exact test based on more than 2000 shufflings, for standard error <0.01. a Bonferroni’s correction (0:05=15 ¼ 0:0033).
Moroccan Arabs [5]
Saharawis Southern Moroccan Berbers Northern central Moroccan Berbers Mozabites
VWA (0.01646) – – D13S317 (0.00258)
Tunisia
CSF1PO (0.00020); D13S317 (0.00079) D13S317 (0.01508)
Kesra
Zriba
CSF1PO (0.00714); D5S818 (0.01488); D13S317 (0.00000)
Saharawis [5]
– – D13S317 (0.00278); VWA (0.00258) CSF1PO (0.00000); D13S317 (0.00635) D5S818 (0.02440); D7S820 (0.03273); D13S317 (0.01408) CSF1PO (0.00456); D13S317 (0.00020); FGA (0.03174)
Southern Moroccan Berbers [5]
– D13S317 (0.03729); VWA (0.04106) CSF1PO (0.00040); D13S317 (0.08431) –
CSF1PO (0.01270); D5S818 (0.03868); D13S317 (0.00615)
Northern central Moroccan Berbers [5]
Mozabites [5]
Tunisia [6]
Kesra
D13S317 (0.00198) CSF1PO (0.00476); D13S317 (0.00694) D13S317 (0.00932)
CSF1PO (0.02321); D13S317 (0.00040); TPO (0.02837)
L. Cherni et al. / Forensic Science International 147 (2005) 101–106
Table 3 Heterogeneity of North African populations assessed through the markers included in Powerplex 16 System
CSF1PO (0.00060) D5S818 (0.00575); VWA (0.04086)
CSF1PO (0.00000); D5S818 (0.02420)
CSF1PO (0.00040); FGA (0.01646)
CSF1PO (0.00000); D13S317 (0.01349); D18S51 (0.00436); TPO (0.02420)
CSF1PO (0.00040); D5S818 (0.00139)
105
Significant FST P values (inside brackets); in bold, the P values that remain significant after Bonferroni’s correction (P ¼ 0:0018 for the majority of comparisons, except for D16S539, PD and PE, where it is P ¼ 0:0167).
106
L. Cherni et al. / Forensic Science International 147 (2005) 101–106
This paper follows the guidelines for publication of population data requested by the journal [7].
Acknowledgements This work was partially supported by the Tunisian Ministry of Higher Education, Scientific Research and Technology. Fundac¸a˜ o para a Cieˆ ncia e a Tecnologia conceded a research grant to L.P. (SFRH/BPD/7121/2001) and partially supports IPATIMUP by Programa Operacional Cieˆ ncia, Tecnologia e Inovac¸a˜ o (POCTI), Quadro Comunita´ rio de Apoio III. We are very grateful to the Tunisian Ministry of Health and the staff of Kesra and Siliana hospitals for their help in collecting blood samples.
[2]
[3]
[4]
[5]
[6]
References [1] M.V. Lareu, C.P. Phillips, A. Carracedo, A.J. Lincoln, D. Syndercombe Court, J.A. Thomson, Investigation of the STR
[7]
locus HUMTH01 using PCR and two electrophoresis formats: UK and Galician Caucasian population surveys and usefulness in paternity investigations, Forensic Sci. Int. 66 (1994) 41–52. S. W Guo, E.A. Thompson, Performing the exact test of Hardy–Weinberg proportions for multiple alleles, Biometrics 8 (1992) 361–372. M. Raymond, F. Rousset, GENEPOP (version 1.2): populations genetics software for exact tests and ecumenicism, J. Hered. 86 (1995) 248–249. S. Schneider, D. Roessli, L. Excoffier, Arlequin Ver. 2.000. A Software for Population Genetics Data Analysis, University of Geneva, 2000. E. Bosch, J. Clarimo´ n, A. Pe´ rez-Lezaun, F. Calafell, STR data for 21 loci in northwestern Africa, Forensic Sci. Int. 116 (2001) 41–51. C. Brandt-Casadevall, M. Ben Dhiab, F. Taroni, C. Gehrig, N. Dimo-Simonin, M. Zemni, P. Mangin, Tunisian population data on 15 PCR-based loci, Forensic Sci. Int. 126 (2002) 272–274. P. Lincoln, A. Carracedo, Publication of population data of human polymorphisms, Forensic Sci. Int. 110 (2000) 3–5.
Announcement of population data
Data for 15 autosomal STR markers (Powerplex 16 System) from two Tunisian populations: Kesra (Berber) and Zriba (Arab) L. Chernia, B. Loueslati Yaaˆcoubia, L. Pereirab, C. Alvesb, H. Khodjet El Killa, A. Ben Ammar El Gaaieda, A. Amorimb,c,* a
Laboratory of Molecular Genetic Immunology and Biotechnology, Faculty of Sciences of Tunis, Tunis, Tunisia b Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), R. Dr. Roberto Frias s/n, 4200-465 Oporto, Portugal c Faculdade de Cieˆncias da Universidade do Porto, Pr. Gomes Teixeira, 4099-002 Oporto, Portugal Received 3 March 2004; received in revised form 31 March 2004; accepted 2 April 2004 Available online 28 May 2004
Abstract Allele frequencies, together with some parameters of forensic interest, for 15 STRs included in the Powerplex 16 System (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, Penta D, Penta E, TH01, TPO and VWA) were estimated from two samples of unrelated individuals from Tunisia, of different ethnicity: Kesra (Berber) and Zriba (Arab). No deviations from Hardy–Weinberg equilibrium were observed after Bonferroni’s correction for the number of loci analysed. Comparative analyses between our population data and other North African databases showed that significant differences were concentrated on loci with lowest values of diversity (mainly CSF1PO and D13S317), irrespective of ethnicity and geographic location. # 2004 Elsevier Ireland Ltd. All rights reserved. Keywords: STRs; Population data; Powerplex 16 System; Tunisia; Arab; Berber
Populations: Unrelated individuals from Kesra (n ¼ 44), a Berber community and from Zriba (n ¼ 45), an Arab community, both in Central Tunisia, and about 40 km apart. DNA extraction: Chelex method [1]. PCR: According to manufacturers (Powerplex 16 System PCR amplification kit, Promega). Typing: ABI 310 and reference sequenced ladders (Promega). Results: See Tables 1–3. Quality control: Proficiency testing of the GEP-ISFG WG. Analysis of data: Hardy–Weinberg equilibrium was assayed by an exact test [2], using GENEPOP software
* Corresponding author. Tel.: þ351-22-5570700; fax: þ351-22-5570799. E-mail address: [email protected] (A. Amorim).
[3]. Population differentiation tests were carried out with the Arlequin software ver. 2.000 [4].
1. Other remarks Population data for the 15 STRs are shown in Table 1 for Kesra and in Table 2 for Zriba. Some deviations from Hardy–Weinberg equilibrium were observed: for Kesra at D3S1358, D16S539 and FGA; while for Zriba at D3S1358, D7S820 and PE; nevertheless, none stand out after Bonferroni’s correction for the number of loci analysed. The comparison between our samples and other North African populations [5,6], showed similar observed heterozygosities, and the few significant FST P values (Table 3) corresponded to loci with the lowest diversity levels across the populations (mainly CSF1PO and D13S317, with values generally under 0.700).
0379-0738/$ – see front matter # 2004 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.forsciint.2004.04.009
102
Table 1 Population data for Powerplex 16 loci in Kesra Allele
D3S1358
D5S818
D7S820
D8S1179
D13S317
D16S539
D18S51
D21S11
FGA
Penta D
Penta E
TH01
TPO
VWA
0.024 0.012
0.023
0.233 0.279 0.372 0.070 0.023
0.011
0.148 0.205 0.273 0.227 0.125 0.011
0.034 0.034
0.205 0.011
0.023 0.398 0.250 0.182
0.352 0.295 0.068 0.068
0.080
0.058 0.081
0.023 0.186
0.143
0.171 0.098 0.024
0.071 0.071 0.155 0.250
0.070 0.337 0.407 0.035
0.035 0.291 0.209 0.198
0.143 0.167 0.155 0.345
0.037 0.195 0.159 0.159
0.190 0.179 0.083
0.012
0.058
0.012
0.037 0.073
0.190 0.167 0.060 0.190 0.214 0.048 0.071 0.036 0.012 0.012
0.024 0.012 0.060 0.036 0.179 0.214 0.190 0.131 0.048
0.036 0.012 0.238 0.167 0.024 0.083 0.119 0.167 0.060
0.083 0.060 0.036
0.012
0.012
0.119 0.226 0.167 0.262 0.143 0.083
0.023 0.477 0.193 0.159 0.136 0.011
0.083 0.250 0.190 0.226 0.155 0.095
L. Cherni et al. / Forensic Science International 147 (2005) 101–106
2.2 3.2 5 6 7 8 9 9.3 10 11 12 13 13.2 14 15 16 17 18 19 20 21 21.2 22 23 24 24.2 25 26 27 28 28.2 29 30 30.2 31 31.2 32.2 33.2
CSF1PO
34.2 35 2N 86 Ho 0.651 P-value 0.270
0.024 0.024 88 0.659 0.032a
88 0.773 0.297
88 0.773 0.781
84 0.714 0.099
86 0.674 0.691
86 0.814 0.028a
84 0.857 0.285
84 0.833 0.182
84 0.714 0.009a
84 0.810 0.136
82 0.780 0.082
84 0.833 0.833
88 84 0.795 0.786 0.773 0.845
Ho, observed heterozygosity; P, Hardy–Weinberg equilibrium, exact test based on more than 2000 shufflings, for standard error <0.01. a Bonferroni’s correction (0:05=15 ¼ 0:0033).
L. Cherni et al. / Forensic Science International 147 (2005) 101–106 103
104
Table 2 Population data for Powerplex 16 loci in Zriba Allele
D3S1358
D5S818
D7S820
D8S1179
D13S317
D16S539
D18S51
D21S11
FGA
Penta D
Penta E
TH01
TPO
VWA
0.060 0.012
0.636 0.205 0.159 0.022 0.122 0.389 0.211 0.144 0.089 0.022
0.068 0.023
0.100 0.056
0.023 0.102 0.523 0.261
0.422 0.211 0.211
0.133 0.067
0.023 0.182
0.144 0.111 0.089 0.178
0.078 0.211 0.478 0.022
0.045 0.455 0.136 0.148
0.178 0.200 0.100
0.011
0.011
0.012 0.023 0.058 0.105 0.116 0.116 0.267 0.116 0.035 0.128 0.023
0.011 0.111 0.089 0.133 0.144 0.089 0.156
0.022
0.133 0.100
0.089 0.333 0.244 0.056 0.044 0.122 0.078 0.011
0.033
0.012 0.024 0.226
0.037 0.012 0.012
0.202 0.071 0.083 0.167
0.098 0.159 0.159 0.159
0.119 0.036
0.098 0.037 0.049 0.037 0.061 0.024 0.037 0.012
0.156 0.256 0.067 0.300 0.189 0.033
0.011 0.522 0.267 0.133 0.067
0.067 0.200 0.256 0.311 0.133 0.011 0.022
L. Cherni et al. / Forensic Science International 147 (2005) 101–106
2.2 3.2 5 6 7 8 9 9.3 10 11 12 13 13.2 14 15 16 17 18 19 20 21 21.2 22 23 24 24.2 25 26 27 28 28.2 29 30 30.2 31 31.2 32.2 33.2
CSF1PO
34.2 35 2N 88 Ho 0.568 P-value 0.273
90 0.711 0.049a
88 0.705 0.801
90 0.733 0.023a
90 0.867 0.877
90 0.667 0.566
88 0.750 0.212
86 0.884 0.096
90 0.844 0.214
90 0.933 0.448
84 0.810 0.755
82 0.854 0.019a
90 0.822 0.535
90 90 0.644 0.889 0.681 0.076
Ho, observed heterozygosity; P, Hardy–Weinberg equilibrium, exact test based on more than 2000 shufflings, for standard error <0.01. a Bonferroni’s correction (0:05=15 ¼ 0:0033).
Moroccan Arabs [5]
Saharawis Southern Moroccan Berbers Northern central Moroccan Berbers Mozabites
VWA (0.01646) – – D13S317 (0.00258)
Tunisia
CSF1PO (0.00020); D13S317 (0.00079) D13S317 (0.01508)
Kesra
Zriba
CSF1PO (0.00714); D5S818 (0.01488); D13S317 (0.00000)
Saharawis [5]
– – D13S317 (0.00278); VWA (0.00258) CSF1PO (0.00000); D13S317 (0.00635) D5S818 (0.02440); D7S820 (0.03273); D13S317 (0.01408) CSF1PO (0.00456); D13S317 (0.00020); FGA (0.03174)
Southern Moroccan Berbers [5]
– D13S317 (0.03729); VWA (0.04106) CSF1PO (0.00040); D13S317 (0.08431) –
CSF1PO (0.01270); D5S818 (0.03868); D13S317 (0.00615)
Northern central Moroccan Berbers [5]
Mozabites [5]
Tunisia [6]
Kesra
D13S317 (0.00198) CSF1PO (0.00476); D13S317 (0.00694) D13S317 (0.00932)
CSF1PO (0.02321); D13S317 (0.00040); TPO (0.02837)
L. Cherni et al. / Forensic Science International 147 (2005) 101–106
Table 3 Heterogeneity of North African populations assessed through the markers included in Powerplex 16 System
CSF1PO (0.00060) D5S818 (0.00575); VWA (0.04086)
CSF1PO (0.00000); D5S818 (0.02420)
CSF1PO (0.00040); FGA (0.01646)
CSF1PO (0.00000); D13S317 (0.01349); D18S51 (0.00436); TPO (0.02420)
CSF1PO (0.00040); D5S818 (0.00139)
105
Significant FST P values (inside brackets); in bold, the P values that remain significant after Bonferroni’s correction (P ¼ 0:0018 for the majority of comparisons, except for D16S539, PD and PE, where it is P ¼ 0:0167).
106
L. Cherni et al. / Forensic Science International 147 (2005) 101–106
This paper follows the guidelines for publication of population data requested by the journal [7].
Acknowledgements This work was partially supported by the Tunisian Ministry of Higher Education, Scientific Research and Technology. Fundac¸a˜ o para a Cieˆ ncia e a Tecnologia conceded a research grant to L.P. (SFRH/BPD/7121/2001) and partially supports IPATIMUP by Programa Operacional Cieˆ ncia, Tecnologia e Inovac¸a˜ o (POCTI), Quadro Comunita´ rio de Apoio III. We are very grateful to the Tunisian Ministry of Health and the staff of Kesra and Siliana hospitals for their help in collecting blood samples.
[2]
[3]
[4]
[5]
[6]
References [1] M.V. Lareu, C.P. Phillips, A. Carracedo, A.J. Lincoln, D. Syndercombe Court, J.A. Thomson, Investigation of the STR
[7]
locus HUMTH01 using PCR and two electrophoresis formats: UK and Galician Caucasian population surveys and usefulness in paternity investigations, Forensic Sci. Int. 66 (1994) 41–52. S. W Guo, E.A. Thompson, Performing the exact test of Hardy–Weinberg proportions for multiple alleles, Biometrics 8 (1992) 361–372. M. Raymond, F. Rousset, GENEPOP (version 1.2): populations genetics software for exact tests and ecumenicism, J. Hered. 86 (1995) 248–249. S. Schneider, D. Roessli, L. Excoffier, Arlequin Ver. 2.000. A Software for Population Genetics Data Analysis, University of Geneva, 2000. E. Bosch, J. Clarimo´ n, A. Pe´ rez-Lezaun, F. Calafell, STR data for 21 loci in northwestern Africa, Forensic Sci. Int. 116 (2001) 41–51. C. Brandt-Casadevall, M. Ben Dhiab, F. Taroni, C. Gehrig, N. Dimo-Simonin, M. Zemni, P. Mangin, Tunisian population data on 15 PCR-based loci, Forensic Sci. Int. 126 (2002) 272–274. P. Lincoln, A. Carracedo, Publication of population data of human polymorphisms, Forensic Sci. Int. 110 (2000) 3–5.