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Allelic frequencies at 12 STR loci in Colombian population
Forensic Science International 136 (2003) 86–88
Announcement of population data
Allelic frequencies at 12 STR loci in Colombian population Alfonso Benı´tez-Pa´ez*, Humberto Ossa Reyes Laboratorio de Gene´tica y Biologı´a Molecular, Carrera 16, 82-29 104 Bogota, DC, Colombia Received 19 November 2002; received in revised form 20 May 2003; accepted 26 May 2003
Abstract Three hundred and twenty-six to four hundred and fifty-one individuals were typed for 12 STR markers and revealed by silver stain method and assisted by a computer analysis. Forensic and Hardy–Weinberg values were found. The Kodak ds 1D Image Analysis Software V 2.0.3 EDAS DC 120 System was a useful tool for determining the correct size of pattern bands that were out allelic ladders, alleles 18 and 17 from F13A01, 15 from TPOX and 4 from TH01 were determined by this method and some corroborated by automatic analysis. # 2003 Elsevier Ireland Ltd. All rights reserved. Keywords: STR; Allelic frequencies; Colombian population
Population: Unrelated Mestizo individuals, implicated in parentage tests and born in Colombia. Extraction: Wizard1 genomic DNA purification kit (Promega Corporation, Madison, WI, USA, Cat. A1120). PCR: Twenty to thirty nanograms of target DNA and following the Promega Corporation instructions for CTT, FFv and SilverSTR III triplex. HPRTB, D8S1179 and D5S818 were typed in a PCR multiplex reaction developed by us with cycling temperatures of 95 8C for 5 min, 35 cycles of 94 8C for 1 min, 56 8C for 1 min, 72 8C for 75 s and final incubation at 60 8C for 30 min. Typing: The PCR products detection was realized by silver staining reagents and their molecular sizes compared with CTT, FFv and SilverSTR III allelic ladders (Promega Corporation). HPRTB, D8S1179 and D5S818 PCR products were typed in agreement with primers published in STR database (http://www.cstl.nist.gov/biotech/strbase/) and allelic assignation was compared with M1, M2 (GEP-ISFG reference sample 2002) and K562 cell line genotypes for this markers in all electrophoresis. Results: See Tables 1 and 2. Quality control: Proficiency testing of the GEP-ISFG (http://www.gep-isfg.org). * Corresponding author. Tel.: þ57-1-6164162; fax: þ57-1-6164172. E-mail addresses: [email protected], [email protected] (A. Benı´tez-Pa´ez).
Analysis of data: Genetic Data Analysis version 1.0 [1], Fstat version 2.9.3.2 [2] and other references [3,4]. Access to the data: Web page unavailable or by author e-mail. Other remarks: Alleles 15 (in TPOX), 18 and 17 (in F13A01), 21 and 23 (in vWA), 4 (in TH01) could be assigned by Kodak ds 1D Image Analysis Software V 2.0.3 EDAS DC 120 System that resulted in a powerful tool in STR typing by silver stain method. Allele 18 was corroborated by automatic detection in ABI310 (data not shown). D8S1179 region to amplify was expanded in order to eliminate cross-size products with D5S818 PCR amplicons, sequence forward primer D8S1179 was derived of AF216671 sequence in GeneBank. Linkage disequilibrium was found between TPOX and D7S820 markers with a significant value (P ¼ 0:0015). The fixation index (f) measured some heterozygotes deficit in CSF1PO, TH01, FESFPS, vWA and D16S539 markers, but those inbreeding values are not significant. Some remarked differences values in heterozygotes, PD and P values were observed with previous population data from Colombian Mestizo [5] and data from African descent [6]. Triplex with HPRTB, D8S1179 and D5S818 showed a higher probability of match than triplex CTT. This triplex reaction increased power of exclusion and typical paternity index values significantly from 0.998913 and 774.3 to 0.999821 and 4105.2, respectively. It is a new STR profile reported for Colombian population in addition to other ones reported from several ethnical populations with some markers presented here and
0379-0738/$ – see front matter # 2003 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/S0379-0738(03)00220-2
Table 1 Allelic frequencies and population’s equilibrium at 12 STR loci analyzed Allele
Obs H Est h Obs h f P
TPOX (n ¼ 451)
TH01 (n ¼ 450)
F13A01 (n ¼ 451)
FESFPS (n ¼ 326)
vWA (n ¼ 451)
D16S539 (n ¼ 451)
D7S820 (n ¼ 451)
D13S317 (n ¼ 451)
HPRTB (n ¼ 412)
D8S1179 (n ¼ 413)
D5S818 (n ¼ 411)
– – – – 0.0044 0.0100 0.0310 – 0.2384 0.2827 0.3625 0.0610 0.0089 0.0011 – – – – – – – –
– – – 0.0089 0.0011 0.4978 0.0654 – 0.0410 0.2705 0.1120 0.0022 – 0.0011 – – – – – – – –
– 0.0011 – 0.3844 0.2378 0.0756 0.1300 0.1689 0.0033 – – – – – – – – – – – – –
0.2295 0.1042 0.2007 0.2040 0.2295 0.0100 0.0011 – – – – 0.0044 0.0033 0.0055 0.0044 0.0011 0.0022 – – – – –
– – – – – 0.0077 0.0061 – 0.2255 0.4693 0.2101 0.0782 0.0031 – – – – – – – – –
– – – – – – – – – – – – 0.0987 0.0898 0.3160 0.2539 0.1796 0.0521 0.0078 0.0011 – 0.0011
– – – – – 0.0111 0.1408 – 0.1718 0.2550 0.2528 0.1375 0.0299 0.0011 – – – – – – – –
– – – – 0.0144 0.1264 0.0843 – 0.2616 0.2772 0.1829 0.0466 0.0067 – – – – – – – – –
– – – – – 0.0976 0.1608 – 0.0577 0.1940 0.2905 0.1330 0.0643 0.0022 – – – – – – – –
– – – – – – 0.0032 – 0.0032 0.0828 0.2890 0.3442 0.2094 0.0568 0.0114 – – – – – – –
– – – – – 0.0048 0.0097 – 0.0666 0.0944 0.1174 0.3354 0.2228 0.1199 0.0266 0.0012 – 0.0012 – – – –
– – – – 0.0280 0.0073 0.0742 – 0.0560 0.4307 0.2701 0.1277 0.0049 0.0012 – – – – – – – –
0.2506 0.7278 0.7494 0.0298 0.5138
0.3459 0.6612 0.6541 0.0107 0.6997
0.2483 0.7453 0.7511 0.0077 0.9959
0.2550 0.8026 0.7450 0.0719 0.0738
0.2883 0.6796 0.7116 0.0473 0.6106
0.2129 0.7837 0.7871 0.0043 0.5506
0.1929 0.8027 0.8071 0.0055 0.7478
0.2084 0.7967 0.7916 0.0064 0.4891
0.1863 0.8184 0.8137 0.0057 0.8225
0.3250 0.7417 0.6750 0.0902 0.3353
0.2276 0.7965 0.7724 0.0304 0.3284
0.3187 0.7167 0.6812 0.0494 0.3750
A. Benı´tez-Pa´ ez, H.O. Reyes / Forensic Science International 136 (2003) 86–88
3.2 4 5 6 7 8 9 9.3 10 11 12 13 14 15 16 17 18 19 20 21 22 23
CSF1PO (n ¼ 451)
Equilibrium values based in diploid individuals. Obs H: observed homozygosity; Est h: unbiased estimated heterozygosity; Obs h: observed heterozygosity; f: fixation index (inbreeding coefficient); P: Hardy–Weinberg disequilibrium, chi-squared measure, exact test based on 3200 shufflings.
87
A. Benı´tez-Pa´ ez, H.O. Reyes / Forensic Science International 136 (2003) 86–88
88
Table 2 Forensic values of polymorphism at 12 STR loci
PM PD PE PIC TPI
CSF1PO TPOX
TH01
F13A01 FESFPS VWA
D16S539 D7S820 D13S317 HPRTB
D8S1179 D5S818
0.1243 0.8757 0.5088 0.6793 1.9956
0.1018 0.8982 0.5126 0.7069 2.0134
0.0688 0.9312 0.5013 0.7715 1.9609
0.0702 0.9298 0.6123 0.7725 2.5920
0.0690 0.9310 0.5489 0.7694 2.1968
Triplex PM Triplex PE
0.1633 0.8367 0.3609 0.6121 1.4455
2.07 103 0.8470
0.1575 0.8425 0.4465 0.6283 1.7340
0.0784 0.9216 0.5754 0.7511 2.3490
8.49 104 0.8828
12 loci PM 12 loci PE 12 loci TPI
0.0737 0.9263 0.5835 0.7661 2.3989
0.0578 0.9422 0.6248 0.7938 2.6845
2.99 104 0.9394
0.1041 0.8959 0.3907 0.7015 1.5385
0.1193 0.8807 0.3999 0.6750 1.5687
8.57 104 0.8350
4.5 1013 0.999821 4105.2
Analysis based in diploid individuals. PM: probability of match; PD: power of discrimination; PE: power of exclusion; PIC: polymorphic information content; TIP: typical paternity index.
other ones different [7–9] in order to increase STR profile for paternity testing proposes in agree with Colombian laws [10]. Twelve loci high typical paternity index determinates to have inclusion probabilities up to 99.9% required by 721/2001 Colombian law. This paper follows the guidelines for publication of population data proposed by the journal [11]. Acknowledgements Thanks are extended to Institute of Legal Medicine, Universidad Santiago de Compostela for its technical help in the automatic analysis. References [1] P.O. Lewis, D. Zaykin, 2001. Genetic Data Analysis: computer program for the analysis of allelic data, version 1.0 (d16c). Free program distributed by the authors over the internet from http://lewis.eeb.uconn.edu/lewishome/software.html. [2] J. Goudet, Fstat version 2.9.3.2, Institute of Ecology, UNIL, Lausanne, Switzerland, 2002. [3] C. Li, A. Chakravarti, An expository review of two methods of calculating the paternity probability, Am. J. Hum. Genet. 43 (1988) 197–205.
[4] K. Huston, Statistical analysis of STR data, Profiles DNA 1 (3) (1998) 14–15. [5] C. Vargas, A. Castillo, A. Gil, A. Pico, O. Garcia, Profiler data for a Colombian population (Department of North Santander), Forensic Sci. Int. 124 (2001) 219–220. [6] J. Yunis, A. Baena, O. Garcia, I. Uriarte, E. Yunis, Population data of F13A01, FES/FPS, VWA, CSF1PO, TPOX and TH01 short tandem repeat loci in a sample of African descent individuals, Forensic Sci. Int. 117 (2001) 235–236. [7] J. Yunis, O. Garcia, A. Baena, G. Arboleda, I. Uriarte, E. Yunis, Population frequency for the short tandem repeat loci D18S849, D3S1744 and D12S1090 in Caucasian–Mestizo and African descent population of Colombia, J. Forensic Sci. 45 (2) (2000) 429–431. [8] J. Yunis, O. Garcia, S. Moreno, I. Uriarte, E. Yunis, Population data on D7S820, FGA, D1S533 and D9S304 in a sample of Caucasian–Mestizo from Colombia, Prog. Forensic Genet. 9 (2003) 201–205. [9] J. Yunis, O. Garcia, S. Moreno, C. Pineda, C. Rodriguez, I. Uriarte, E. Yunis, Population data on PowerPlex 2.1 (FGA, VWA, TPOX, TH01, PENTA E, D18S51, D21S11, D3S1358, D8S1179) and GammaStar (D16S539, D7S820, D13S317, D5S818) in a sample of Caucasian–Mestizo from Colombia, Prog. Forensic Genet. 9 (2003) 207–212. [10] Congreso de la Repu´ blica de Colombia, Ley 721 de 2001. [11] P. Lincoln, A. Carracedo, Publication of population data of human polymorphisms, Forensic Sci. Int. 110 (2000) 3–5.
Announcement of population data
Allelic frequencies at 12 STR loci in Colombian population Alfonso Benı´tez-Pa´ez*, Humberto Ossa Reyes Laboratorio de Gene´tica y Biologı´a Molecular, Carrera 16, 82-29 104 Bogota, DC, Colombia Received 19 November 2002; received in revised form 20 May 2003; accepted 26 May 2003
Abstract Three hundred and twenty-six to four hundred and fifty-one individuals were typed for 12 STR markers and revealed by silver stain method and assisted by a computer analysis. Forensic and Hardy–Weinberg values were found. The Kodak ds 1D Image Analysis Software V 2.0.3 EDAS DC 120 System was a useful tool for determining the correct size of pattern bands that were out allelic ladders, alleles 18 and 17 from F13A01, 15 from TPOX and 4 from TH01 were determined by this method and some corroborated by automatic analysis. # 2003 Elsevier Ireland Ltd. All rights reserved. Keywords: STR; Allelic frequencies; Colombian population
Population: Unrelated Mestizo individuals, implicated in parentage tests and born in Colombia. Extraction: Wizard1 genomic DNA purification kit (Promega Corporation, Madison, WI, USA, Cat. A1120). PCR: Twenty to thirty nanograms of target DNA and following the Promega Corporation instructions for CTT, FFv and SilverSTR III triplex. HPRTB, D8S1179 and D5S818 were typed in a PCR multiplex reaction developed by us with cycling temperatures of 95 8C for 5 min, 35 cycles of 94 8C for 1 min, 56 8C for 1 min, 72 8C for 75 s and final incubation at 60 8C for 30 min. Typing: The PCR products detection was realized by silver staining reagents and their molecular sizes compared with CTT, FFv and SilverSTR III allelic ladders (Promega Corporation). HPRTB, D8S1179 and D5S818 PCR products were typed in agreement with primers published in STR database (http://www.cstl.nist.gov/biotech/strbase/) and allelic assignation was compared with M1, M2 (GEP-ISFG reference sample 2002) and K562 cell line genotypes for this markers in all electrophoresis. Results: See Tables 1 and 2. Quality control: Proficiency testing of the GEP-ISFG (http://www.gep-isfg.org). * Corresponding author. Tel.: þ57-1-6164162; fax: þ57-1-6164172. E-mail addresses: [email protected], [email protected] (A. Benı´tez-Pa´ez).
Analysis of data: Genetic Data Analysis version 1.0 [1], Fstat version 2.9.3.2 [2] and other references [3,4]. Access to the data: Web page unavailable or by author e-mail. Other remarks: Alleles 15 (in TPOX), 18 and 17 (in F13A01), 21 and 23 (in vWA), 4 (in TH01) could be assigned by Kodak ds 1D Image Analysis Software V 2.0.3 EDAS DC 120 System that resulted in a powerful tool in STR typing by silver stain method. Allele 18 was corroborated by automatic detection in ABI310 (data not shown). D8S1179 region to amplify was expanded in order to eliminate cross-size products with D5S818 PCR amplicons, sequence forward primer D8S1179 was derived of AF216671 sequence in GeneBank. Linkage disequilibrium was found between TPOX and D7S820 markers with a significant value (P ¼ 0:0015). The fixation index (f) measured some heterozygotes deficit in CSF1PO, TH01, FESFPS, vWA and D16S539 markers, but those inbreeding values are not significant. Some remarked differences values in heterozygotes, PD and P values were observed with previous population data from Colombian Mestizo [5] and data from African descent [6]. Triplex with HPRTB, D8S1179 and D5S818 showed a higher probability of match than triplex CTT. This triplex reaction increased power of exclusion and typical paternity index values significantly from 0.998913 and 774.3 to 0.999821 and 4105.2, respectively. It is a new STR profile reported for Colombian population in addition to other ones reported from several ethnical populations with some markers presented here and
0379-0738/$ – see front matter # 2003 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/S0379-0738(03)00220-2
Table 1 Allelic frequencies and population’s equilibrium at 12 STR loci analyzed Allele
Obs H Est h Obs h f P
TPOX (n ¼ 451)
TH01 (n ¼ 450)
F13A01 (n ¼ 451)
FESFPS (n ¼ 326)
vWA (n ¼ 451)
D16S539 (n ¼ 451)
D7S820 (n ¼ 451)
D13S317 (n ¼ 451)
HPRTB (n ¼ 412)
D8S1179 (n ¼ 413)
D5S818 (n ¼ 411)
– – – – 0.0044 0.0100 0.0310 – 0.2384 0.2827 0.3625 0.0610 0.0089 0.0011 – – – – – – – –
– – – 0.0089 0.0011 0.4978 0.0654 – 0.0410 0.2705 0.1120 0.0022 – 0.0011 – – – – – – – –
– 0.0011 – 0.3844 0.2378 0.0756 0.1300 0.1689 0.0033 – – – – – – – – – – – – –
0.2295 0.1042 0.2007 0.2040 0.2295 0.0100 0.0011 – – – – 0.0044 0.0033 0.0055 0.0044 0.0011 0.0022 – – – – –
– – – – – 0.0077 0.0061 – 0.2255 0.4693 0.2101 0.0782 0.0031 – – – – – – – – –
– – – – – – – – – – – – 0.0987 0.0898 0.3160 0.2539 0.1796 0.0521 0.0078 0.0011 – 0.0011
– – – – – 0.0111 0.1408 – 0.1718 0.2550 0.2528 0.1375 0.0299 0.0011 – – – – – – – –
– – – – 0.0144 0.1264 0.0843 – 0.2616 0.2772 0.1829 0.0466 0.0067 – – – – – – – – –
– – – – – 0.0976 0.1608 – 0.0577 0.1940 0.2905 0.1330 0.0643 0.0022 – – – – – – – –
– – – – – – 0.0032 – 0.0032 0.0828 0.2890 0.3442 0.2094 0.0568 0.0114 – – – – – – –
– – – – – 0.0048 0.0097 – 0.0666 0.0944 0.1174 0.3354 0.2228 0.1199 0.0266 0.0012 – 0.0012 – – – –
– – – – 0.0280 0.0073 0.0742 – 0.0560 0.4307 0.2701 0.1277 0.0049 0.0012 – – – – – – – –
0.2506 0.7278 0.7494 0.0298 0.5138
0.3459 0.6612 0.6541 0.0107 0.6997
0.2483 0.7453 0.7511 0.0077 0.9959
0.2550 0.8026 0.7450 0.0719 0.0738
0.2883 0.6796 0.7116 0.0473 0.6106
0.2129 0.7837 0.7871 0.0043 0.5506
0.1929 0.8027 0.8071 0.0055 0.7478
0.2084 0.7967 0.7916 0.0064 0.4891
0.1863 0.8184 0.8137 0.0057 0.8225
0.3250 0.7417 0.6750 0.0902 0.3353
0.2276 0.7965 0.7724 0.0304 0.3284
0.3187 0.7167 0.6812 0.0494 0.3750
A. Benı´tez-Pa´ ez, H.O. Reyes / Forensic Science International 136 (2003) 86–88
3.2 4 5 6 7 8 9 9.3 10 11 12 13 14 15 16 17 18 19 20 21 22 23
CSF1PO (n ¼ 451)
Equilibrium values based in diploid individuals. Obs H: observed homozygosity; Est h: unbiased estimated heterozygosity; Obs h: observed heterozygosity; f: fixation index (inbreeding coefficient); P: Hardy–Weinberg disequilibrium, chi-squared measure, exact test based on 3200 shufflings.
87
A. Benı´tez-Pa´ ez, H.O. Reyes / Forensic Science International 136 (2003) 86–88
88
Table 2 Forensic values of polymorphism at 12 STR loci
PM PD PE PIC TPI
CSF1PO TPOX
TH01
F13A01 FESFPS VWA
D16S539 D7S820 D13S317 HPRTB
D8S1179 D5S818
0.1243 0.8757 0.5088 0.6793 1.9956
0.1018 0.8982 0.5126 0.7069 2.0134
0.0688 0.9312 0.5013 0.7715 1.9609
0.0702 0.9298 0.6123 0.7725 2.5920
0.0690 0.9310 0.5489 0.7694 2.1968
Triplex PM Triplex PE
0.1633 0.8367 0.3609 0.6121 1.4455
2.07 103 0.8470
0.1575 0.8425 0.4465 0.6283 1.7340
0.0784 0.9216 0.5754 0.7511 2.3490
8.49 104 0.8828
12 loci PM 12 loci PE 12 loci TPI
0.0737 0.9263 0.5835 0.7661 2.3989
0.0578 0.9422 0.6248 0.7938 2.6845
2.99 104 0.9394
0.1041 0.8959 0.3907 0.7015 1.5385
0.1193 0.8807 0.3999 0.6750 1.5687
8.57 104 0.8350
4.5 1013 0.999821 4105.2
Analysis based in diploid individuals. PM: probability of match; PD: power of discrimination; PE: power of exclusion; PIC: polymorphic information content; TIP: typical paternity index.
other ones different [7–9] in order to increase STR profile for paternity testing proposes in agree with Colombian laws [10]. Twelve loci high typical paternity index determinates to have inclusion probabilities up to 99.9% required by 721/2001 Colombian law. This paper follows the guidelines for publication of population data proposed by the journal [11]. Acknowledgements Thanks are extended to Institute of Legal Medicine, Universidad Santiago de Compostela for its technical help in the automatic analysis. References [1] P.O. Lewis, D. Zaykin, 2001. Genetic Data Analysis: computer program for the analysis of allelic data, version 1.0 (d16c). Free program distributed by the authors over the internet from http://lewis.eeb.uconn.edu/lewishome/software.html. [2] J. Goudet, Fstat version 2.9.3.2, Institute of Ecology, UNIL, Lausanne, Switzerland, 2002. [3] C. Li, A. Chakravarti, An expository review of two methods of calculating the paternity probability, Am. J. Hum. Genet. 43 (1988) 197–205.
[4] K. Huston, Statistical analysis of STR data, Profiles DNA 1 (3) (1998) 14–15. [5] C. Vargas, A. Castillo, A. Gil, A. Pico, O. Garcia, Profiler data for a Colombian population (Department of North Santander), Forensic Sci. Int. 124 (2001) 219–220. [6] J. Yunis, A. Baena, O. Garcia, I. Uriarte, E. Yunis, Population data of F13A01, FES/FPS, VWA, CSF1PO, TPOX and TH01 short tandem repeat loci in a sample of African descent individuals, Forensic Sci. Int. 117 (2001) 235–236. [7] J. Yunis, O. Garcia, A. Baena, G. Arboleda, I. Uriarte, E. Yunis, Population frequency for the short tandem repeat loci D18S849, D3S1744 and D12S1090 in Caucasian–Mestizo and African descent population of Colombia, J. Forensic Sci. 45 (2) (2000) 429–431. [8] J. Yunis, O. Garcia, S. Moreno, I. Uriarte, E. Yunis, Population data on D7S820, FGA, D1S533 and D9S304 in a sample of Caucasian–Mestizo from Colombia, Prog. Forensic Genet. 9 (2003) 201–205. [9] J. Yunis, O. Garcia, S. Moreno, C. Pineda, C. Rodriguez, I. Uriarte, E. Yunis, Population data on PowerPlex 2.1 (FGA, VWA, TPOX, TH01, PENTA E, D18S51, D21S11, D3S1358, D8S1179) and GammaStar (D16S539, D7S820, D13S317, D5S818) in a sample of Caucasian–Mestizo from Colombia, Prog. Forensic Genet. 9 (2003) 207–212. [10] Congreso de la Repu´ blica de Colombia, Ley 721 de 2001. [11] P. Lincoln, A. Carracedo, Publication of population data of human polymorphisms, Forensic Sci. Int. 110 (2000) 3–5.