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Autosomic STR population data in two Caribbean samples from Colombia
Forensic Science International 152 (2005) 79–81 www.elsevier.com/locate/forsciint
Announcement of Population Data
Autosomic STR population data in two Caribbean samples from Colombia Beatriz Martı´nez a,*, Luis Caraballo a, Leonor Gusma˜o b, Antonio Amorim b, Angel Carracedo c a
Instituto de Investigaciones Inmunolo´gicas de la Universidad de Cartagena, Cartagena, Colombia Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Portugal c Instituto de Medicina Legal, Universidad de Santiago de Compostela, Santiago de Compostela, Spain b
Received 15 October 2004; accepted 21 January 2005 Available online 9 March 2005
Abstract In this work, a sample of 124 unrelated individuals from San Andres Island and Santa Marta City (Colombia) was studied for the nine STRs included in the AmpF‘STR Profiler kit (CSF1PO, D3S1358, D5S818, D7S820, D13S317, FGA, TH01, TPOX and vWA). Although these two populations are geographically apart, San Andres is an Island in the middle of Caribbean Sea (about 480 miles northwest the Colombian mainland) and Santa Marta City located in the coast, exact test showed no differentiation between both population samples (P = 0.39445 0.0805). Therefore, allele frequencies and parameters of forensic interest were estimated for the global sample. # 2005 Elsevier Ireland Ltd. All rights reserved. Keywords: STRs; Population data; AmpF‘STR Profiler; Colombian Caribbean coast
Population: One hundred and twenty-four unrelated individuals living in Colombia, from two different populations: Santa Marta City in the Caribbean Cost (N = 97) and San Andres Island in the Caribbean Sea (N = 27). DNA extraction: Mini-Salting-Out method [1]. PCR: According to the manufacturer’s instructions (AmpF‘STR Profiler PCR amplification kit, AB Applied Biosystems). Typing: ABI 310 and reference sequenced ladders provided with the kit (AmpF‘STR Profiler PCR amplification kit, AB Applied Biosystems). Results: Tables 1 and 2. Quality control: Proficiency testing of the GEP-ISFG Working Group (www.gep-isfg.org). * Corresponding author. Tel.: +57 56 698491; fax: +57 56 698491. E-mail address: [email protected] (B. Martı´nez).
Analysis of data: Gene frequencies, expected and observed heterozygosity values, Hardy–Weinberg equilibrium test and exact test of population differentiation were carried out using the Arlequin Software version 2.000 [2]. Bonferroni correction assumes that a 0.05 significance level used for nine tests (one per locus) yields an actual significance of 0.0056 [3]. Statistical parameters for forensic and paternity testing, power of discrimination (PD) and a priori exclusion chance (CE), were calculated with Powerstats version 1.2 (Promega Corp.) [4]. Other remarks: Colombian Caribbean coast population was originated from the admixture of Spanish colonists, African slaves and Aboriginal populations, mainly during the XVI–XVIII centuries. Nowadays the population is very heterogeneous, even among the known geographic sub-regions (Bolivar, Atla´ntico, Magdalena, Guajira, Cesar and San Andres Island). The present
0379-0738/$ – see front matter # 2005 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.forsciint.2005.01.016
B. Martı´nez et al. / Forensic Science International 152 (2005) 79–81
80
Table 1 Population data for nine STR loci in a sample of 124 individuals from Colombian Caribbean coast Allele
CSF1PO
D3S1358
D5S818
D7S820
D13S317
FGA
TH01
TPOX
vWA
5 6 7 8 9 9.3 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 30
– – 0.020 0.032 0.069 – 0.250 0.294 0.278 0.053 0.004 – – – – – – – – – – – – – – –
– – – – – – – – 0.008 0.020 0.206 0.343 0.274 0.101 0.044 0.004 – – – – – – – – – –
– – 0.024 0.028 0.072 – 0.077 0.347 0.331 0.101 0.016 0.004 – – – – – – – – – – – – – –
– – 0.016 0.169 0.105 – 0.282 0.218 0.178 0.032 – – – – – – – – – – – – – – –
– – 0.004 0.093 0.085 – 0.097 0.246 0.310 0.121 0.044 – – – – – – – – – – – – – – –
– – – – – – – – – – – – – – 0.024 0.101 0.065 0.169 0.161 0.137 0.105 0.125 0.069 0.028 0.008 0.008
0.052 0.214 0.314 0.121 0.198 0.077 0.024 – – – – – – – – – – – – – – – – – – –
– 0.048 0.081 0.379 0.097 – 0.073 0.254 0.068 – – – – – – – – – – – – – – – – –
– – – – – – – – 0.004 0.024 0.077 0.182 0.266 0.262 0.133 0.040 0.012 – – – – – – – – –
Ho He PD CE P
0.742 0.768 0.907 0.526 0.223
0.734 0.755 0.899 0.507 0.816
0.734 0.754 0.899 0.514 0.119
0.806 0.804 0.931 0.584 0.739
0.790 0.806 0.935 0.598 0.253
0.831 0.883 0.973 0.741 0.507
0.726 0.797 0.928 0.577 0.028*
0.710 0.767 0.913 0.544 0.063
0.726 0.809 0.932 0.597 0.415
Ho: observed heterozygosity; He: expected heterozygosity; PD: power of discrimination; CE: a priori chance of exclusion; P: Hardy-Weinberg equilibrium, exact test based on more than 2000 shufflings, for standard error < 0.01. * Bonferroni correction (0.05/9 = 0.0056).
studied sample belongs to two of these Colombian subregions: Santa Marta City, the capital of Magdalena, and San Andres, a small island in the Caribbean Sea, 140 miles east of Nicaragua.
Exact test of sample differentiation based on the nine autosomal loci included in the AmpF‘STR Profiler kit (CSF1PO, D3S1358, D5S818, D7S820, D13S317, FGA, TH01, TPOX and vWA) did not revealed significant
Table 2 Non-differentiation exact probability values obtained from population differentiation tests between Santa Marta (SM) and San Andres (SA) samples, as well as between the global sample (CC) and samples from Antioquia, Colombia (Ant) [5,6], Bogota´ , Colombia (Bog) [7], Boyaca´ , Colombia (Boy) [7] and Caribbean coast, Colombia (Car) [8] Locus
SM vs. SA
CC vs. Ant
CC vs. Bog
CC vs. Boy
CC vs. Car
CSF1PO D3S1358 D5S818 D7S820 TH01 TPOX vWA FGA D13S317
0.04115 0.21355 0.07160 0.79000 0.25510 0.36605 0.63695 0.65315 0.85040
0.00130* – 0.22945 0.74090 0.00000* 0.00000* 0.30300 0.96190 0.00360*
0.00495* 0.00755 0.24605 0.54935 0.01190 0.00035* 0.37705 0.60280 0.13365
0.09160 0.00325* 0.47740 0.18605 0.00085* 0.00260* 0.00555* 0.40940 0.09375
0.15185 0.00040* 0.28555 0.63150 0.00375* 0.01060 0.61280 0.87300 0.70245
*
Significant values after Bonferroni correction (<0.0056).
B. Martı´nez et al. / Forensic Science International 152 (2005) 79–81
differences between Santa Marta and San Andres (P = 0.39445 0.0805). Therefore, the two samples were pooled as representing a single population. Table 1 shows the allele frequency distributions in the global sample of 124 individuals, as well as other population and forensic genetic parameters. In the present sample, the power of exclusion and matching probability values obtained when combining the nine STR loci were 0.9996176 and one in 2.04 1010, respectively. These values can be considered below the required for forensic applications, consequently the use of a wider battery of genetic markers is therefore recommended for such studies in this region. Deviation from Hardy–Weinberg equilibrium was only observed for THO1 (P = 0.028). However, if Bonferroni correction is used (P < 0.0056) the difference is not significant (Table 2). Single locus comparisons with published data on other Colombian populations [5,8] revealed significant differences in two to four out of nine loci (Table 2). As expected, no significant differences were obtained in locus by locus comparison of the Santa Marta and San Andres samples. The present study results show that, since there are no significant differences in the allele distributions in the two population samples, a single database including both populations can be used for human identification purposes. However, due to the genetic heterogeneity of the Colombian population, specific forensic databases are required for different regions. This paper follows the guidelines for publication of population data requested by the journal [9].
Acknowledgements Financial support was granted by The University of Cartagena, Colombia and by Fundac¸a˜ o para a Cieˆ ncia e a
81
Tecnologia, Programa Operacional Cieˆ ncia, Tecnologia e Inovac¸a˜ o (POCTI).
References [1] S.A. Miller, D.D. Dykes, H.F. Polesky, A simple salting out procedure for estracting DNA from human nucleated cells, Nucl. Acid Res. 16 (1998) 1215. [2] S. Schneider, D. Roessli, L. Excoffier. Arlequin Version 2000. A Software for Population Genetics Data Analysis, University of Geneva, 2000. [3] B.S. Weir, Multiple tests, in: B.S. Weir (Ed.), Genetic Data Analysis II, Sinauer Associates, USA, 1996 , pp. 134– 138. [4] Powerstats Version 1.2, Promega Corporation website. Downloaded 28th December 2003 at http://www.promega.com/geneticidtools/powerstats/. [5] M.L.J. Bravo, J.J. Builes, M.M. Pancorbo, M.A. Moreno, Analysis of 12 STR loci in Antioquia (Colombia) population sample, Int. Congr. Ser. 1261 (2004) 151–153. [6] J.J. Builes, M.L.J. Bravo, J.D. Garcia, M.A. Moreno, Genetic analysis of the short tandem repeat Loci FGA, D7S820, D1S355, D9S304, D12S1090, D3S1744 and D18S849 in an Antioquia (Colombia) Population Sample, Int. Congr. Ser. 1261 (2004) 163–165. [7] M. Rey, A. Gutierrez, B. Schroeder, W. Usaquen, A. Carracedo, I. Bustos, A. Giraldo, Allele frequencies for 13 STRs from two Colombian populations: Bogota´ and Boyaca´ , Forensic Sci. Int. 136 (2003) 83–85. [8] M. Paredes, A. Galindo, M. Bernal, S. Avila, D. Andrade, C. Vergara, M. Rincon, R.E. Romero, N. Navarrete, M. Cardenas, J. Ortega, D. Suarez, A. Cifuentes, A. Salas, A. Carracedo, Analysis of the CODIS autosomal STR loci in four main Colombian regions, Forensic Sci. Int. 137 (2003) 67– 73. [9] P. Lincoln, A. Carracedo, Publication of population data of human polymorphisms, Forensic Sci. Int. 110 (2000) 3–5.
Announcement of Population Data
Autosomic STR population data in two Caribbean samples from Colombia Beatriz Martı´nez a,*, Luis Caraballo a, Leonor Gusma˜o b, Antonio Amorim b, Angel Carracedo c a
Instituto de Investigaciones Inmunolo´gicas de la Universidad de Cartagena, Cartagena, Colombia Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Portugal c Instituto de Medicina Legal, Universidad de Santiago de Compostela, Santiago de Compostela, Spain b
Received 15 October 2004; accepted 21 January 2005 Available online 9 March 2005
Abstract In this work, a sample of 124 unrelated individuals from San Andres Island and Santa Marta City (Colombia) was studied for the nine STRs included in the AmpF‘STR Profiler kit (CSF1PO, D3S1358, D5S818, D7S820, D13S317, FGA, TH01, TPOX and vWA). Although these two populations are geographically apart, San Andres is an Island in the middle of Caribbean Sea (about 480 miles northwest the Colombian mainland) and Santa Marta City located in the coast, exact test showed no differentiation between both population samples (P = 0.39445 0.0805). Therefore, allele frequencies and parameters of forensic interest were estimated for the global sample. # 2005 Elsevier Ireland Ltd. All rights reserved. Keywords: STRs; Population data; AmpF‘STR Profiler; Colombian Caribbean coast
Population: One hundred and twenty-four unrelated individuals living in Colombia, from two different populations: Santa Marta City in the Caribbean Cost (N = 97) and San Andres Island in the Caribbean Sea (N = 27). DNA extraction: Mini-Salting-Out method [1]. PCR: According to the manufacturer’s instructions (AmpF‘STR Profiler PCR amplification kit, AB Applied Biosystems). Typing: ABI 310 and reference sequenced ladders provided with the kit (AmpF‘STR Profiler PCR amplification kit, AB Applied Biosystems). Results: Tables 1 and 2. Quality control: Proficiency testing of the GEP-ISFG Working Group (www.gep-isfg.org). * Corresponding author. Tel.: +57 56 698491; fax: +57 56 698491. E-mail address: [email protected] (B. Martı´nez).
Analysis of data: Gene frequencies, expected and observed heterozygosity values, Hardy–Weinberg equilibrium test and exact test of population differentiation were carried out using the Arlequin Software version 2.000 [2]. Bonferroni correction assumes that a 0.05 significance level used for nine tests (one per locus) yields an actual significance of 0.0056 [3]. Statistical parameters for forensic and paternity testing, power of discrimination (PD) and a priori exclusion chance (CE), were calculated with Powerstats version 1.2 (Promega Corp.) [4]. Other remarks: Colombian Caribbean coast population was originated from the admixture of Spanish colonists, African slaves and Aboriginal populations, mainly during the XVI–XVIII centuries. Nowadays the population is very heterogeneous, even among the known geographic sub-regions (Bolivar, Atla´ntico, Magdalena, Guajira, Cesar and San Andres Island). The present
0379-0738/$ – see front matter # 2005 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.forsciint.2005.01.016
B. Martı´nez et al. / Forensic Science International 152 (2005) 79–81
80
Table 1 Population data for nine STR loci in a sample of 124 individuals from Colombian Caribbean coast Allele
CSF1PO
D3S1358
D5S818
D7S820
D13S317
FGA
TH01
TPOX
vWA
5 6 7 8 9 9.3 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 30
– – 0.020 0.032 0.069 – 0.250 0.294 0.278 0.053 0.004 – – – – – – – – – – – – – – –
– – – – – – – – 0.008 0.020 0.206 0.343 0.274 0.101 0.044 0.004 – – – – – – – – – –
– – 0.024 0.028 0.072 – 0.077 0.347 0.331 0.101 0.016 0.004 – – – – – – – – – – – – – –
– – 0.016 0.169 0.105 – 0.282 0.218 0.178 0.032 – – – – – – – – – – – – – – –
– – 0.004 0.093 0.085 – 0.097 0.246 0.310 0.121 0.044 – – – – – – – – – – – – – – –
– – – – – – – – – – – – – – 0.024 0.101 0.065 0.169 0.161 0.137 0.105 0.125 0.069 0.028 0.008 0.008
0.052 0.214 0.314 0.121 0.198 0.077 0.024 – – – – – – – – – – – – – – – – – – –
– 0.048 0.081 0.379 0.097 – 0.073 0.254 0.068 – – – – – – – – – – – – – – – – –
– – – – – – – – 0.004 0.024 0.077 0.182 0.266 0.262 0.133 0.040 0.012 – – – – – – – – –
Ho He PD CE P
0.742 0.768 0.907 0.526 0.223
0.734 0.755 0.899 0.507 0.816
0.734 0.754 0.899 0.514 0.119
0.806 0.804 0.931 0.584 0.739
0.790 0.806 0.935 0.598 0.253
0.831 0.883 0.973 0.741 0.507
0.726 0.797 0.928 0.577 0.028*
0.710 0.767 0.913 0.544 0.063
0.726 0.809 0.932 0.597 0.415
Ho: observed heterozygosity; He: expected heterozygosity; PD: power of discrimination; CE: a priori chance of exclusion; P: Hardy-Weinberg equilibrium, exact test based on more than 2000 shufflings, for standard error < 0.01. * Bonferroni correction (0.05/9 = 0.0056).
studied sample belongs to two of these Colombian subregions: Santa Marta City, the capital of Magdalena, and San Andres, a small island in the Caribbean Sea, 140 miles east of Nicaragua.
Exact test of sample differentiation based on the nine autosomal loci included in the AmpF‘STR Profiler kit (CSF1PO, D3S1358, D5S818, D7S820, D13S317, FGA, TH01, TPOX and vWA) did not revealed significant
Table 2 Non-differentiation exact probability values obtained from population differentiation tests between Santa Marta (SM) and San Andres (SA) samples, as well as between the global sample (CC) and samples from Antioquia, Colombia (Ant) [5,6], Bogota´ , Colombia (Bog) [7], Boyaca´ , Colombia (Boy) [7] and Caribbean coast, Colombia (Car) [8] Locus
SM vs. SA
CC vs. Ant
CC vs. Bog
CC vs. Boy
CC vs. Car
CSF1PO D3S1358 D5S818 D7S820 TH01 TPOX vWA FGA D13S317
0.04115 0.21355 0.07160 0.79000 0.25510 0.36605 0.63695 0.65315 0.85040
0.00130* – 0.22945 0.74090 0.00000* 0.00000* 0.30300 0.96190 0.00360*
0.00495* 0.00755 0.24605 0.54935 0.01190 0.00035* 0.37705 0.60280 0.13365
0.09160 0.00325* 0.47740 0.18605 0.00085* 0.00260* 0.00555* 0.40940 0.09375
0.15185 0.00040* 0.28555 0.63150 0.00375* 0.01060 0.61280 0.87300 0.70245
*
Significant values after Bonferroni correction (<0.0056).
B. Martı´nez et al. / Forensic Science International 152 (2005) 79–81
differences between Santa Marta and San Andres (P = 0.39445 0.0805). Therefore, the two samples were pooled as representing a single population. Table 1 shows the allele frequency distributions in the global sample of 124 individuals, as well as other population and forensic genetic parameters. In the present sample, the power of exclusion and matching probability values obtained when combining the nine STR loci were 0.9996176 and one in 2.04 1010, respectively. These values can be considered below the required for forensic applications, consequently the use of a wider battery of genetic markers is therefore recommended for such studies in this region. Deviation from Hardy–Weinberg equilibrium was only observed for THO1 (P = 0.028). However, if Bonferroni correction is used (P < 0.0056) the difference is not significant (Table 2). Single locus comparisons with published data on other Colombian populations [5,8] revealed significant differences in two to four out of nine loci (Table 2). As expected, no significant differences were obtained in locus by locus comparison of the Santa Marta and San Andres samples. The present study results show that, since there are no significant differences in the allele distributions in the two population samples, a single database including both populations can be used for human identification purposes. However, due to the genetic heterogeneity of the Colombian population, specific forensic databases are required for different regions. This paper follows the guidelines for publication of population data requested by the journal [9].
Acknowledgements Financial support was granted by The University of Cartagena, Colombia and by Fundac¸a˜ o para a Cieˆ ncia e a
81
Tecnologia, Programa Operacional Cieˆ ncia, Tecnologia e Inovac¸a˜ o (POCTI).
References [1] S.A. Miller, D.D. Dykes, H.F. Polesky, A simple salting out procedure for estracting DNA from human nucleated cells, Nucl. Acid Res. 16 (1998) 1215. [2] S. Schneider, D. Roessli, L. Excoffier. Arlequin Version 2000. A Software for Population Genetics Data Analysis, University of Geneva, 2000. [3] B.S. Weir, Multiple tests, in: B.S. Weir (Ed.), Genetic Data Analysis II, Sinauer Associates, USA, 1996 , pp. 134– 138. [4] Powerstats Version 1.2, Promega Corporation website. Downloaded 28th December 2003 at http://www.promega.com/geneticidtools/powerstats/. [5] M.L.J. Bravo, J.J. Builes, M.M. Pancorbo, M.A. Moreno, Analysis of 12 STR loci in Antioquia (Colombia) population sample, Int. Congr. Ser. 1261 (2004) 151–153. [6] J.J. Builes, M.L.J. Bravo, J.D. Garcia, M.A. Moreno, Genetic analysis of the short tandem repeat Loci FGA, D7S820, D1S355, D9S304, D12S1090, D3S1744 and D18S849 in an Antioquia (Colombia) Population Sample, Int. Congr. Ser. 1261 (2004) 163–165. [7] M. Rey, A. Gutierrez, B. Schroeder, W. Usaquen, A. Carracedo, I. Bustos, A. Giraldo, Allele frequencies for 13 STRs from two Colombian populations: Bogota´ and Boyaca´ , Forensic Sci. Int. 136 (2003) 83–85. [8] M. Paredes, A. Galindo, M. Bernal, S. Avila, D. Andrade, C. Vergara, M. Rincon, R.E. Romero, N. Navarrete, M. Cardenas, J. Ortega, D. Suarez, A. Cifuentes, A. Salas, A. Carracedo, Analysis of the CODIS autosomal STR loci in four main Colombian regions, Forensic Sci. Int. 137 (2003) 67– 73. [9] P. Lincoln, A. Carracedo, Publication of population data of human polymorphisms, Forensic Sci. Int. 110 (2000) 3–5.