- Email: [email protected]
Genetic variation for 12 STRs loci in a Colombian population (Department of Valle del Cauca)
Forensic Science International 137 (2003) 235–237
Announcement of population data
Genetic variation for 12 STRs loci in a Colombian population (Department of Valle del Cauca) Marı´a Victoria Go´meza,*, Marı´a Edith Reyesa, Heiber Ca´rdenasb, Oscar Garcı´ac a
Laboratorio de Inmunologı´a e Inmunogene´tica, Hospital Universitario del Valle, Cali, Colombia b Departamento de Biologı´a, Universidad del Valle, Cali, Colombia c Area de Laboratorio Ertzaintza, Avda. Montevideo 3, E-48002 Bilbao, Spain Received 12 February 2003; received in revised form 30 June 2003; accepted 2 July 2003
Population: Department of Valle del Cauca, Colombia. Number: 939–1920. Extraction: Genomic DNA was extracted from 1 ml of EDTA anticoagulated peripheral blood using the salting out methodology. PCR: After DNA quantitation by spectrophotometry, 1 or 2 ng of DNA were amplified using the commercial kits AmpFlSTR Profiler, AmpFlSTR Profiler Plus, AmpFlSTR COfiler (PE Applied Biosystems) and PowerPlex 16 (Promega Corporation) following the manufacturer’s instructions. Typing: ABI310 and reference sequenced ladders (PE Applied Biosystems and Promega Corporation). Allele CSF1PO D13S317 D5S818 D7S820 TH01 5 6 6.1 7 8 9 9.3 10 11 12 13 13.2 14 15 16 17 18 18.2
0.0044 0.0161 0.0144 0.0233
0.0005 0.0740 0.1321
0.0255 0.0107 0.0659
0.0112 0.1361 0.0954
0.2337 0.2762 0.3636 0.0613
0.0597 0.2277 0.2955 0.1428
0.0563 0.3986 0.2858 0.1446
0.2823 0.2779 0.1593 0.0302
0.0096 0.0017
0.0662 0.0016
0.0115 0.0010
0.0031
0.0014 0.3541 0.0014 0.2586 0.0928 0.1291 0.1548 0.0079
Quality control: Proficiency testing of the GEP-ISFG WG. Analysis of data: PowerStats [1] and GDA [2]. Access to the data: [email protected]. Other remarks: A comparison of allele frequencies in the population under study has been performed with other studies from Colombian Caucasian individuals [3–11], with African descent individuals of Colombia [11,12] and with Amerindian populations of Colombia [13]. These comparisons revealed statistically significant differences (data not shown). This paper follows the guidelines for publication of population data requested by the journal [14]. TPOX VWA
FGA
D3S1358 D8S1179 D21S11 D18S51
0.0127 0.0038 0.4736 0.0905 0.0535 0.2769 0.0005 0.0860 0.0003 0.0031 0.0026 0.0576 0.1260 0.3440 0.2492 0.1539
* Corresponding author. E-mail address: [email protected] (M.V. Go´mez).
0379-0738/$ – see front matter # 2003 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/S0379-0738(03)00297-4
0.0005 0.0010 0.0031 0.0091 0.0026
0.0003
0.0053 0.0106
0.0016 0.0050
0.0487 0.0751 0.1021 0.3286
0.1019 0.3726 0.2720 0.1470 0.0933
0.2656 0.1349 0.0249 0.0037 0.0005
0.0053 0.0085 0.0825 0.1097 0.0011 0.1550 0.1672 0.1438 0.1400 0.0788
M.V. Go´ mez et al. / Forensic Science International 137 (2003) 235–237
236
Allele CSF1PO D13S317 D5S818 D7S820 TH01
TPOX VWA
19 19.2 20 20.2 21 22 22.2 23 23.2 24 24.2 25 25.2 26 26.2 27 28 29 30 30.2 31 31.2 32 32.2 33 33.2 34 34.2 35 35.2 36 38 N He Ho PD CE PIC P
FGA
D3S1358 D8S1179 D21S11 D18S51
0.0576 0.0621 0.0060 0.0016 0.0068 0.0864 0.0005 0.0008 0.0016 0.1245 0.1360 0.0026 0.1380 0.0013 0.1691
0.0522 0.0304 0.0117 0.0069 0.0037 0.0032 0.0026
0.1380 0.0003 0.0895
0.0016 0.0011 0.0249 0.1224 0.1875 0.2712 0.0260 0.0720 0.0752 0.0207 0.1361 0.0016 0.0456 0.0026 0.0026 0.0042 0.0005 0.0011 0.0005
0.0222 0.0076 0.0026
0.0005 0.0005
1459 0.7323 0.7176 0.8836 0.4560 0.6865 0.3419
1919 0.8098 0.8129 0.9383 0.6232 0.7844 0.2888
1919 0.7303 0.7415 0.8851 0.4954 0.6899 0.7447
1918 0.7892 0.7857 0.9241 0.5728 0.7579 0.1703
1460 0.7587 0.7438 0.9041 0.4993 0.7212 0.3313
1459 0.6806 0.6703 0.8500 0.3839 0.6346 0.3778
1920 0.7735 0.7688 0.9150 0.5424 0.7406 0.3691
1916 0.8795 0.8753 0.9731 0.7452 0.8793 0.8241
1919 0.7466 0.7436 0.8959 0.4989 0.7076 0.3416
945 0.7845 0.7640 0.9245 0.5341 0.7546 0.3219
944 0.8436 0.8390 0.9566 0.6733 0.8258 0.5419
939 0.8792 0.8754 0.9722 0.7455 0.8664 0.3431
N: sample size; Ho: observed heterozygosity; He: expected heterozygosity; PD: power of discrimination; CE: a priori chance of exclusion; PIC: polymorphic information content; P: Hardy–Weinberg equilibrium, Fisher’s exact test based on 3200 shufflings.
References [1] A. Tereba, Tools for Analysis of Population Statistics. Profiles in DNA, vol. 2, Promega Corporation, 1999, pp. 14–16. [2] P.O. Lewis, D. Zaykin, Genetic Data Analysis, version 1.0 (d16c), Computer program for the analysis of allelic data, Free program distributed by the authors over the internet from the GDA Home Page at http://www.lewis.eeb.uconn.edu/ lewishome/software.html, 2001. [3] J.J. Yunis, O. Garcia, I. Uriarte, E. Yunis, Population data on six short tandem repeat loci in a sample of
Caucasian-Mestizos from Colombia, Int. J. Legal Med. 113 (2000) 175–178. [4] J.J. Yunis, O. Garcia, I. Uriarte, E.J. Yunis, Population data on D16S539, D7S820, D13S317, LPL, F13B and D1S80 loci in a sample of Caucasian-Mestizos from Colombia, Forensic Sci. Int. 115 (2001) 117–118. [5] C.I. Vargas, A. Castillo, A.M. Gil, A.L. Pico, O. Garcı´a, Profiler data for a Colombian population (Department of North Santander), Forensic Sci. Int. 124 (2001) 219–220. [6] C.I. Vargas, A. Castillo, A.M. Gil, A.L. Pico, O. Garcı´a, Allele frequencies for the AmpFlSTR Profiler loci in a
M.V. Go´ mez et al. / Forensic Science International 137 (2003) 235–237
[7]
[8]
[9]
[10]
Colombian population (Department of Boyaca), J. Forensic Sci. 47 (2002) 406–407. C.I. Vargas, A. Castillo, A.M. Gil, A.L. Pico, O. Garcı´a, Population genetic data for 13 STR loci in a northeast Colombian (Department of Santander) population, Prog. Forensic Genet. 9 (2003) 197–200. J.J. Yunis, O. Garcia, S. Moreno, I. Uriarte, E.J. Yunis, Population data on D7S820, FGA, D1S533 and D9S304 in a sample of Caucasian-Mestizos from Colombia, Prog. Forensic Genet. 9 (2003) 201–206. J.J. Yunis, O. Garcia, S. Moreno, C. Pineda, C. Rodrı´guez, I. Uriarte, E.J. 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-Mestizos from Colombia, Prog. Forensic Genet. 9 (2003) 207–212. M.A. Acosta, M. Brion, M.V. Lareu, A. Carracedo, Genetic data on eight STRs (D5S818, D7S820, F13B, LPL, TH01,
[11]
[12]
[13]
[14]
237
TPOX, VWA31, CSF1PO) from a Colombian population, Forensic Sci. Int. 129 (2002) 216–218. M.L. Bravo, M.A. Moreno, J.J. Builes, A. Salas, M.V. Lareu, A. Carracedo, Autosomal STR genetic variation in Negroid Choco´ and Bogota´ populations, Int. J. Legal Med. 115 (2001) 102–104. J.J. Yunis, A. Baena, O. Garcia, I. Uriarte, E.J. Yunis, Population data of F13A01, FES/FPS, VWA, CSF1PO, TPOX and TH01 short tandem repeat loci in a sample of African descent individuals of Colombia, Forensic Sci. Int. 117 (2001) 235–236. J.J. Yunis, A. Baena, O. Garcia, I. Uriarte, E.J. Yunis, Population frequencies for CSF1PO, TPOX, TH01, F13A01, FES/FPS and VWA in seven Amerindian populations from Colombia, in: Proceedings of the 10th International Symposium on Human Identification, Lake Buena Vista, FL, USA, 1999. P. Lincoln, A. Carracedo, Publication of population data of human polymorphisms, Forensic Sci. Int. 110 (2000) 3–5.
Announcement of population data
Genetic variation for 12 STRs loci in a Colombian population (Department of Valle del Cauca) Marı´a Victoria Go´meza,*, Marı´a Edith Reyesa, Heiber Ca´rdenasb, Oscar Garcı´ac a
Laboratorio de Inmunologı´a e Inmunogene´tica, Hospital Universitario del Valle, Cali, Colombia b Departamento de Biologı´a, Universidad del Valle, Cali, Colombia c Area de Laboratorio Ertzaintza, Avda. Montevideo 3, E-48002 Bilbao, Spain Received 12 February 2003; received in revised form 30 June 2003; accepted 2 July 2003
Population: Department of Valle del Cauca, Colombia. Number: 939–1920. Extraction: Genomic DNA was extracted from 1 ml of EDTA anticoagulated peripheral blood using the salting out methodology. PCR: After DNA quantitation by spectrophotometry, 1 or 2 ng of DNA were amplified using the commercial kits AmpFlSTR Profiler, AmpFlSTR Profiler Plus, AmpFlSTR COfiler (PE Applied Biosystems) and PowerPlex 16 (Promega Corporation) following the manufacturer’s instructions. Typing: ABI310 and reference sequenced ladders (PE Applied Biosystems and Promega Corporation). Allele CSF1PO D13S317 D5S818 D7S820 TH01 5 6 6.1 7 8 9 9.3 10 11 12 13 13.2 14 15 16 17 18 18.2
0.0044 0.0161 0.0144 0.0233
0.0005 0.0740 0.1321
0.0255 0.0107 0.0659
0.0112 0.1361 0.0954
0.2337 0.2762 0.3636 0.0613
0.0597 0.2277 0.2955 0.1428
0.0563 0.3986 0.2858 0.1446
0.2823 0.2779 0.1593 0.0302
0.0096 0.0017
0.0662 0.0016
0.0115 0.0010
0.0031
0.0014 0.3541 0.0014 0.2586 0.0928 0.1291 0.1548 0.0079
Quality control: Proficiency testing of the GEP-ISFG WG. Analysis of data: PowerStats [1] and GDA [2]. Access to the data: [email protected]. Other remarks: A comparison of allele frequencies in the population under study has been performed with other studies from Colombian Caucasian individuals [3–11], with African descent individuals of Colombia [11,12] and with Amerindian populations of Colombia [13]. These comparisons revealed statistically significant differences (data not shown). This paper follows the guidelines for publication of population data requested by the journal [14]. TPOX VWA
FGA
D3S1358 D8S1179 D21S11 D18S51
0.0127 0.0038 0.4736 0.0905 0.0535 0.2769 0.0005 0.0860 0.0003 0.0031 0.0026 0.0576 0.1260 0.3440 0.2492 0.1539
* Corresponding author. E-mail address: [email protected] (M.V. Go´mez).
0379-0738/$ – see front matter # 2003 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/S0379-0738(03)00297-4
0.0005 0.0010 0.0031 0.0091 0.0026
0.0003
0.0053 0.0106
0.0016 0.0050
0.0487 0.0751 0.1021 0.3286
0.1019 0.3726 0.2720 0.1470 0.0933
0.2656 0.1349 0.0249 0.0037 0.0005
0.0053 0.0085 0.0825 0.1097 0.0011 0.1550 0.1672 0.1438 0.1400 0.0788
M.V. Go´ mez et al. / Forensic Science International 137 (2003) 235–237
236
Allele CSF1PO D13S317 D5S818 D7S820 TH01
TPOX VWA
19 19.2 20 20.2 21 22 22.2 23 23.2 24 24.2 25 25.2 26 26.2 27 28 29 30 30.2 31 31.2 32 32.2 33 33.2 34 34.2 35 35.2 36 38 N He Ho PD CE PIC P
FGA
D3S1358 D8S1179 D21S11 D18S51
0.0576 0.0621 0.0060 0.0016 0.0068 0.0864 0.0005 0.0008 0.0016 0.1245 0.1360 0.0026 0.1380 0.0013 0.1691
0.0522 0.0304 0.0117 0.0069 0.0037 0.0032 0.0026
0.1380 0.0003 0.0895
0.0016 0.0011 0.0249 0.1224 0.1875 0.2712 0.0260 0.0720 0.0752 0.0207 0.1361 0.0016 0.0456 0.0026 0.0026 0.0042 0.0005 0.0011 0.0005
0.0222 0.0076 0.0026
0.0005 0.0005
1459 0.7323 0.7176 0.8836 0.4560 0.6865 0.3419
1919 0.8098 0.8129 0.9383 0.6232 0.7844 0.2888
1919 0.7303 0.7415 0.8851 0.4954 0.6899 0.7447
1918 0.7892 0.7857 0.9241 0.5728 0.7579 0.1703
1460 0.7587 0.7438 0.9041 0.4993 0.7212 0.3313
1459 0.6806 0.6703 0.8500 0.3839 0.6346 0.3778
1920 0.7735 0.7688 0.9150 0.5424 0.7406 0.3691
1916 0.8795 0.8753 0.9731 0.7452 0.8793 0.8241
1919 0.7466 0.7436 0.8959 0.4989 0.7076 0.3416
945 0.7845 0.7640 0.9245 0.5341 0.7546 0.3219
944 0.8436 0.8390 0.9566 0.6733 0.8258 0.5419
939 0.8792 0.8754 0.9722 0.7455 0.8664 0.3431
N: sample size; Ho: observed heterozygosity; He: expected heterozygosity; PD: power of discrimination; CE: a priori chance of exclusion; PIC: polymorphic information content; P: Hardy–Weinberg equilibrium, Fisher’s exact test based on 3200 shufflings.
References [1] A. Tereba, Tools for Analysis of Population Statistics. Profiles in DNA, vol. 2, Promega Corporation, 1999, pp. 14–16. [2] P.O. Lewis, D. Zaykin, Genetic Data Analysis, version 1.0 (d16c), Computer program for the analysis of allelic data, Free program distributed by the authors over the internet from the GDA Home Page at http://www.lewis.eeb.uconn.edu/ lewishome/software.html, 2001. [3] J.J. Yunis, O. Garcia, I. Uriarte, E. Yunis, Population data on six short tandem repeat loci in a sample of
Caucasian-Mestizos from Colombia, Int. J. Legal Med. 113 (2000) 175–178. [4] J.J. Yunis, O. Garcia, I. Uriarte, E.J. Yunis, Population data on D16S539, D7S820, D13S317, LPL, F13B and D1S80 loci in a sample of Caucasian-Mestizos from Colombia, Forensic Sci. Int. 115 (2001) 117–118. [5] C.I. Vargas, A. Castillo, A.M. Gil, A.L. Pico, O. Garcı´a, Profiler data for a Colombian population (Department of North Santander), Forensic Sci. Int. 124 (2001) 219–220. [6] C.I. Vargas, A. Castillo, A.M. Gil, A.L. Pico, O. Garcı´a, Allele frequencies for the AmpFlSTR Profiler loci in a
M.V. Go´ mez et al. / Forensic Science International 137 (2003) 235–237
[7]
[8]
[9]
[10]
Colombian population (Department of Boyaca), J. Forensic Sci. 47 (2002) 406–407. C.I. Vargas, A. Castillo, A.M. Gil, A.L. Pico, O. Garcı´a, Population genetic data for 13 STR loci in a northeast Colombian (Department of Santander) population, Prog. Forensic Genet. 9 (2003) 197–200. J.J. Yunis, O. Garcia, S. Moreno, I. Uriarte, E.J. Yunis, Population data on D7S820, FGA, D1S533 and D9S304 in a sample of Caucasian-Mestizos from Colombia, Prog. Forensic Genet. 9 (2003) 201–206. J.J. Yunis, O. Garcia, S. Moreno, C. Pineda, C. Rodrı´guez, I. Uriarte, E.J. 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-Mestizos from Colombia, Prog. Forensic Genet. 9 (2003) 207–212. M.A. Acosta, M. Brion, M.V. Lareu, A. Carracedo, Genetic data on eight STRs (D5S818, D7S820, F13B, LPL, TH01,
[11]
[12]
[13]
[14]
237
TPOX, VWA31, CSF1PO) from a Colombian population, Forensic Sci. Int. 129 (2002) 216–218. M.L. Bravo, M.A. Moreno, J.J. Builes, A. Salas, M.V. Lareu, A. Carracedo, Autosomal STR genetic variation in Negroid Choco´ and Bogota´ populations, Int. J. Legal Med. 115 (2001) 102–104. J.J. Yunis, A. Baena, O. Garcia, I. Uriarte, E.J. Yunis, Population data of F13A01, FES/FPS, VWA, CSF1PO, TPOX and TH01 short tandem repeat loci in a sample of African descent individuals of Colombia, Forensic Sci. Int. 117 (2001) 235–236. J.J. Yunis, A. Baena, O. Garcia, I. Uriarte, E.J. Yunis, Population frequencies for CSF1PO, TPOX, TH01, F13A01, FES/FPS and VWA in seven Amerindian populations from Colombia, in: Proceedings of the 10th International Symposium on Human Identification, Lake Buena Vista, FL, USA, 1999. P. Lincoln, A. Carracedo, Publication of population data of human polymorphisms, Forensic Sci. Int. 110 (2000) 3–5.