Forensic Science International 137 (2003) 67–73

Analysis of the CODIS autosomal STR loci in four

main Colombian regions
Manuel Paredesa,*, Aida Galindoa, Margarita Bernala, Sandra Avilaa,
Diana Andradea, Carlos Vergaraa, Magner Rincóna, Rosa Elena Romeroa,
Mayda Navarretea, Martha Cárdenasa, Janeth Ortegaa, Dayana Suareza,
Adriana Cifuentesa, Antonio Salasb, Ángel Carracedob
a
Laboratorio de ADN, Instituto Nacional de Medicina Legal y Ciencias Forenses de Colombia, Calle 7-A Nro. 12-61 piso 3, Bogotá, Colombia
b
Unidad de Genética, Instituto de Medicina Legal, Universidade de Santiago de Compostela,
Santiago de Compostela, San Fsco 15701, Galicia, Spain
Received 30 June 2003; accepted 3 July 2003

Abstract

Genotype polymorphism studies at the 13 loci STRs included in the combined DNA index system [CODIS and PCR-based
short tandem repeat loci, in: Proceedings of the Second European Symposium on Human Identification, Promega Corporation,
Madison, WI, 1998, pp. 73–88; J. Forensic Sci. 46 (2001) 453] (CODIS: D3S1358, HUMvWA31, HUMFGA, D8S1179
D21S11, D18S51, D5S818, D13S317, D7S820, HUMTH01, HUMTPOX, HUMCSF1PO and D16S539) were carried out in a
sample of 1429 unrelated Colombian individuals belonging to 25 different departments. As many other countries in Latino-
America, Colombia shows an important admixture component, basically integrated by Amerindians, European-descendants and
African-descendants. Due to the fact that only partial population analyses have been carried out in the country, the main aim of
the present analysis is to establish a database of forensic interest based on the widely used CODIS systems covering the main
Colombian regions.
# 2003 Published by Elsevier Ireland Ltd.

Keywords: Short tandem repeat; STRs; Microsatellite; Population data; Colombia

General information on the sampled Colombian
populations: Although other regional studies have been
carried out in Colombia [1–8], in this work we have
analyzed a representative sample scattered through Colom-
bia representing the predominant population groups of the
country. Each main region in Colombia seems to show
different population contributions and degrees of admix-
ture (for instance, the predominant group in the Chocó
prefecture is of African ancestry) and the definition of
specific reference databases is necessary for forensic pur-
poses.
We have analyzed a total of 1429 unrelated individuals
belonging to 25 out of the 32 departments of Colombia
*
Corresponding author.
E-mail address: mparedes@rocketmail.com (M. Paredes).
(at present, 96% of the Colombians live in these regions [9]).
Our samples do not include the Colombian Amerindian
communities, which represent about 1.7% of the present
national population.
It could be verified that more than 80% of the individuals
sampled in the present study were born in the same locality
were they were sampled. The parents of 63% of them were
also born in the same geographic region (in same isolated
cases, the participants in this study were born in neighboring
towns to the area sampled). This demography is compatible
with a model of fragmented settlement and later unification,
which specifically characterized the Colombian population
[10–12].
Sample collection and DNA extraction: Voluntary
informed consent was obtained for each individual case.
Bloodstain samples were collected in FTA (Gibco BRL),

0379-0738/$ – see front matter # 2003 Published by Elsevier Ireland Ltd.

doi:10.1016/S0379-0738(03)00271-8
68 M. Paredes et al. / Forensic Science International 137 (2003) 67–73
and DNA was extracted by using the protocol recommended
by the company.
PCR and typing: The PCR strategy, primer sequences,
and cycling conditions were as recommended in the Profiler
Plus and Cofiler Kits (Applied Biosystems, Foster City, CA).
PCR amplifications were performed in a thermocycler MJ
Research PTC-100. Separation and detection of the ampli-
fied products were carried out in an automatic multicapillary
sequencer ABI 3100 (AB) using performance optimized
polymer (POP 4) and capillaries of 47 cm. Genescan Col-
lection, Genescan Analysis and Genotyper version 3.1. soft-
ware was used for typing analysis. Typing was made by
comparison with the sequenced allelic ladders provided in
the kits. In order to avoid mistakes in each of the different
analytical processes (extraction, PCR, fragment analysis,
etc.) as well as the edition of the results, an internal quality
control was carried by independent experts.
Analysis of data: Different parameters of forensic and
population interest were determined. Heterozygosity values
(observed and expected) and chance of exclusion (CE) were
estimated as described by Nei [13]. Independence of the loci
and exact test for Hardy–Weinberg equilibrium was checked
as implemented in the genetic data analysis (GDA) software
(P.O. Lewis and D. Saykin, GDA software for the analysis of
discrete genetic data, computer program distributed by the
authors and available at http://chee.unm.edu/gda/ [14,15]),
and ARLEQUIN versions 1.1 and 2.0 [16]. Power of
Fig. 1. Map showing the main Colombian regions analyzed in the present work: (1) North Colombian Pacific coast, (2) Caribbean, (3)
southwest Andean region, (4) Central Andean region (including Orinoquian and Amazonian regions).
discrimination (PD) [17] and probability of paternity a priori
of exclusion (PE) were also computed.
Quality control: Proficiency testing of the GEP-ISFG
WG (http://www.gep-isfg.org).
Results and discussion: According to historical docu-
mentation, the genotypic data was grouped in 4 main
population groups: (a) African-descendants population inha-
biting the North Colombian Pacific coast and the Caribbean
island of San Andrés, (b) ‘Mestizo’ populations from the
Colombian mountain range of Los Andes and populations
settled in the Amazonian region and Oriental flats (Orino-
quian region), (c) populations from the Southwest Andean
region (with an important Amerindian component), and (d)
African-descendant populations inhabiting the Colombian
Caribbean coast. The used of clustering methods (UPGMA)
showed a complete correlation of the genetic data with the
historical classification (data not shown) (Fig. 1).
Allele frequencies as well as observed and expected
heterozygosity for these four groups are shown in
Tables 1–4. No deviations from Hardy–Weinberg equili-
brium were observed in almost all the systems, with the
exception of locus D21S11 in the southwest Andine popula-
tion with a significant P value (P ¼ 0:0268). However, with
the Bonferroni correction [18], we did not detect significant
deviations from the Hardy–Weinberg equilibrium.
Exact tests used to examine independence of the loci
showed that there is no evidence of association between
 M. Paredes et al. / Forensic Science International 137 (2003) 67–73 69

Table 1
Allele frequencies and statistical parameter for 13 STRs loci in a population (N ¼ 243) from the Caribbean coasta
Allele D3S1358 vWA31 FGA D8S1179 D21S11 D18S51 D5S818 D13S317 D7S820 D16S539 THO1 TPOX CSF1PO

5 – – – – – – – – – 0.002 0.002 – –
6 – – – – – – – – – – 0.285 0.031 –
7 – – – – – – 0.033 – 0.008 – 0.258 0.006 0.011
8 – – – 0.002 – – 0.023 0.076 0.129 0.025 0.124 0.404 0.013
9 – – – 0.008 – – 0.041 0.109 0.085 0.177 0.159 0.097 0.019
9.3 – – – – – – – – – – 0.161 – –
10 – – – 0.056 – 0.013 0.039 0.045 0.283 0.148 0.010 0.050 0.256
11 – 0.002 – 0.088 – 0.013 0.360 0.263 0.304 0.292 – 0.317 0.273
12 0.002 – 0.169 – 0.087 0.300 0.323 0.171 0.210 – 0.091 0.355
13 0.006 0.004 – 0.265 – 0.118 0.185 0.128 0.019 0.134 – 0.004 0.065
14 0.064 0.074 – 0.233 – 0.150 0.016 0.049 – 0.012 – – 0.008
14.2 – – – – – – – – – – – – –
15 0.374 0.152 – 0.140 – 0.161 – 0.006 – – – – –
17 0.174 0.228 – 0.010 – 0.139 – – – – – – –
18 0.089 0.169 0.008 – – 0.087 – – – – – – –
18.2 – – 0.002 – – – – – – – – – –
19 0.006 0.062 0.080 – – 0.047 – – – – – – –
19.2 – – 0.002 – – – – – – – – – –
20 – 0.014 0.084 – – 0.027 – – – – – – –
20.2 – – – – – – – – – – – – –
21 – 0.002 0.130 – – 0.020 – – – – – – –
21.2 – – 0.002 – – – – – – – – – –
22 – – 0.142 – – 0.007 – – – – – – –
22.2 – – – – – – – – – – – – –
23 – – 0.142 – – 0.004 – – – – – – –
24 – – 0.134 – – 0.007 – – – – – – –
24.2 – – – – 0.004 – – – – – – – –
25 – – 0.150 – – – – – – – – – –
25.2 – – – – – – – – – – – – –
26 – – 0.086 – 0.002 – – – – – – – –
26.2 – – – – – – – – – – – – –
27 – – 0.029 – 0.010 – – – – – – – –
28 – – 0.004 – 0.134 – – – – – – – –
29 – – 0.004 – 0.241 – – – – – – – –
30 – – – – 0.253 – – – – – – – –
30.2 – – – – 0.033 – – – – – – – –
31 – – – – 0.076 – – – – – – – –
31.2 – – – – 0.056 – – – – – – – –
32 – – – – 0.004 – – – – – – – –
32.2 – – – – 0.136 – – – – – – – –
33 – – – – 0.004 – – – – – – – –
33.1 – – – – 0.002 – – – – – – – –
33.2 – – – – 0.033 – – – – – – – –
34 – – – – 0.002 – – – – – – – –
34.2 – – – – – – – – – – – – –
35 – – – – 0.006 – – – – – – – –
36 – – – – 0.004 – – – – – – – –
CE 0.507 0.611 0.756 0.636 0.668 0.768 0.514 0.595 0.562 0.603 0.577 0.485 0.487
PD 0.883 0.933 0.969 0.939 0.946 0.971 0.893 0.926 0.909 0.928 0.925 0.878 0.872
Hobs 0.760 0.790 0.901 0.831 0.815 0.870 0.757 0.765 0.750 0.790 0.686 0.711 0.738
Hexp 0.738 0.803 0.882 0.817 0.832 0.887 0.742 0.789 0.775 0.800 0.787 0.715 0.728
P exact test for 0.147 0.353 0.416 0.781 0.872 0.178 0.607 0.333 0.434 0.653 0.058 0.679 0.676
Hardy–Weinberg
equilibrium
(runs: 3000)
Number of 484 486 486 486 486 447 486 486 480 486 484 485 476
chromosomes
a
CE: change of exclusion; PD: power of discrimination; Hobs: observed heterozygosity; Hexp: expected heterozygosity.
70 M. Paredes et al. / Forensic Science International 137 (2003) 67–73

Table 2
Allele frequencies and statistical parameter for 13 STRs loci in populations (N ¼ 846) from Andean regions and Amazonian and Orinoquian
areasa
Allele D3S1358 vWA31 FGA D8S1179 D21S11 D18S51 D5S818 D13S317 D7S820 D16S539 THO1 TPOX CSF1PO

5 – – – – – – – – 0.001 0.001 – – –
6 – – – – – – – – 0.001 – 0.374 0.003 0.001
7 – – – – – – 0.029 – 0.022 – 0.246 0.002 0.006
8 – – – 0.006 – – 0.008 0.083 0.107 0.011 0.076 0.505 0.009
9 – – – 0.012 – – 0.078 0.151 0.088 0.159 0.117 0.072 0.021
9.3 – – – – – – – – – – 0.179 – –
10 – – – 0.060 – 0.011 0.073 0.066 0.281 0.159 0.009 0.046 0.228
11 – – – 0.079 – 0.009 0.418 0.219 0.285 0.266 – 0.263 0.297
12 0.001 – – 0.122 – 0.126 0.256 0.295 0.174 0.260 – 0.105 0.364
13 0.003 0.002 – 0.333 – 0.121 0.132 0.124 0.038 0.119 – 0.003 0.066
14 0.101 0.047 – 0.251 – 0.164 0.007 0.059 0.003 0.024 – 0.001 0.009
14.2 – – – – – 0.001 – 0.002 – – – – –
15 0.372 0.089 – 0.110 – 0.136 – – – 0.001 – – 0.001
16 0.268 0.358 – 0.027 – 0.134 0.001 – – – – – –
17 0.139 0.280 0.002 0.001 – 0.149 – – – – – – –
18 0.105 0.165 0.012 – – 0.062 – – – – – – –
18.2 – – – – – – – – – – – –
19 0.011 0.047 0.066 – – 0.039 – – – – – – –
19.2 – – 0.001 – – – – – – – – – –
20 0.001 0.010 0.082 – – 0.027 – – – – – – –
20.2 – – 0.001 – – – – – – – – – –
21 – 0.002 0.118 – – 0.013 – – – – – – –
21.2 – – 0.002 – – – – – – – – – –
22 – – 0.135 – – 0.004 – – – – – – –
22.2 – – 0.004 – – – – – – – – – –
23 – – 0.148 – – 0.003 – – – – – – –
24 – – 0.169 – – 0.003 – – – – – – –
24.2 – – – – – – – – – – – – –
25 – – 0.149 – – – – – – – – – –
25.2 – – 0.001 – – – – – – – – – –
26 – – 0.076 – 0.001 – – – – – – – –
26.2 – – – – 0.002 – – – – – – – –
27 – – 0.024 – 0.015 – – – – – – – –
28 – – 0.010 – 0.098 – – – – – – – –
29 – – 0.002 – 0.207 – – – – – – – –
30 – – – – 0.293 – – – – – – – –
30.2 – – – – 0.031 – – – – – – – –
31 – – – – 0.067 – – – – – – – –
31.2 – – – – 0.089 – – – – – – – –
32 – – – – 0.021 – – – – – – – –
32.2 – – – – 0.127 – – – – – – – –
33 – – – – 0.002 – – – – – – – –
33.1 – – – – – – – – – – – – –
33.2 – – – – 0.042 – – – – – – – –
34 – – – – 0.001 – – – – – – – –
34.2 – – – – 0.004 – – – – – – – –
35 – – – – 0.002 – – – – – – – –
36 – – – – – – – – – – – – –
CE 0.532 0.533 0.756 0.599 0.672 0.753 0.508 0.629 0.592 0.594 0.521 0.413 0.488
PD 0.904 0.892 0.973 0.928 0.952 0.972 0.892 0.934 0.928 0.927 0.899 0.830 0.879
Hobs 0.706 0.752 0.841 0.798 0.832 0.841 0.715 0.816 0.761 0.788 0.725 0.647 0.728
Hexp 0.752 0.750 0.879 0.789 0.830 0.878 0.727 0.809 0.790 0.794 0.746 0.652 0.730
P exact test for 0.051 0.249 0.346 0.719 0.333 0.038 0.113 0.083 0.490 0.812 0.464 0.151 0.865
Hardy–Weinberg
equilibrium
(runs: 3000)
Number of 1690 1692 1679 1692 1689 1565 1691 1691 1668 1674 1687 1688 1609
chromosomes
a
CE: change of exclusion; PD: power of discrimination; Hobs: observed heterozygosity; Hexp: expected heterozygosity.
 M. Paredes et al. / Forensic Science International 137 (2003) 67–73 71

Table 3
Allele frequencies and statistical parameter for 13 STRs loci in a population (N ¼ 217) from the South Andean Occidental regiona
Allele D3S1358 vWA31 FGA D8S1179 D21S11 D18S51 D5S818 D13S317 D7S820 D16S539 THO1 TPOX CSF1PO

5 – – – – – – – – – – – – –
6 – – – – – – – – – – 0.406 0.009 –
7 – – – – – – 0.032 – 0.012 – 0.325 0.002 0.007
8 – – – 0.009 – – 0.014 0.067 0.102 0.007 0.067 0.503 0.005
9 – – – 0.005 – – 0.111 0.187 0.065 0.164 0.065 0.058 0.021
9.3 – – – – – – – – – – 0.127 – –
10 – – – 0.053 – 0.012 0.048 0.051 0.271 0.189 0.012 0.030 0.299
11 – 0.002 – 0.102 – 0.007 0.403 0.196 0.282 0.267 – 0.293 0.257
12 – – – 0.171 – 0.076 0.272 0.274 0.231 0.260 – 0.100 0.336
13 – 0.002 – 0.282 – 0.110 0.108 0.150 0.035 0.099 – 0.005 0.063
14 0.065 0.030 – 0.264 – 0.238 0.012 0.076 0.002 0.014 – – 0.009
14.2 – – – – – – – – – – – – –
15 0.458 0.081 – 0.090 – 0.147 – – – – – – 0.005
16 0.278 0.387 – 0.023 – 0.142 – – – – – – –
17 0.107 0.274 0.009 – – 0.150 – – – – – – –
18 0.089 0.168 – – – 0.064 – – – – – – –
18.2 – – 0.002 – – – – – – – – – –
19 0.002 0.039 0.069 – – 0.017 – – – – – – –
19.2 – – – – – – – – – – – – –
20 – 0.016 0.056 – – 0.025 – – – – – – –
20.2 – – – – – – – – – – – – –
21 – – 0.088 – – 0.007 – – – – – – –
21.2 – – – – – – – – – – – – –
22 – – 0.141 – – 0.005 – – – – – – –
22.2 – – 0.002 – – – – – – – – – –
23 – – 0.164 – – – – – – – – – –
24 – – 0.187 – – – – – – – – – –
24.2 – – 0.002 – – – – – – – – – –
25 – – 0.120 – – – – – – – – – –
25.2 – – – – – – – – – – – – –
26 – – 0.109 – – – – – – – – – –
26.2 – – – – – – – – – – – – –
27 – – 0.039 – 0.016 – – – – – – – –
28 – – 0.012 – 0.076 – – – – – – – –
29 – – – – 0.173 – – – – – – – –
30 – – – – 0.260 – – – – – – – –
30.2 – – – – 0.023 – – – – – – – –
31 – – – – 0.060 – – – – – – – –
31.2 – – – – 0.111 – – – – – – – –
32 – – – – – – – – – – – – –
32.2 – – – – 0.194 – – – – – – – –
33 – – – – 0.002 – – – – – – – –
33.1 – – – – – – – – – – – – –
33.2 – – – – 0.074 – – – – – – – –
34 – – – – 0.005 – – – – – – – –
34.2 – – – – – – – – – – – – –
35 – – – – 0.007 – – – – – – – –
36 – – – – – – – – – – – – –
CE 0.452 0.514 0.747 0.609 0.678 0.714 0.518 0.637 0.567 0.582 0.470 0.404 0.482
PD 0.854 0.879 0.968 0.933 0.948 0.960 0.896 0.938 0.911 0.912 0.872 0.823 0.862
Hobs 0.678 0.783 0.861 0.792 0.811 0.818 0.705 0.797 0.801 0.825 0.691 0.648 0.745
Hexp 0.691 0.739 0.876 0.801 0.839 0.857 0.738 0.818 0.779 0.790 0.707 0.646 0.728
P exact test for 0.645 0.816 0.342 0.920 0.027 0.113 0.855 0.116 0.154 0.062 0.394 0.436 0.235
Hardy–Weinberg
equilibrium
(runs: 3000)
Number of 428 434 433 432 434 408 434 434 433 434 434 433 433
chromosomes
a
CE: change of exclusion; PD: power of discrimination; Hobs: observed heterozygosity; Hexp: expected heterozygosity.
72 M. Paredes et al. / Forensic Science International 137 (2003) 67–73

Table 4
Allele frequencies and statistical parameter for 13 STRs loci in a Colombian African-descendant population from the Chocó region in the
North Colombian Pacific coast and the Caribbean Island of San Andrés (N ¼ 123)a
Allele D3S1358 vWA31 FGA D8S1179 D21S11 D18S51 D5S818 D13S317 D7S820 D16S539 THO1 TPOX CSF1PO

5 – – – – – – – – – – 0.004 – –
6 – – – – – – – – – – 0.199 0.069 –
7 – – – – – – 0.020 – – – 0.407 0.016 0.042
8 – – – 0.004 – – 0.041 0.033 0.205 0.008 0.171 0.309 0.008
9 – – – 0.004 – – 0.037 0.049 0.115 0.232 0.114 0.195 0.050
9.3 – – – – – – – – – – 0.106 – –
10 – – – 0.012 – – 0.069 0.049 0.311 0.146 – 0.073 0.315
11 – 0.004 – 0.049 – 0.004 0.256 0.293 0.230 0.264 – 0.297 0.264
12 0.004 – – 0.142 – 0.068 0.354 0.382 0.111 0.191 – 0.041 0.242
13 – 0.028 – 0.260 – 0.077 0.211 0.154 0.020 0.134 – – 0.062
13.2 – – – – – 0.004 – – – – – – –
14 0.069 0.061 – 0.313 – 0.090 0.012 0.041 0.008 0.024 – – 0.013
14.2 – – – – – 0.009 – – – – – – –
15 0.390 0.183 – 0.171 – 0.135 – – – – – – 0.004
16 0.305 0.309 0.004 0.041 – 0.135 – – – – – – –
17 0.167 0.183 0.004 0.004 – 0.149 – – – – – – –
18 0.053 0.154 0.004 – – 0.111 – – – – – – –
18.2 – – 0.017 – – – – – – – – – –
19 0.012 0.065 0.054 – – 0.081 – – – – – – –
19.2 – – 0.004 – – – – – – – – – –
20 – 0.012 0.063 – – 0.060 – – – – – – –
20.2 – – 0.004 – – – – – – – – – –
21 – – 0.165 – – 0.060 – – – – – – –
21.2 – – – – – – – – – – – – –
22 – – 0.130 – – 0.004 – – – – – – –
22.2 – – – – – – – – – – – – –
23 – – 0.210 – – 0.009 – – – – – – –
23.2 – – 0.004 – – – – – – – – – –
24 – – 0.145 – – 0.004 – – – – – – –
24.2 – – – – 0.004 – – – – – – – –
25 – – 0.117 – 0.004 – – – – – – – –
25.2 – – – – – – – – – – – – –
26 – – 0.050 – – – – – – – – – –
26.2 – – – – – – – – – – – – –
27 – – 0.008 – 0.037 – – – – – – – –
28 – – 0.008 – 0.280 – – – – – – – –
29 – – 0.008 – 0.134 – – – – – – – –
30 – – – – 0.175 – – – – – – – –
30.2 – – – – 0.045 – – – – – – – –
31 – – – – 0.065 – – – – – – – –
31.2 – – – – 0.041 – – – – – – – –
32 – – – – 0.028 – – – – – – – –
32.2 – – – – 0.110 – – – – – – – –
33 – – – – 0.016 – – – – – – – –
33.1 – – – – – – – – – – – – –
33.2 – – – – 0.024 – – – – – – – –
34 – – – – 0.004 – – – – – – – –
34.2 – – – – – – – – – – – – –
35 – – – – 0.016 – – – – – – – –
36 – – – – 0.016 – – – – – – – –
CE 0.485 0.620 0.741 0.574 0.711 0.793 0.536 0.517 0.577 0.601 0.524 0.549 0.549
PD 0.873 0.931 0.961 0.915 0.954 0.974 0.897 0.879 0.908 0.928 0.874 0.904 0.899
Hobs 0.740 0.837 0.867 0.821 0.886 0.906 0.789 0.740 0.844 0.756 0.667 0.772 0.782
Hexp 0.722 0.808 0.866 0.784 0.853 0.899 0.759 0.740 0.786 0.803 0.745 0.770 0.766
P exact test for 0.621 0.658 0.815 0.917 0.239 0.867 0.260 0.254 0.502 0.411 0.054 0.298 0.759
Hardy–Weinberg
equilibrium
(runs: 3000)
Number of 246 246 243 246 246 235 246 246 244 246 246 246 239
chromosomes
a
CE: change of exclusion; PD: power of discrimination; Hobs: observed heterozygosity; Hexp: expected heterozygosity.
 M. Paredes et al. / Forensic Science International 137 (2003) 67–73
them. Tables 1–4 summarized the values for other statistical
parameters of forensic interest. The values obtained for these
indices show the utility of this set of loci as a useful tool in
human identification studies. This paper follows the guide-
lines for publication of population data requested by the
journal [19].
Acknowledgements
We are grateful to A.R. Chakraborty for useful discussion
of the population model and the results, A.F. Zambrano for
revising the population model for the settlement of the
Colombian populations, and A. Castro from the Instituto
Colombiano de Bienestar Familiar for invaluable assistance
for sampling collection.
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