Int J Legal Med
DOI 10.1007/s00414-013-0858-z
ORIGINAL ARTICLE
Comparison of the genetic background of different
Colombian populations using the SNPforID 52plex
identification panel
Adriana Ibarra & Ana Freire-Aradas &
Martha Martínez & Manuel Fondevila & German Burgos &
Mauricio Camacho & Henry Ostos & Zuleyma Suarez &
Angel Carracedo & Sidney Santos & Leonor Gusmão
Received: 10 March 2013 / Accepted: 28 March 2013
# Springer-Verlag Berlin Heidelberg 2013
Abstract Various strategies for analysing SNP markers
and genotyping have been published with the goal of
obtaining informative profiles from biological samples
that contain only small amounts of template and/or
degraded DNA. In this study, a multiplex assay of 52
autosomal single-nucleotide polymorphisms (SNPs) was
used to analyse 438 individuals from urban populations
from different regions of Colombia, as well as a sample
of 50 Native American individuals of the Pastos ethnic
group from Nariño. To determine if significant differ-
ences in these 52 SNPs exist between the distinct re-
gions of Colombia, genetic distance and admixture
analyses were performed based on the available data
for 17 different Colombian population groups and for
Electronic supplementary material The online version of this article
(doi:10.1007/s00414-013-0858-z) contains supplementary material,
which is available to authorized users.
A. Ibarra : M. Martínez
IdentiGEN-Genetic Identification Laboratory and Research Group
of Genetic Identification, School of Natural and Exact Sciences
(FCEN), University of Antioquia, Calle 67, 53-108, Bloque 7-321,
Medellin, Colombia
A. Freire-Aradas : M. Fondevila : A. Carracedo
Institute of Forensic Sciences, Genomic Medicine Group Luis
Concheiro, University of Santiago de Compostela, Galicia, Spain
G. Burgos
Molecular Genetics Laboratory, Cruz Vital. Ecuadorian Red Cross,
C11. Papallacta OE1-62 y Av de la Prensa,
Quito, Ecuador
M. Camacho
Institute of Legal Medicine and Forensic Sciences, Street 21 No.
22-67 B. La Esperanza, Northeast Regional,
Arauca, Colombia
population groups from Africa, Europe and America.
The results demonstrate significant differences between
the populations from the Southwest Andean, Central-
West Andean, Central-East Andean, Orinoquian and
northern Colombian Pacific Coast regions. Most of the
regions exhibited a European and Native American ad-
mixture. One exception is the population from the re-
gion of Chocó (on the northern Pacific Coast), which
exhibits a high proportion of African admixture (54 %).
From the observed genetic backgrounds, it is possible to
conclude that a single reference database for the entire
country would not be suitable for forensic purposes.
The allele frequencies and the forensically relevant pa-
rameters were calculated for all of the markers in each
H. Ostos
Genomic Medicine Laboratory, Health Faculty, Surcolombiana
University, Street 9 No. 14-03,
Neiva, Huila, Colombia
Z. Suarez
Clinical Laboratory Olga Zuleima Suárez Molina, Av. 0 No. 11-
161 Consultorio 103 Edificio Negomón,
Cúcuta, Colombia
S. Santos : L. Gusmão
Medical and Human Genetics Laboratory, Federal University of
Pará (UFPA), Av. Augusto Corrêa, 01, Caixa Postal 8615, 66075-
970, Belém, Pará, Brazil
L. Gusmão (*)
IPATIMUP-Institute of Molecular Pathology and Immunology,
University of Porto, R. Dr. Roberto Frias s/n,
4200-465, Porto, Portugal
e-mail: lgusmao@ipatimup.pt

Colombian region with significant values for the com-
bined matching probability (power of discrimination
≥0.99999999999999990) and the combined probability
of exclusion (≥0.9990) in trios that were obtained from
all of the population groups.
Keywords Identification . SNPs . Single-base extension .
Admixture . Population substructure . Degraded samples
Introduction
Currently, forensic genetics includes a large pool of poly-
morphic markers, from which short tandem repeats (STRs)
have become the markers of choice because of their high
discriminatory power. Although these markers are clearly
useful in forensics and possess the capacity to resolve both
identification and kinship cases, there are some complex
scenarios, often due to the presence of highly degraded
DNA, that remain difficult to solve. In these cases, it is
necessary to employ other genetic markers that are
characterised by shorter PCR products than those of the
STRs (e.g., less than 150 bp). These additional markers
include the single-nucleotide polymorphisms (SNPs) that
are widespread in the human genome and possess a low
mutation rate (10−8) [2], which are relevant features for
analysing samples that have been degraded and for deter-
mining complex relationships, respectively (e.g., [1–6]).
Useful information on these markers is available through
the International HapMap Project and dbSNP databases (at
NCBI; www.ncbi.nlm.nih.gov/).
One of the first reports on a set of SNPs that were
selected to be applied in the field of forensic genetics was
published by the SNPforID consortium; this set includes 52
SNPs that are highly polymorphic in populations worldwide
[7]. Several populations have already been characterised by
this assay (e.g., [8–11]), including various regional groups
from Colombia [12]. Like most American countries, Co-
lombia harbours populations that are highly admixed due to
the recent influx of Europeans and Africans, who have
merged with the existing native populations that have
inhabited this continent from more than 16,000 years (e.g.,
[13]). Therefore, the evaluation of the substructure of the
population is necessary before the introduction of new
markers into the forensic routine. The autosomal STRs that
are used in forensic genetics are not generally present at
significantly different allelic frequencies in most of the
urban admixed populations in Colombia (e.g., [14–16]),
which demonstrates a genetic proximity of the Colombian
populations to the Europeans, especially to the Spanish
populations, with the exception of the populations that are
of Native and African descent. The same scope has been
observed for the Y-chromosome haplotypes that are present
Int J Legal Med
in Colombian populations, which are predominantly of Eu-
ropean ancestry (e.g., [17]). Nevertheless, the population
substructure can be detected using maternally inherited
mtDNA markers because admixture was a gender-biassed
process that occurred differently in the distinct regions of
the territory of Colombia [18, 19]. The heterogeneity of the
country is enriched by a few small groups of a Native
American or an African ancestry, which have been more
or less isolated.
The aim of this study was to analyse the genetic diversity
in the 52 SNPs that were included in the SNPforID consor-
tium Human Identification 52 SNP multiplex in different
regions of Colombia and to infer the genetic structure of the
country’s population, which will impact the definition of a
forensic database for the studied markers. Therefore, we
have selected samples from six different Colombian
admixed populations, and a native group, that had not been
previously studied at this set of SNP markers. The calcula-
tion of the genetic distance in the population and the admix-
ture analyses were undertaken using data from this work, as
well as data from studies that had been previously published
by Porras et al. [12] for some populations located in the
central-west region of the country.
Materials and methods
Population samples, DNA extraction and quantification
A total of 265 samples were collected using blood and
buccal swabs from unrelated individuals in the following
Colombian regions: Arauca (n=73), Huila (n=82), Nariño
(n=78) and Norte de Santander (n=32); additionally, 50
samples were collected from a native group of Nariño, the
Pastos (see Supplementary Fig. S1).
Additionally, DNA samples were selected from routine
paternity cases at the IdentiGEN laboratory at the University
of Antioquia from unrelated individuals born and living in
the departments of Boyacá-Cundinamarca (n = 80) and
Chocó (n=93).
For comparison, data from other Colombian [12], as well
as African, European and Native American, population
samples (Supplementary Table S1) were extracted from the
SNPforID 52plex database (http://spsmart.cesga.es/
snpforid.php). Prior informed consent was obtained for all
of the participants for their cooperation in this study under
strictly confidential conditions.
The blood samples were collected in EDTA and were
deposited on Whatman™ FTA™ Gene Cards (GE
Healthcare Life Sciences, Buckinghamshire, UK). Genomic
DNA was extracted using a standard salting-out procedure
[20] or by resin Chelex 100 [21], and DNA concentrations
were determined using a Lambda Bio 10 spectrophotometer.
Int J Legal Med
Genotyping procedure
All of the samples were typed for the 52 SNPs in a single
PCR multiplex reaction, using the previously described
protocol from Sanchez et al. [7] for the 52plex de SNPforID,
after adapting the final volume of the single base extension
reaction to 6 μl.
Statistical analysis
For each marker, the allele frequencies, power of discrimi-
nation (PD) and a priori probability of exclusion (PE) were
calculated using Power Stats software v1.2 from Promega
[22].
The gene diversity values, the observed and expected
heterozygosities, the Hardy–Weinberg equilibrium test, the
pairwise genetic distances (FST) and the analysis of molec-
ular variance (AMOVA) were all calculated using Arlequin
software v3.5.1.3 [23].
The pairwise genetic distances were visualised in a two-
dimensional space using the multidimensional scaling
(MDS) method implemented in the software STATISTICA
v7.0. (http://www.statsoft.com/).
The population structure inferences were performed using
STRUCTURE v2.3.3 [24], with a burn-in length of 100,000,
followed by 100,000 Markov Chain Monte Carlo repetitions.
The initial runs were performed without any prior information
about the origin of the samples, using the “admixture model”
and considering either correlated or independent “allele fre-
quency models”; a minimum of three independent runs were
performed for each testing K value, ranging from K=1 to K=
5. In the second phase, when the reference samples were used
as training sets to test for “unknown” individuals or
populations, STRUCTURE analyses were carried out for K
=3 using the same parameters as before and selecting the “use
population information” option. Here, three independent runs
were performed only for the appropriate number of clusters, as
indicated by the initial analyses.
Results and discussion
The genotyping results that were obtained for the seven
analysed population groups are included in Supplementary
Table S2. To determine if the Colombian population is
genetically substructured at the 52 autosomal SNPs, com-
parative analyses were performed between the populations
from the various regions for which data were available (this
study and Porras et al. [12]; see Supplementary Fig. S1).
Colombian genetic structure was evaluated using two dif-
ferent approaches, specifically (a) for the pairwise FST, genetic
distances and the corresponding probability for non-
differentiation were calculated between samples representing
different populations, and (b) for the same samples, African,
European and Native American ancestral contributions were
estimated.
Analysis of genetic distances
Allele frequencies were used to calculate the pairwise ge-
netic distances (FST) between the populations for the studied
groups, other Colombian populations [12] and various
populations from Africa, America and Europe (Supplemen-
tary Table S1). For the reference populations from Africa,
low FST values were observed, except in comparisons of the
two samples from Pygmies and Somalians (Supplementary
Table S3). Very low genetic distances were found between
all of the European samples, with pairwise FST values below
0.007. The Native American population from Colombia
showed significantly high FST values in all of the pairwise
comparisons. Figure 1 depicts the MDS plot of the pairwise
FST matrix from Supplementary Table S3. When the results
that were obtained for the Colombian samples were com-
pared with each other, as well as with the African, European
and Native American reference samples, it is clear that most
of the samples from the admixed populations group togeth-
er, between the European and Native population groups.
Nevertheless, the two samples from Chocó and Mulaló
exhibit a lower differentiation from the African populations,
and the sample from Nariño was shown to be closer to the
Native Americans, which would be expected based on his-
torical data describing significant African and Native con-
tributions, respectively [25]. Finally, the Native American
sample from Pastos that was included in the present study,
although less distant from the European population than the
other native groups, exhibited a high genetic similarity to
the other populations of South American natives, as
expected.
Analysis of admixture
To perform the admixture analysis, reference population
data for Africans, Europeans and Native Americans were
extracted from the SNPforID 52plex database (http://
spsmart.cesga.es/snpforid.php) (Supplementary Table S1).
Initially, population structure analyses were performed with-
in each ancestral group after removing the genotype profiles
with missing data for more than five SNPs and using infor-
mation about the entire set of 52 markers.
The results from the STRUCTURE made it clear that the
population structure of the African samples would be better
explained by the assumption of two clusters, one containing
the Somali individuals and the other the remaining samples
(Supplementary Fig. S2). It is known that the African people
who were brought into Colombia were mainly from the
Bantu groups of sub-Saharan Africa, which includes
 Int J Legal Med

Native American group

0.6
A
African group Colombia Ecuador
0.4
Bantu NE Brazil
Pygmies
Mexico
Chocó
0.2 Uganda Pastos
South Mulalo
Angola
Dimension 2

Nigeria Huila Nariño

0.0
Valle Arauca
Senegal Tolima Norte de Santander
Cundinamarca-Boyaca
-0.2 Coffee area
Somalia Antioquia

-0.4

Italy
B
Portugal
-0.6 European group
Britain
Spain

-0.8
-2.0 -1.5 -1.0 -0.5 0.0 0.5 1.0 1.5 2.0

Dimension 1

Fig. 1 MDS plot of the FST genetic distances. a Dimension 1 vs. dimension 2 vs. dimension 3, just including populations from Colom-
dimension 2, including samples from African, European, Native Amer- bia (stress=0.00847)
ican and Colombian populations (stress=0.06732). b Dimension 1 vs.

territories along the Atlantic Sea in Central-Western and
Western Africa, as well as from Mozambique on the east
coast [26, 27]. For these reasons, the data from Somalia,
which is located in Northeast Africa, were excluded from
the population that was used as a reference for the subse-
quent admixture analyses of the Colombian populations.
No signs of population substructure were detected in
attempts assuming two or three populations and using
an admixture model for the European group, which is
represented by the British, Spanish, Italian and Portu-
guese data. In this case, all of the individuals represent-
ed approximately one half or one third of each
population contribution for K=2 and K=3, respectively
(Supplementary Fig. S3).
The Native American data showed better fit for a model
that creates two population clusters that separate the Native
Colombian groups Awa, Coyaima, Emberá and Pijao from the
remaining groups from Brazil, Ecuador and Mexico, as well
as from the Colombian samples from CEPH and Pastos. These
two Native American clusters separating the Colombian
Central Andean populations from the rest can also be ob-
served when it is assumed that there are three populations
(Supplementary Fig. S4).
A second analysis was performed by pooling all of the
reference data, assuming three clusters and using the admix-
ture model without indicating a putative population origin for
each individual (Supplementary Fig. S5). After calculating the
proportion of individual membership of all of the samples in
each cluster, those individuals carrying less than 90 % of their
contribution from the group they were initially assigned to
were removed from the final samples that were being used as
references for African, European and Native ancestral
populations in the admixture analyses (Supplementary Table
S1). Notably, the sample from Pastos, which was included in
the present study, preserves a low level of admixture. The
average continental membership proportions of the Pastos are
0.029 for Africa, 0.923 for America and 0.048 for Europe.
Finally, the reference and study populations were
analysed simultaneously to determine the ethnic contri-
butions to all of the Colombian samples (this study and
Int J Legal Med

Table 1 Interethnic estimates of the three main ancestral contributors that do not exhibit statistically significant differences in the
in 11 mixed populations from Colombia
allele frequencies for the 52 SNP alleles were grouped. There-
Population Africa Europe Native America fore, the samples from Antioquia, the Coffee area and Valle
del Cauca have been classified as a single group, representing
Huila 0.194 0.409 0.396 the Central-West Andean region (following the same criteria
Chocó 0.538 0.230 0.232 as Paredes et al., 2003). The Central-East Andean region
Norte de Santander 0.181 0.420 0.399 comprises the samples from Boyacá-Cundinamarca, Huila,
Arauca 0.218 0.405 0.377 Norte de Santander and Tolima. The consistency of the group-
Nariño 0.188 0.301 0.511 ing was tested by AMOVA, which demonstrated that almost
Boyacá-Cundinamarca 0.199 0.419 0.382 all of the genetic variation could be attributed to differences
Antioquia 0.197 0.466 0.337 within the populations or between groups, rather than between
Tolima 0.213 0.412 0.375 the populations within the established group (0.52 %). The
Valle de Cauca 0.234 0.418 0.348 results obtained are shown in Supplementary Tables S4 and
Coffee area 0.206 0.446 0.348 S5.
Mulaló 0.466 0.279 0.256 The 52 SNPs exhibit high diversity in all of the
Africa 0.997 0.002 0.001 samples, leading to a cumulative discrimination power
Europe 0.004 0.993 0.003 ranging from 99.999999999999994 % in the native
Native America 0.004 0.002 0.994 group of Pastos to 99.99999999999999999995 % in
the Central-West Andean region (see Table 2). When
considering the full set of markers, high values of
exclusion probability were also found, varying from
Porras et al. [12]). The results obtained demonstrate that 99.90 to 99.996 % (see Table 2).
most of the regions are characterised by an admixture, In most cases, no deviation from the Hardy–Weinberg
in which the European and Native American contribu- equilibrium (HWE) was detected (Supplementary Table S5).
tion prevails, except for the population from Chocó, on Exceptions were found in 11 out of the 312 tests that were
the north Pacific Coast, which harbours an African performed (see Supplementary Table S5 footnote, for
admixture proportion of 54 % (Table 1 and Supplemen- discussion).
tary Fig. S6). A significant African contribution was In conclusion, based on the overall estimates from
also observed in a small population group called Mulaló our samples, neither significant frequencies of silent
that is located in the region of the Valle del Cauca. In alleles nor significant substructure are expected to be
the remaining populations, the proportion of African present in the groups of the native, Southwest Andean,
ancestry varied between 18 and 23 %. The highest Central-West Andean, Orinoquian and north Colombian
Native American membership was observed in the re- Pacific Coast populations. Although no significant ge-
gion of Nariño. Slightly higher native proportions were netic distances were found between the samples from
also found in populations from the east of the Central the Central-East Andean region, results of the HWE test
Andean region in comparison to the west. do not exclude the possibility that some heterogeneity
may exist between the populations that were included in
Allele frequency database and diversity indices of forensic this group (see Supplementary Table S5 footnote). Ad-
relevance ditional sampling efforts in this region are, therefore,
important before decisions are made about the consis-
Before calculating the allele frequencies and forensically rel- tency of grouping the Central-East Andean populations
evant parameters, samples from neighbouring departments in a single database for forensic purposes.

Table 2 Accumulated forensic

parameters for the 52 SNPs in-
cluded in the SNPforID multi-
plex, estimated for five regions
of Colombia and in a native
group
Population Power of discrimination (%) Power of exclusion (%)
Native American group 99.999999999999994 99.90
Southwest Andean region 99.9999999999999992 99.97
Central-West Andean region 99.99999999999999999995 99.98
Central-East Andean region 99.99999999999999999992 99.996
Orinoquian region 99.9999999999999999993 99.990
North Colombian Pacific Coast 99.9999999999999992 99.98

Conclusions
An assay of 52 unlinked autosomal markers was performed
to investigate the population substructure of Colombia and
establish the use of a single national or local databases when
adding these markers to the forensic routine. The results
demonstrate that there are significant differences in the
allele frequencies of these 52 SNPs among the populations
of some departments of Colombia. Population comparisons
and admixture analyses demonstrate a genetic composition
of the studied populations that is compatible with five Co-
lombian forensic databases for the 52 SNPs. The
populations from most regions are characterised by an
admixed profile, in which the European and Native Amer-
ican ancestries prevail, except for the population from
Chocó, on the north Pacific Coast, which harbours an Afri-
can admixed proportion of 54 %. A significant percentage of
African ancestry was also observed in a small population
group called Mulaló, contrasting with the high proportion of
native contribution that was detected in the Pastos, as would
be expected for a native group. Therefore, it was possible to
conclude that a single Colombian database would not be
suitable as a reference for forensic purposes and that the
samples from admixed urban Colombian populations that
have been previously studied can be grouped in, at least,
five regions: the Southwest Andean, Central-West Andean,
Central-East Andean, Orinoquian and north Colombian Pa-
cific Coast regions. The high values of the combined
matching probabilities in all of the samples, as well as the
combined probability of the exclusion in trios, demonstrates
the usefulness of the studied set of markers for forensic
casework in Colombia.
Acknowledgments The authors wish to thank Oscar Palacio, Tomas
Restrepo, Yeny Posada, Silvana Zapata, Zoraida Florez, Gloria
Galeano, Luz Mariela Ochoa and Liliana Porras for their help in
sample typing and data revising and analysis. Likewise, the authors
would like to thank the Ipiales’ residents, Cuaspud-Carlosama rural
community and especially Dr. Martha Castañeda for her support in
field sampling logistics. This work was supported by funding from
Xunta de Galicia INCITE 09 208163PR (PI: Victoria Lareu).
IPATIMUP is an Associate Laboratory of the Portuguese Ministry of
Education and Science and is partially supported by FCT. LG is
supported by a grant from CAPES, Brazil. AFA was supported by a
María Barbeito grant from Xunta de Galicia (Spain). MF is funded by a
grant from the postdoctoral programme of the Foundation Barrié de La
Maza.
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