Forensic Science International: Genetics 6 (2012) 132135

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Forensic Science International: Genetics

journal homepage: www.elsevier.com/locate/fsig

Short communication

Allelic frequencies and statistical data obtained from 48 AIM INDEL loci in an
admixed population from the Brazilian Amazon
Pablo Abdon da Costa Francez a,b, Elzemar Martins Ribeiro-Rodrigues b,
Sidney Emanuel Batista dos Santos b,*
a
Laboratorio de Genetica Forense, Departamento de Laboratorios Forenses, Polcia Cientca do Amapa, Brazil
b
Laboratorio de Genetica Humana e Medica, Instituto de Ciencias Biologicas, Universidade Federal do Para, Rua Augusto Correa, 01 - Guama, CEP 66075-110 Belem, Para, Brazil

A R T I C L E I N F O A B S T R A C T

Article history: Allelic frequencies of 48 informative insert-delete (INDEL) loci were obtained from a sample set of 130
Received 8 October 2010 unrelated individuals living in Macapa, a city located in the northern Amazon region, in Brazil. The values
Received in revised form 22 February 2011 of heterozygosity (H), polymorphic information content (PIC), power of discrimination (PD), power of
exclusion (PE), matching probability (MP) and typical paternity index (TPI) were calculated and showed
Accepted 2 April 2011
the forensic efciency of these genetic markers. Based on the allele frequency obtained for the population
of Macapa, we estimated an interethnic admixture for the three parental groups (European, Native
Keywords:
American and African) of, respectively, 50%, 21% and 29%. Comparing these allele frequencies with those
INDEL
Population genetics
of other Brazilian populations and the parental populations, statistically signicant distances were found.
Macapa population The interpopulation genetic distance (FST coefcients) to the present database ranged from FST = 0.0431
Forensic genetics (p < 0.00001) between Macapa and Belem to FST = 0.266 (p < 0.00001) between Macapa and the Native
American group.
2011 Elsevier Ireland Ltd. All rights reserved.

1. Population
The Brazilian population is one of the most heterogeneous
populations in the world. Estimates indicate that, before the arrival
of the rst colonizers, around 2.5 million natives were living within
the Brazilian territory [1]. The European immigration rst consisted
primarily of Portuguese. During the rst 300 years, 500,000 people
came from Portugal. Then, in the second half of the 15th century the
slave trade started and continued until 1850. During this period, 3.5
million Africans were brought to Brazil by force [2].
Due to the special occupation policies of such a vast territory, the
admixture process occurred in different ways in different geographic
regions of the country. In northeast Brazil, the African contribution is
high and the Native American component is low; in the North, the
contribution of Native Americans is pronounced, whereas in the
South the Amerindian and African inuence is reduced in
comparison with all the other geographic regions of Brazil [3,4].
After obtaining signed informed consent from all participants of
the study, peripheral blood samples were collected from 130
unrelated healthy individuals (63 female, 67 male; mean age 37.5,
range 1869 years) seen for routine examinations at the UNILAB
Clinical Analysis Laboratory in Macapa (08020 2000 N; 518030 5900 W),
State of Amapa, northern Brazil.
For estimating ancestry and genetic distances (FST), we used the
genotype frequencies of the 48 INDEL markers investigated in this
study, obtained for the three main parental ethnic groups which
formed the Brazilian population: Africans 189 individuals from
Sub-Saharan Africa [5,6], Europeans 161 individuals from
Portugal [7], and Native Americans 243 individuals from
indigenous tribes of the Brazilian Amazon region [8,9]. We also
compared the genotype frequencies of the 48 INDEL markers
obtained for admixed Brazilian populations (81 individuals from
the State of Rio Grande do Sul, 196 individuals from the city of
Belem, State of Para, and 103 individuals of African descent living
in the Amazon region) [10].
Although the biogeography of some groups in certain parts of
the world is cultural and genetically established, other groups have
a relatively recent admixture history, with ancestors from widely
separated regions. This is the case of the Brazilian population,
characterized by a genetic background based mainly on three
parental ancestry populations (European, African and Native
American) in an assorted degree of admixture among them [11,12].

2. DNA extraction and quantication

* Corresponding author. Tel.: +55 91 3201 7843; fax: +55 91 3201 7843.
E-mail addresses: pabdon@uol.com.br, elze_mar@yahoo.com.br, DNA was extracted from peripheral blood mononuclear cells,
sidneysantos@ufpa.br (S.E.B. dos Santos). using the phenol-chloroform protocol [13]. DNA quantication

1872-4973/$ see front matter 2011 Elsevier Ireland Ltd. All rights reserved.
doi:10.1016/j.fsigen.2011.04.002
 P.A.C. Francez et al. / Forensic Science International: Genetics 6 (2012) 132135 133

Table 1
Allele frequencies distribution of the 48 INDEL loci investigated in the present study.

INDEL identication Deletion Insertion N Hobs Hexp PIC PD PE MP TPI p

rs140762 Mid473 0.396 0.604 260 0.5462 0.4803 0.36 0.577 0.231 0.423 1.10 0.1415
rs1160871 Mid619 0.492 0.508 260 0.4769 0.5018 0.37 0.636 0.168 0.364 0.96 0.6016
rs2307644 Mid1448 0.319 0.681 260 0.3769 0.4363 0.34 0.598 0.10 0.402 0.80 0.1560
rs2308115 Mid1923 0.242 0.758 260 0.3308 0.3686 0.30 0.534 0.077 0.466 0.75 0.2405
rs1610941 Mid856 0.662 0.338 260 0.4154 0.4495 0.35 0.604 0.124 0.396 0.86 0.4353
rs16388 Mid99 0.662 0.338 260 0.3231 0.4088 0.35 0.604 0.124 0.396 0.86 0.0289
rs16383 Mid93 0.438 0.562 260 0.5231 0.4943 0.37 0.605 0.209 0.395 1.05 0.5919
rs1160910 Mid682 0.74 0.26 260 0.3333 0.3860 0.31 0.551 0.078 0.449 0.75 0.1658
rs2067128 Mid1039 0.358 0.642 260 0.4846 0.4613 0.35 0.592 0.174 0.408 0.97 0.7034
rs2307976 Mid1780 0.65 0.35 260 0.5308 0.4568 0.35 0.563 0.216 0.437 1.07 0.0819
rs2307666 Mid1470 0.385 0.615 260 0.4000 0.4752 0.36 0.633 0.114 0.367 0.83 0.0942
rs16416 Mid132 0.565 0.435 260 0.5000 0.4934 0.37 0.616 0.188 0.384 1.00 1.000
rs2067186 Mid1098 0.466 0.534 260 0.4622 0.4998 0.37 0.64 0.157 0.36 0.93 0.4631
rs2307754 Mid1558 0.477 0.523 260 0.4688 0.5009 0.37 0.638 0.162 0.362 0.94 0.4812
rs16654 Mid217 0.368 0.632 260 0.4419 0.4671 0.36 0.614 0.141 0.386 0.90 0.5735
rs140857 Mid568 0.281 0.719 260 0.4385 0.4054 0.32 0.554 0.32 0.446 0.89 0.3924
rs2307553 Mid1357 0.662 0.338 260 0.4462 0.4495 0.35 0.595 0.145 0.405 0.90 1.000
rs16710 Mid273 0.658 0.342 260 0.4077 0.4520 0.35 0.609 0.119 0.391 0.84 0.3284
rs2307880 Mid1684 0.335 0.665 260 0.5154 0.4470 0.35 0.562 0.201 0.438 1.03 0.1138
rs1610902 Mid818 0.242 0.758 260 0.3462 0.3686 0.30 0.534 0.084 0.466 0.76 0.4830
rs2067259 Mid1172 0.173 0.827 260 0.2692 0.2874 0.25 0.447 0.052 0.553 0.68 0.5386
rs2067263 Mid1176 0.465 0.535 260 0.5736 0.4995 0.37 0.578 0.26 0.422 1.17 0.1132
rs2307912 Mid1716 0.673 0.327 260 0.3923 0.4418 0.34 0.602 0.109 0.398 0.82 0.2328
rs2307554 Mid1358 0.729 0.271 260 0.3256 0.3970 0.32 0.562 0.075 0.438 0.74 0.0500
rs2307981 Mid1785 0.192 0.808 260 0.3077 0.3119 0.26 0.476 0.067 0.524 0.72 1.000
rs2067353 Mid1271 0.615 0.385 260 0.5385 0.4752 0.36 0.577 0.223 0.423 1.08 0.1389
rs1610866 Mid780 0.788 0.212 260 0.3308 0.3349 0.28 0.50 0.077 0.50 0.75 1.000
rs140783 Mid494 0.589 0.411 260 0.5000 0.4862 0.37 0.609 0.188 0.391 1.00 0.8519
rs140783 Mid625 0.712 0.288 260 0.3462 0.4121 0.33 0.577 0.084 0.423 0.76 0.0867
rs2307575 Mid1379 0.849 0.151 260 0.2403 0.2576 0.22 0.41 0.042 0.59 0.66 0.4878
rs2308203 Mid2011 0.717 0.283 260 0.4388 0.4074 0.32 0.572 0.086 0.428 0.77 0.1270
rs2307922 Mid1726 0.578 0.422 260 0.5156 0.4897 0.37 0.605 0.202 0.395 1.03 0.5897
rs2308144 Mid1952 0.354 0.646 260 0.4308 0.4590 0.35 0.61 0.134 0.39 0.88 0.5652
rs140765 Mid476 0.412 0.588 260 0.4846 0.4862 0.37 0.617 0.174 0.383 0.97 1.000
rs16712 Mid275 0.635 0.365 260 0.4846 0.4655 0.36 0.596 0.174 0.404 0.97 0.7088
rs16432 Mid152 0.446 0.554 260 0.5692 0.4961 0.37 0.577 0.256 0.423 1.16 0.1109
rs16635 Mid196 0.373 0.627 260 0.4230 0.4700 0.36 0.622 0.129 0.378 0.87 0.2654
rs1610864 Mid778 0.704 0.296 260 0.4385 0.4185 0.33 0.567 0.139 0.433 0.89 0.6748
rs2307799 Mid1603 0.473 0.527 260 0.5615 0.5005 0.37 0.587 0.247 0.413 1.14 0.2180
rs2307582 Mid1386 0.338 0.662 260 0.4308 0.4495 0.35 0.60 0.134 0.40 0.88 0.6971
rs1160894 Mid660 0.665 0.335 260 0.4231 0.4470 0.35 0.6 0.129 0.4 0.87 0.5584
rs140864 Mid575 0.185 0.815 260 0.3076 0.3022 0.26 0.467 0.067 0.533 0.72 1.000
rs16653 Mid216 0.665 0.335 260 0.5000 0.4470 0.35 0.57 0.188 0.43 1.0 0.2372
rs140770 Mid481 0.209 0.791 260 0.3411 0.3323 0.28 0.498 0.082 0.502 0.76 1.000
rs1610996 Mid913 0.081 0.919 260 0.1308 0.1491 0.14 0.254 0.014 0.746 0.58 0.1877
rs25574 Mid350 0.173 0.827 260 0.2539 0.2874 0.25 0.443 0.046 0.557 0.67 0.2150
rs1611070 Mid988 0.408 0.592 260 0.4923 0.4848 0.37 0.612 0.181 0.388 0.98 1.000
rs16460 Mid1184 0.492 0.508 260 0.4462 0.5018 0.37 0.647 0.145 0.353 0.9 0.2216

N: number of chromosomes; Hobs: observed heterozygosity; Hexp: expected heterozygosity; PIC: polymorphism information content; PD: power of discrimination; PE: power
of exclusion; MP: matching probability; TPI: typical paternity index; p: probability of deviation from HardyWeinberg equilibrium.

was performed using a NANODROP 1000 spectrophotometer 4. Typing

(Thermo Scientic, Wilmington, DE, USA).
3. PCR
The PCR primer sequences and DNA amplication conditions
used were the same as described by Santos et al. [10] that using a
48-INDEL ancestry-informative-marker (AIM) panel allows geno-
typing and can be used to distinguish continental populations,
specically Europeans, Africans and Native Americans, and also
allows identifying substructure in mixed populations. These
authors further demonstrated that in admixed populations from
different parental groups the marker panel allows estimating, in an
accurate and reliable manner, the individual and global interethnic
admixture relative to those groups, and that all the produced
estimates have low thresholds.
Electrophoresis and typing were performed in an ABI 3130
Avant Automated Sequencer (Applied Biosystems, Foster City, CA,
USA). For data acquisition we used the ABI PRISMTM 3130 Avant
Data Collection v2.0 software (Applied Biosystems), and for prole
analysis the GeneMapper ID v3.2 software (Applied Biosystems).
Typing quality and allele designation were warranted by simulta-
neous electrophoretic analysis of a control sample of known size.
Allele designations were made with the ABIGS LIZ-500 reference
ladder (Applied Biosystems) as size standard.
5. Statistical analysis
Allelic frequencies, heterozygosity (H), polymorphism infor-
mation content (PIC), power of discrimination (PD), power of
exclusion (PE) and deviation probability from the HardyWeinberg
134 P.A.C. Francez et al. / Forensic Science International: Genetics 6 (2012) 132135

Table 2
Comparison of interethnic admixture between Macapa population and others admixed Brazilian populations.

Population Interethnic admixture

European African Native American

Macapaa 0.50  0.0115 0.21  0.0131 0.29  0.0113

Belemb 0.546  0.0082 0.148  0.0110 0.306  0.0098
South Brazilb 0.913  0.0030 0.00 0.087  0.0099
Amazon Afro-descendentsb 0.149  0.0074 0.69  0.0073 0.161  0.0072
a
Current study.
b
Santos et al. [10].

Table 3
Comparison of interpopulation genetic distances (FST coefcients) between the Macapa population, parental population and admixed Brazilian populations.

Populations Africans Europeans N. Americans Belem South Brazil Afro-descendents Macapa

Africans 0.00000
Europeans 0.32792 0.00000
N. Americans 0.48174 0.36002 0.00000
Belem 0.23794 0.04969 0.19711 0.00000
South Brazil 0.35653 0.00395 0.34342 0.04004 0.00000
Afro-descendents 0.06224 0.20322 0.34582 0.09906 0.21208 0.00000
Macapa 0.23108 0.08918 0.26604 0.04308 0.08290 0.11234 0.00000

equilibrium (p) as well as genetic distance (FST) coefcients were
calculated using the Arlequin Version 2.000 software [14].
Matching probability (MP) and typical paternity index (TPI) were
calculated for each locus using the Powerstats V12 software [15],
and for calculating admixture components we used the Structure
software (http://pritch.bsd.uchicago.edu/software/struc-
ture2_1.html) and Admix 95 (www.genetica.fmed.edu.uy/soft-
ware.htm). The FST matrix and WPGMA tree analysis were carried
out with the GDA program [16]. The tree was displayed by means
of the TreeView software (http://taxonomy.zoology.gla.ac.uk/rod/
treeview.html).
6. Results
Allele frequencies and statistic parameters for the 48 INDEL loci
of the population of Macapa are shown in Table 1.
7. Data access
Available upon request: pabdon@uol.com.br.
8. Other remarks
All loci analyzed were in HardyWeinberg equilibrium in the
studied population (p > 0.05), except rs16388 (p = 0.0289). How-
ever, after applying the Bonferroni correction using the number of
analyzed loci, the differences observed were not statistically
signicant regarding rs16388 (p = 0.75528).
The forensic parameter averages calculated were: polymor-
phism information content (PIC) = 33.3%; power of discrimination
(PD) = 56.7%; power of exclusion (PE) = 14.2%; observed hetero-
zygozity (Ho) = 42%. The rs2067263 marker showed the highest
level of heterozygosity (57.4%) and the rs1610996 marker showed
the lowest (13.1%). The power of discrimination and the power of
exclusion for the 48 INDELs studied were
99.9999999999999998035% and 99.9456321%, respectively.
Comparing the allele frequencies obtained for the 48 INDEL
systems investigated in the population of Macapa with the
frequencies calculated for the three parental ethnic groups, the
African, European and Native American contributions were
estimated to be 0.21  0.0115, 0.50  0.0131 and 0.29  0.0113,
respectively (Table 2). The individual admixture components
estimated for the Macapa population varied substantially: between

Fig. 1. Phylogenetic tree elaborated by the WPGMA method.

 P.A.C. Francez et al. / Forensic Science International: Genetics 6 (2012) 132135
5% and 74% for African DNA, from 14% to 79% for European DNA, and
from 6% to 63% for Native American DNA. These results are in agreement
with other population studies and historical data and are consistent
with the anthropological origins (European, African and Native
American) of the Brazilian populations tested (supplementary Fig. 1).
The results obtained in the population of Macapa were
compared with those of other admixed Brazilian populations
(Amazonian Afro-descendents, South Brazil and Belem) and with
parental populations (European, African and Native American). In
terms of interpopulation genetic distances (FST coefcients), the
population of Macapa was found to be closest to the population of
Belem (FST = 0.0431, p < 0.00001), and the Native American
(FST = 0.266; p < 0.00001) and African (FST = 0.23108,
p < 0.00001) were the most different populations (Table 3 and
Fig. 1).
This paper follows the publication guidelines of population data
requested by the journal [17].
Acknowledgments
Financial aid was provided by Polcia Cientca do Amapa
(POLITEC) and Laboratorio de Genetica Humana e Medica (LGHM).
This study was approved by the SEAMA College Ethics Research
Committee (ERC Resolution no. 078/2009).
Appendix A. Supplementary data
Supplementary data associated with this article can be found, in
the online version, at doi:10.1016/j.fsigen.2011.04.002.
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