Forensic Science International 164 (2006) 266–270

www.elsevier.com/locate/forsciint
Announcement of population data
Allele frequencies for 15 autosomal STR loci and admixture
estimates in Puerto Rican Americans
J. Zúñiga a,b,**, M. Ilzarbe c, V. Acunha-Alonzo d, F. Rosetti d, Z. Herbert c,
V. Romero a, I. Almeciga a, O. Clavijo a, J.N.H. Stern a, J. Granados f,
M. Fridkis-Hareli a, P. Morrison c, J. Azocar e,**, E.J. Yunis a,*
a
Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute and Department of Pathology,
Harvard Medical School, 44 Binney Street, Boston, MA 02115, United States
b
Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
c
Molecular Biology Core Facilities, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, United States
d
Escuela Nacional de Antropologia e Historia, Instituto Nacional de Antropologia e Historia, Mexico City, Mexico
e
Northgate Medical Center, Springfield, MA, USA
f
Department of Immunology and Rheumatology,
Instituto Nacional de Ciencias Médicas y de la Nutrición Salvador Zubirán, Mexico City, Mexico
Received 22 November 2005; received in revised form 23 November 2005; accepted 23 November 2005
Available online 19 January 2006

Abstract

Allelic frequencies of 15 short tandem repeats (STR) markers (CSF1PO, FGA, THO1, TPOX, VWA, D3S11358, D5S818,
D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, D19S433 and D2S1338) were determined using the AmpF‘ STR1
TM
Identifiler PCR Amplification Kit in Puerto Rican American individuals (N = 205) from Massachusetts. The FGA, D18S51
and D2S1338 loci had a high power of discrimination (PD) with values of 0.967, 0.965 and 0.961, respectively. Significant
deviations from the Hardy–Weinberg (HW) equilibrium were not detected. An important genetic contribution of Caucasian
European (76.4%) was detected in Puerto Rican Americans. However, comparative analysis between Puerto Rican American
and other neighboring populations from United States mainly with African and Caucasian Americans, revealed significant
differences in the distribution of STR markers.
Our results are important for future comparative genetic studies of different American ethnic groups, in particular a cultural
group called Hispanic-Americans and should be helpful for forensic and paternity testing.
# 2005 Elsevier Ireland Ltd. All rights reserved.

Keywords: Short tandem repeat; STR; Allelic frequencies; Puerto Rican; AmpF‘ STR1 IdentifilerTM

Population: Two hundred and five non-related Puerto
Rican American individuals from Springfield, Massachu-
* Corresponding author. Tel.: +1 617 632 3347;
fax: +1 617 632 4466.
** Corresponding authors.
E-mail addresses: Joaquin_zuniga@dfci.harvard.edu
(J. Zúñiga), jazocar@comcast.net (J. Azocar),
edmond_yunis@dfci.harvard.edu (E.J. Yunis).
setts were studied. All subjects were recruited from the same
community and with Puerto Rican ancestry (all four grand-
parents were born in Puerto Rico and none from Europe or
other continents) as self-reported by questionnaire.
DNA extraction: Genomic DNA was extracted from
200 mL of EDTA-blood by using Qiagen columns (Qiagen,
Chatsworth, CA).
PCR: CSF1PO, FGA, THO1, TPOX, VWA, D3S11358,
D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51,

0379-0738/$ – see front matter # 2005 Elsevier Ireland Ltd. All rights reserved.
doi:10.1016/j.forsciint.2005.11.022
 J. Zúñiga et al. / Forensic Science International 164 (2006) 266–270
D21S11, D19S433 and D2S1338 loci along with amelogenin
were co-amplified using the AmpF‘ STR1 IdentifilerTM Kit
(Applied Biosystems, Foster City, CA) according to manu-
facturer’s instructions [1].
Typing: The amplified products and reference ladders
provided in the kit were analyzed in a ABIPrism 3100
Genetic Analyzer (Applied Biosystems). Electrophoresis
results were analyzed using GeneMapper1 software Version
3.5.
Results: See Tables 1 and 2.
Quality control: Laboratory internal control standards
and kit controls.
Analysis of data: Gene frequencies, observed and
expected heterozygosity and Hardy–Weinberg (HW) equili-
brium and exact test of population differentiation were
calculated using the Arlequin population genetics software
v2.1. The significance level 0.05 was corrected by the
Bonferroni method, p-values < 0.003 were considered sta-
tistically significant (0.05/15 = 0.003).
Matching probability, power of discrimination, poly-
morphism information content, power of exclusion and
typical paternity indexes were calculated using the Power
Stats v1.2 software.
Admixture estimations were calculated using the max-
imum likelihood method with the program Leadmix [2] and a
Bayesian approach using the program Structure 2.0 [3] (http://
pritch.bsd.uchicago.edu). We used Caucasian European (Spa-
niards), West Africans and Amerindian populations as Puerto
Rican ancestral contributors. Previous reported STR data on
parental populations Europeans from Spain [4], West Africans
[5] and from Mexican Amerindian population [6] were used
for the analyses of admixture estimates.
Access to data: The complete data can be accessed:
joaquin_zuniga@dfci.harvard.edu.
Other remarks: In this study, we analyzed the frequen-
cies of 15 STR markers in 205 Puerto Rican Subjects from
Springfield, Massachusetts, Table 1. Significant deviations
from HW equilibrium were not observed. The loci D19S433
and D18S51 had the highest number of alleles (15) com-
pared with the locus TH01 with only six alleles. The locus
FGA showed the higher power of discrimination
(PD = 0.967) followed by the loci D18S51 and D2S1338
with PD = 0.965 and 0.961, respectively. The combined
power of discrimination of all 15 STR was >0.99999999
and the combined power of exclusion was >0.9999992.
These STR frequencies compared with those published
before in other populations [4–6] were used for the admix-
ture estimation analysis with the maximum likelihood
method [2]. They demonstrated an important contribution
of Caucasian European (76.4%), African (17.0%) and Amer-
indian genes (6.6%) in Puerto Rican American population.
Individual ancestry proportions calculated with Structure 2.0
[3] are shown in a triangle plot that shows the distribution of
the individual admixture estimates in relation to the parental
populations. The results obtained by the above-mentioned
Bayesian approach confirm that Puerto Rican Subjects from
267
Massachusetts has a greater Caucasian ancestry contribu-
tion, Fig. 1.
Using the population differentiation test, we compared
our results in Puerto Rican American individuals with pre-
viously published data available online on three populations
in the United States [7]: Hispanic American (in the United
States, Hispanic Americans refers to individuals originating
from Latin America, it is not ethnic but a cultural denomi-
nation), African American and Caucasian American http://
www.cstl.nist.gov/biotech/strbase. Comparative analyses
between pairs of populations are shown as non-differentia-
tion exact probability values in Table 2. We found significant
differences between Puerto Rican American and African
American populations (6/15 loci with p < 0.003) and
between Puerto Rican American and Caucasian American
populations (4/15 loci with p < 0.003). The comparison
between Puerto Rican Americans and Random Hispanic
Americans showed a significant value in the locus
D19S433 ( p = 0.00293). In addition, important differences
between Caucasian American versus African American and
Hispanic American versus African American comparisons
were observed, Table 2.
Several STR markers have been investigated for applica-
tion to human identity testing [8,9]. In this study, we used a
commercially available multiplex STR typing kit to analyze
the allelic frequencies of 15 STR markers in a Puerto Rican
American population from Massachusetts. The most infor-
mative loci for power of exclusion were FGA, D18S51 and
D19S433 and the least informative were D5S818, TPOX,
TH01 and CSF1PO. In our study, we also detected an
Fig. 1. Estimation of individual ancestry proportions in Puerto
Rican Americans. In this analysis, with a three parental population
model, the contributions of Caucasian European, African and Amer-
indian populations in N = 205 Puerto Rican American individuals
from Massachusetts were calculated. Triangle plot obtained with the
Structure 2.0 software shows the ancestry proportions of each
individual (*) in the context of the parental populations, which
are represented in different angles of the figure.
 268
Table 1
Allele frequencies of 15 STR in Puerto Rican American (N = 205)
Allele D8S1179 D21S11 D7S820 CSF1PO D3S1358 TH01 D13S317 D16S539 D2S1338 D19S433 vWA TPOX D18S51 D5S818 FGA
5 – – – – – – – – – – – – – – –
6 – – – – – 0.200 – – – – – 0.007 – – –
7 – – 0.022 0.017 – 0.217 – – – – – 0.002 – 0.049 –
8 0.010 – 0.161 0.022 – 0.127 0.093 0.020 – – – 0.398 – 0.002 –
9 0.010 – 0.137 0.015 – 0.210 0.085 0.146 – 0.002 – 0.117 – 0.039 –
9.3 – – – – – 0.237 – – – – – – – – –
10 0.100 – 0.310 0.234 – 0.010 0.059 0.098 – 0.083 – 0.066 0.005 0.049 –
10.2 – – – – – – – – – – – – 0.002 – –

J. Zúñiga et al. / Forensic Science International 164 (2006) 266–270

11 0.051 – 0.173 0.261 – – 0.220 0.329 – 0.027 0.007 0.315 0.005 0.315 –
12 0.122 – 0.141 0.415 0.005 – 0.310 0.237 – 0.098 – 0.090 0.083 0.363 –
12.2 – – – – – – – – – 0.010 – – – – –
13 0.222 – 0.054 0.032 0.016 – 0.166 0.144 – 0.234 – 0.005 0.127 0.173 –
13.2 – – – – – – – – – 0.022 – – – – –
14 0.234 – 0.002 0.002 0.066 – 0.066 0.027 – 0.256 0.088 – 0.163 0.007 –
14.2 – – – – – – – – – 0.046 – – – – –
15 0.212 – – – 0.273 – 0.002 – – 0.112 0.154 – 0.173 0.002 –
15.2 – – – – – – – – – 0.056 – – – – –
16 0.034 – – – 0.327 – – – 0.056 0.027 0.207 – 0.149 – –
16.2 – – – – – – – – – 0.017 – – – –
17 0.005 – – 0.002 0.195 – – – 0.220 0.007 0.261 – 0.129 – –
17.2 – – – – – – – – – 0.002 – – – – –
18 – – – – 0.115 – – – 0.051 – 0.173 – 0.095 – 0.012
19 – – – – 0.005 – – – 0.200 – 0.083 – 0.032 – 0.080
19.2 – – – – – – – – – – – – – – –
20 – – – – 0.005 – – – 0.090 – 0.024 – 0.017 – 0.098
21 – – – – – – – – 0.034 – 0.002 – 0.005 – 0.151
21.2 – – – – – – – – – – – – – – –
22 – – – – – – – – 0.051 – – – 0.012 – 0.168
22.2 – – – – – – – – – – – – – – –
23 – – – – – – – – 0.095 – – – 0.002 – 0.134
23.2 – – – – – – – – – – – – – – –
24 – – – – – – – – 0.095 – – – – – 0.163
24.2 – – – – – – – – – – – – – – –
25 – – – – – – – – 0.088 – – – – – 0.080
25.2 – – – – – – – – – – – – – – –
26 – – – – – – – – 0.020 – – – – – 0.076
26.2 – 0.002 – – – – – – – – – – – – –
27 – 0.024 – – – – – – – – – – – – 0.029
28 – 0.107 – – – – – – – – – – – – –
28.2 – – – – – – – – – – – – – – –
29 – 0.244 – – – – – – – – – – – – 0.004
29.2 – – – – – – – – – – – – – – –
30 – 0.261 – – – – – – – – – – – – –
30.2 – 0.029 – – – – – – – – – – – – –
30.3 – – – – – – – – – – – – – – –
31 – 0.063 – – – – – – – – – – – – –
31.2 – 0.114 – – – – – – – – – – – – –
32 – 0.007 – – – – – – – – – – – – –
32.2 – 0.083 – – – – – – – – – – – – –
33 – 0.002 – – – – – – – – – – – – –
33.2 – 0.051 – – – – – – – – – – – – –
34 – – – – – – – – – – – – – – –
34.2 – 0.007 – – – – – – – – – – – – –

J. Zúñiga et al. / Forensic Science International 164 (2006) 266–270

35 – 0.002 – – – – – – – – – – – – –
36 – – – – – – – – – – – – – – –
Ho 0.800 0.809 0.834 0.673 0.756 0.741 0.824 0.770 0.853 0.863 0.790 0.658 0.873 0.726 0.897
He 0.824 0.835 0.808 0.704 0.764 0.799 0.806 0.784 0.870 0.846 0.822 0.721 0873 0.736 0.878
HW (p) 0.135 0.111 0.146 0.214 0.335 0.006 0.047 0.157 0.187 0.004 0.867 0.579 0.418 0.824 0.086
MP 0.058 0.049 0.071 0.134 0.096 0.076 0.072 0.078 0.039 0.047 0.056 0.119 0.035 0.113 0.033
PD 0.942 0.951 0.929 0.866 0.904 0.924 0.928 0.922 0.961 0.953 0.944 0.881 0.965 0.887 0.967
PIC 0.80 0.81 0.78 0.65 0.72 0.76 0.78 0.75 0.86 0.83 0.80 0.67 0.86 0.69 0.86
PE 0.599 0.617 0.664 0.388 0.520 0.487 0.645 0.545 0.692 0.731 0.590 0.360 0.741 0.479 0.790
TPI 2.50 2.63 3.10 1.53 2.05 1.90 2.85 2.17 3.31 3.80 2.44 1.44 3.94 1.86 4.88
Ho: Observed heterozygosity; He: expected heterozygosity; HW: Hardy–Weinberg equilibrium, Bonferroni correction significant p-value <0.003. MP: Matching probability; PD: power of
discrimination; PIC: polymorphism information content; PE: power of exclusion; TPI: typical paternity index.

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270 J. Zúñiga et al. / Forensic Science International 164 (2006) 266–270

Table 2
Comparative analysis between Puerto Rican American (PRA) and other neighboring populations: Hispanic–Americans (HA)a [7], Caucasian–
Americans (CA) [7] and African–Americans (AA) [7]
Locus PRA vs. HA PRA vs. CA PRA vs. AA CA vs. AA CA vs. HA HA vs. AA
* *
D8S1179 0.21603 0.00098 0.07722 0.00000 0.11632 0.02737
D21S11 0.23167 0.24047 0.00000* 0.00000* 0.49462 0.00000*
D7S820 0.04594 0.00587 0.06256 0.00000* 0.00280* 0.00782
CSF1PO 0.11046 0.52297 0.02444 0.02053 0.22385 0.02151
D3S1358 0.98143 0.04399 0.68231 0.01173 0.13881 0.81232
TH01 0.42131 0.00000* 0.00000* 0.00000* 0.00196* 0.00000*
D13S317 0.04203 0.08993 0.00000* 0.00196* 0.08993 0.00000*
D16S539 0.19257 0.46921 0.04301 0.00196* 0.11046 0.05083
D2S1338 0.28543 0.00391* 0.00000* 0.00000* 0.23265 0.00000*
D19S433 0.00293* 0.00000* 0.04888 0.00000* 0.19648 0.00782
vWA 0.24145 0.95210 0.39003 0.31965 0.52493 0.39394
TPOX 0.19062 0.00196* 0.00000* 0.00000* 0.10362 0.00000*
D18S51 0.88465 0.42913 0.00000* 0.00000* 0.82209 0.00587
D5S818 0.49365 0.31672 0.05083 0.02737 0.61193 0.01760
FGA 0.36168 0.35679 0.06940 0.01955 0.12805 0.08309
The significance level 0.05 was corrected by the Bonferroni method for the number of comparisons (0.05/15 = 0.003).
a
In the United States, Hispanic Americans refers to individuals originating from Latin America, it is not ethnic but a cultural denomination.
*
Significant p-values <0.003.

important Caucasian European genetic contribution in
Puerto Rican Americans with and adequate number of
STR polymorphic markers. Our results support previous
studies of admixture estimates using blood groups [10]
and other ancestry informative markers [11] that have
reported an important contribution of Caucasian genes in
Puerto Ricans.
Taken together, our results are important to determine the
genetic background of Puerto Ricans living in the United
States. STR analysis in this ethnic group showed significant
differences between Puerto Rican Americans compared with
African American and Caucasian American populations
suggesting that the 15 STR system tested would be a useful
tool for forensic, paternity testing and population differen-
tiation analysis between neighboring populations living in
the United States.
This study is reported following the guidelines for pub-
lication of population data requested by the journal [12].
Acknowledgements
This work was supported by NIH grants HL29583 and
HL59838. J.Z. was supported in part by grants from the
Instituto Nacional de Enfermedades Respiratorias, Mexico
and by Fundacion Mexico en Harvard A.C.
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