www.elsevier.com/locate/forsciint

Forensic Science International 168 (2007) 85–88

Announcement of Population Data

Population genetic data for 18 STR loci in Costa Rica

A. Rodrıguez a, G. Arrieta a, I. Sanou a, M.C. Vargas b, O. Garcıa c,I. Yurrebaso c, J.A. Perez c, M. Villalta d, M. Espinoza a,*

a Unidad de Genetica Forense, Departamento de Ciencias Forenses, Organismo de Investigacion Judicial,

Poder Judicial, Costa Ricab Escuela de Ciencias Biologicas, Facultad de Ciencias Exactas y Naturales de la Universidad Nacional, Costa Rica

c Area de Laboratorio Ertzaintza, Larrauri Mendotxe 18, Erandio, Bizkaia, Basque Countryd Escuela de Biologıa, Instituto Tecnologico de Costa Rica, Costa Rica

Received 15 November 2005; received in revised form 24 January 2006; accepted 25 January 2006

Available online 3 March 2006

Abstract

Allele frequencies for 18 STR autosomal loci (D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820, D16S539,

TH01, TPOX, CSF1PO, Penta D, Penta E, D19S433, D2S1338 and SE33) were obtained from a sample of 191–500 unrelated individuals from

Costa Rica, Central America.

# 2006 Elsevier Ireland Ltd. All rights reserved.

Keywords: Costa Rica; Population database; STR; Hardy–Weinberg equilibrium; Linkage equilibrium

Population: Samples were collected from 191–500 unre-

lated healthy individuals from Costa Rica.

Extraction: DNA was extracted by the Chelex method [1].

PCR: PCR amplifications were performed using the

AmpFlSTR Identifiler PCR Amplification kit (Applied

Biosystems), the PowerPlex 16 kit and the PowerPlex 16/ES

Monoplex System (SE33) (Promega Corporation) according to

the manufacturers’ recommendations.

Typing: Amplified products were analyzed using an ABI

310 and an ABI 3100 Avant DNA sequencer (PE-Biosystems,

Foster City, CA). Allele designations were made according to

recommendations of the DNA Commission of the ISFG [2]

with the aid of allelic ladders provided by the manufacturers.

Quality control: Proficiency testing of the GEP-ISFG

working group.

Results: See Table 1.

Analysis of data: Statistical evaluations were carried out

with the aid of GDA and PowerStats software packages [3,4].

Statistical parameters such as power of discrimination (PD) and

a priori chance of exclusion (CE) for each loci were estimated

as described by Huston [5]. Also we calculated the polymorphic

* Corresponding author.

E-mail address: mespinoza@Poder-Judicial.go.cr (M. Espinoza).

0379-0738/$ – see front matter # 2006 Elsevier Ireland Ltd. All rights reserved.

doi:10.1016/j.forsciint.2006.01.013

information content (PIC) according to Botstein et al. [6].

Minimum allele frequencies (MAF) for PCR-based loci, based

on statistical and population genetics theory [7] were

determined. The Hardy–Weinberg equilibrium for each loci

and linkage disequilibrium were verified using the GDA

program.

Access of data: Available upon request to mespinoza

@Poder-Judicial.go.cr.

Other remarks: No significant deviations from Hardy–

Weinberg expectations based on the exact test (in all cases, the

data were shuffled 2000 times) were found. Linkage

disequilibrium has been tested using shuffling test for all

possible combinations between loci obtaining an exact

probability upper than 0.05 indicating independence of loci

in all cases. The combined power of discrimination (PD) and

the combined chance of exclusion (CE) for the 18 studied loci

were >0.999999999 and 0.999999989, respectively.

A comparison of the allele frequencies in the population

under study has been performed with other studies with Central

American and Caribbean populations (Table 2). No statistically

significant differences were found with other population studies

of Costa Rica [8,9]. However, statistically significant differ-

ences were found with the populations of Honduras [10],

Nicaragua [11], El Salvador [12] and Mexico [13,14] (in all

cases, p < 0.00001).

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Table 1

Observed allele frequencies for 18 STR loci in the Costa Rican population

Allele D3S1358 VWA FGA D8S1179 D21S11 D18S51 D5S818 D13S317 D7S820 D16S539 TH01 TPOX CSF1PO Penta D Penta E D19S433 D2S1338 SE33

2.2 0.0050

3.2 0.0010

5 0.0020 0.0111 0.0504

6 0.0010 0.3538 0.0090 0.0060

7 0.0242 0.0131 0.1986 0.0010 0.0091 0.0111 0.1200

8 0.0060 0.0040 0.0978 0.1260 0.0192 0.0827 0.4274 0.0030 0.0232 0.0222

9 0.0091 0.0958 0.1653 0.0897 0.1330 0.1401 0.0847 0.0192 0.1754 0.0121

9.3 0.2157

10 0.0625 0.0111 0.0494 0.0625 0.2530 0.1845 0.0071 0.0494 0.2621 0.2107 0.0524

10.2 0.0010

11 0.0040 0.0696 0.0151 0.3760 0.2278 0.2702 0.2510 0.3236 0.2752 0.2359 0.1109 0.0090

11.2 0.0052

12 0.0010 0.1290 0.1179 0.3206 0.2611 0.2107 0.2681 0.1028 0.3669 0.1593 0.1673 0.0700 0.0026

12.2 0.0080 0.0026

13 0.0071 0.0050 0.3206 0.1290 0.1270 0.1190 0.0312 0.1270 0.0020 0.0534 0.1139 0.0887 0.2680

13.2 0.0020 0.0550 0.0026

14 0.1048 0.0827 0.2247 0.1482 0.0020 0.0665 0.0060 0.0171 0.0111 0.0333 0.1028 0.3060 0.0183

14.2 0.0380

15 0.3448 0.1452 0.1361 0.1179 0.0111 0.1089 0.1480 0.0288

15.2 0.0560

16 0.2248 0.3145 0.0403 0.1341 0.0020 0.0423 0.0250 0.0290 0.0550

16.2 0.0140

17 0.1643 0.2600 0.0020 0.0010 0.1431 0.0010 0.0443 0.0010 0.1770 0.0942

17.2 0.0020 0.0026

18 0.1442 0.1159 0.0060 0.0010 0.0675 0.0151 0.0370 0.1230

18.2 0.0020

19 0.0081 0.0625 0.0887 0.0544 0.0252 0.1270 0.0576

20 0.0010 0.0081 0.0736 0.0222 0.0252 0.2000 0.0340

21 0.0020 0.0887 0.0131 0.0081 0.0220 0.0236

21.2 0.0157

22 0.1431 0.0171 0.0040 0.0940 0.0079

22.2 0.0060 0.0340

23 0.1270 0.0030 0.1440 0.0052

23.2 0.0010 0.0183

24 0.1925 0.0020 0.0840 0.0026

24.2 0.0020 0.0314

25 0.1633 0.0010 0.0680

25.2 0.0020 0.0419

26 0.0786 0.0180

27 0.0202 0.0262 0.0916

27.2 0.0628

28 0.0030 0.0867

28.2 0.0707

29 0.0030 0.2460

29.2 0.0759

30 0.0010 0.2510

30.2 0.0222 0.0497

31 0.0585

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731.2 0.0756 0.0314

32 0.0212

32.1 0.0026

32.2 0.1482 0.0052

33 0.0030

33.2 0.0444 0.0026

34 0.0030

34.2 0.0060

35 0.0030

35.2

36 0.0010

N 496 496 496 496 496 496 496 496 496 496 496 496 496 496 496 500 500 191

MAF 0.0060 0.0061 0.0067 0.0061 0.0063 0.0065 0.0058 0.0062 0.0061 0.0060 0.0059 0.0055 0.0058 0.0063 0.0068 0.0061 0.0064 0.0171

H 0.7802 0.8044 0.8891 0.8004 0.8327 0.8669 0.7319 0.8165 0.7944 0.7823 0.7601 0.6573 0.7198 0.8347 0.9052 0.7960 0.8600 0.9110

PD 0.9104 0.9207 0.9677 0.9324 0.9523 0.9755 0.8803 0.9440 0.9233 0.9270 0.9045 0.8618 0.8684 0.9478 0.9831 0.9350 0.9688 0.9882

CE 0.5629 0.6073 0.7732 0.5998 0.6610 0.7285 0.4792 0.6301 0.5886 0.5665 0.5272 0.3653 0.4595 0.6649 0.8061 0.5916 0.7147 0.8179

PIC 0.7376 0.7582 0.8583 0.7752 0.8150 0.8752 0.6842 0.7968 0.7626 0.7660 0.7256 0.6422 0.6663 0.8063 0.8960 0.7733 0.8543 0.9319

p 0.4280 0.0685 0.1095 0.6415 0.3570 0.6955 0.7395 0.8165 0.2380 0.0780 0.8635 0.1280 0.7750 0.5070 0.8455 0.9325 0.5490 0.5135

N, sample size; MAF, minimum allele frequency; H, observed heterozygosity; PD, power of discrimination; CE, probability of paternity exclusion; PIC, polymorphic information content; p, Hardy–Weinberg

equilibrium. Exact test based on 2000 shufflings.

Table 2

Comparative analysis (where it has been possible) between this sample of Costa Rica (CR) and other neighboring populations: other populations of Costa Rica (CR2 and CR3) [8,9], Honduras (HO) [10], Nicaragua (NI)

[11], El Salvador (ES) [12] and Mexico (ME1 and ME2) [13,14]

Locus CR vs. CR2 CR vs. CR3 CR vs. HO CR vs. NI CR vs. ES CR vs. ME1 CR vs. ME2

D3S1358 0.6210 0.0000* 0.0002*

VWA 0.4367 0.9605 0.1060 0.0262* 0.0150* 0.0006* 0.0280*

FGA 0.5390 0.0427* 0.4852

D8S1179 0.4116 0.3299 0.4633

D21S11 0.0537 0.0094* 0.0045*

D18S51 0.7213 0.0299* 0.3645

D5S818 0.2783 0.0000* 0.0007*

D13S317 0.2545 0.8489 0.0322* 0.0391* 0.0001* 0.0021*

D7S820 0.1358 0.7558 0.0003* 0.1291 0.0551 0.3738

D16S539 0.0805 0.4814 0.0135* 0.0297* 0.5339

TH01 0.3127 0.4013 0.0357* 0.0000* 0.0002* 0.0002*

TPOX 0.8131 0.3192 0.0302* 0.2244 0.0000* 0.0003*

CSF1PO 0.2145 0.0837 0.3252 0.9909 0.6262

Penta D 0.9128

Penta E 0.2315

D19S433 0.0000*

D2S1338 0.0012*

* p-value < 0.05.

A. Rodrıguez et al. / Forensic Science International 168 (2007) 85–8888

In conclusion, a Costa Rican population database has been

established for the 18 STR systems studied. These systems have

been shown to be useful tool for personal identification.

This paper follows the guidelines for publication of

population data requested by the journal [15].

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