Volume 3, Issue 2, Pages e35-e38 (March 2009)

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ABSTRACT

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15 STR loci frequencies with mutation rates in the population from Rio Grande do Sul, Southern Brazil

Received 21 February 2008; accepted 12 May 2008. published online 04 July 2008.

Abstract

Allele frequencies for 15 short tandem repeats (STR) loci were obtained from a sample of 2038 individuals undergoing paternity testing. The population is from Rio Grande do Sul, Brazil. The loci are the most commonly used in forensic and paternity testing, being analysed by the AmpFlSTR® Identifiler (Applied Biosystems) commercial kit. The most polymorphic locus was D2S1338. Mutation rates were ascertained from this population sample. All the loci analysed reached the Hardy–Weinberg equilibrium. The results of genetic distance are consistent with the European-derived origins of Rio Grande do Sul population.

Keywords: Allele frequencies, Short tandem repeats, AmpFlSTR® identifiler, Southern Brazilian population

Article Outline

• Abstract

• 1. Population

• 2. Extraction

• 3. PCR

• 4. Typing

• 5. Results

• 6. Quality control

• 7. Analysis of data

• 8. Access to the data

• 9. Other remarks

• Acknowledgment

• References

• Copyright

1. Population

Blood sample from 2038 unrelated individuals were obtained from 1019 paternity testing cases (mothers and fathers) in Rio Grande do Sul population.

2. Extraction

Genomic DNA was purified from dried blood samples preserved in FTA cards (Whatman Bioscience, Cambridge, UK) following the manufacturer's instructions.

3. PCR

Simultaneous amplification of 15 STR loci (multiplex PCR) plus the gender determination marker, Amelogenin, were performed by using the AmpFlSTR® Identifiler™ PCR Amplification Kit (Applied Biosystems, Foster City, CA, USA) according to the user's manual recommendations.

4. Typing

The separation and genotyping of the Identifiler PCR products were carried out on capillary electrophoresis at ABI PRISM® 3130xl Genetic Analyzer (Applied Biosystems). All genotypes were analyzed using the GeneMapper® ID 3.2 software.

5. Results

The allele frequencies, mutation rates and statistic parameters for the 15 STR loci in Rio Grande do Sul population are shown in Table 1.

Table 1.

Allele frequencies of 15 STR loci, parameters of forensic interest, results of exact for HWE and sex-specific mutation rates for Rio Grande do Sul (Brazil) population sample


Alelle	D8S1179	D21S11	D7S820	CSF1PO	D3S1358	TH01	D13S317	D16S539	D2S1338	D19S433	vWA	TPOX	D18S51	D5S818	FGA
5						0.0014		0.0002				0.0007
6						0.2265		0.0002				0.0132
7			0.0123	0.0106		0.2154	0.0007					0.0042		0.0256
8	0.0103		0.1397	0.0103		0.1383	0.1007	0.0209				0.4821		0.0103
9	0.0071		0.1275	0.0204		0.1612	0.0891	0.1460		0.0002		0.1190		0.0457
9.3						0.2467
10	0.0700		0.2760	0.2640		0.0105	0.0572	0.0841		0.0017		0.0606	0.0125	0.0549
10.2													0.0007
11	0.0805		0.2453	0.2997	0.0003		0.2863	0.2830		0.0119	0.0027	0.2657	0.0056	0.3323
12	0.1414		0.1680	0.3166	0.0020		0.2943	0.2785		0.1000		0.0510	0.1290	0.3424
12.2										0.0117
13	0.2980		0.0275	0.0703	0.0034		0.1206	0.1635	0.0002	0.2421	0.0025	0.0025	0.1069	0.1754
13.2										0.0399			0.0005
14	0.2351		0.0035	0.0074	0.1006		0.0496	0.0219	0.0002	0.2997	0.0810	0.0010	0.1845	0.0122
14.2										0.0280			0.0002
15	0.1254		0.0002	0.0007	0.2934		0.0015	0.0017	0.0025	0.1587	0.1222		0.1455	0.0012
15.2					0.0003					0.0496
16	0.0270				0.2645				0.0429	0.0370	0.2616		0.1418		0.0014
16.2										0.0156
17	0.0037				0.1950				0.2131	0.0020	0.2625		0.1149		0.0015
17.2										0.0017
18	0.0015				0.1278				0.0914		0.1796		0.0670		0.0096
18.2										0.0002					0.0022
19					0.0120				0.1234		0.0773		0.0553		0.0746
19.2															0.0007
20					0.0007				0.1291		0.0096		0.0186		0.1031
21									0.0477		0.0010		0.0098		0.1582
21.2													0.0005		0.0012
22									0.0571				0.0047		0.1695
22.2															0.0044
23									0.1279				0.0010		0.1491
23.2															0.0032
24		0.0003							0.0794				0.0008		0.1479
24.2		0.0007													0.0005
25		0.0010							0.0668						0.1118
25.2		0.0002
26		0.0012							0.0161						0.0427
27		0.0251							0.0020				0.0002		0.0130
28		0.1507							0.0002						0.0030
29		0.2170													0.0010
29.2		0.0010
30		0.2495													0.0002
30.2		0.0333													0.0010
31		0.0635
31.2		0.1027													0.0002
32		0.0089
32.2		0.0936
33		0.0010
33.2		0.0355
34		0.0027
34.2		0.0044
35		0.0057
35.2		0.0005
36		0.0007
37		0.0005
38		0.0003
45.2															0.0002

N	4074	4060	4072	4068	4076	4076	4072	4068	4028	4032	4060	4076	4072	4072	4060
FMR	0.0019	0.0028	0.0000	0.0019	0.0000	0.0000	0.0009	0.0000	0.0000	0.0000	0.0009	0.0000	0.0019	0.0000	0.0009
MMP	0.0019	0.0019	0.0009	0.0037	0.0000	0.0000	0.0019	0.0028	0.0038	0.0010	0.0057	0.0019	0.0019	0.0028	0.0057
HO	0.7997	0.8310	0.7903	0.7365	0.7659	0.7846	0.7785	0.7797	0.8724	0.8046	0.8025	0.6590	0.8644	0.7397	0.8601
HE	0.8081	0.8417	0.7990	0.7348	0.7795	0.7966	0.7933	0.7865	0.8798	0.8099	0.8030	0.6765	0.8755	0.7353	0.8716
PCI	0.7827	0.8231	0.7692	0.6872	0.7447	0.7644	0.7649	0.7543	0.8681	0.7857	0.7747	0.6308	0.8624	0.6920	0.8576
PD	0.937	0.956	0.930	0.882	0.918	0.928	0.929	0.922	0.973	0.939	0.922	0.849	0.972	0.895	0.970
PE	0.598	0.655	0.584	0.482	0.536	0.566	0.554	0.558	0.740	0.600	0.396	0.365	0.721	0.501	0.712

P	0.4992	0.8225	0.0063a	0.3726	0.3393	0.8668	0.0295a	0.4033	0.3773	0.8238	0.8994	0.2813	0.5571	0.9944	0.7445

N, Number of chromosomes; FMR, female mutation rate; MMP, male mutation rate; Ho, observed heterozygosity; He, expected heterozygosity; PIC, polymorphism information content; PD, power of discrimination; PE, power of exclusion; P, Hardy–Weinberg equilibrium exact probability tests.

P: Not statistically significant after Bonferroni's correction.

6. Quality control

All steps were according to the Laboratory internal control standards and kit controls.

7. Analysis of data

Statistical analysis was performed using Cervus version 3.0.3 (www.fieldgenetics.com) [1], [2], PowerStats V12 software [3] and DISPAN program [4] for genetic distances. Mutations were assumed and counted in cases of single discrepancies between parent and child at a locus when at least 14 other STR loci were consistent with paternity and/or maternity. All mutations were confirmed by repeating the genotyping of the trio.

8. Access to the data

Request to email: paternidade@fepps.rs.gov.br

9. Other remarks

All the loci analysed reached the Hardy–Weinberg equilibrium in the population studied (P>0.05), except D7S820 locus (P=0.0063) and D13S317 (P=0.0295). When the Bonferroni correction [5] was employed using the number of loci analysed, the differences observed were not statistically significant. The polymorphism information content (PIC) values ranged from 0.6308 for TPOX to 0.8681 for D2S1338. Of the 1019 paternity testing cases, mutations of single locus were observed in 50 cases. The mutations rates at vWA and FGA were highest (0.66%, each). Comparisons with six other populations [6], [7], [8], [9], [10], [11] from Rio de Janeiro (Brazil), São Paulo—European-derived (Brazil), Amazônia (Brazil), Açores (Portugal), North of Italy and Bavaria (Germany) were performed in terms of genetic distances, using vWA, D5S818, D7S820 and D13S317 allele frequencies data. The populations of Rio de Janeiro and São Paulo are closer to the population of Rio Grande do Sul (0.0006, each) followed by the population of Açores (0.0008), Bavaria (0.0008), North of Italy (0.0012) and Amazônia (0.0020). These results are consistent with the European-derived origins of Rio Grande do Sul, colonized mainly by Portuguese, Italian and German populations. Amazônia State, situated on the north of Brazil, is geographically distant from Rio Grande do Sul State and the population is formed by the miscegenation of Europeans, Africans, and Amerindians. In conclusion, the 15 STR loci analysed are a powerful tool for forensic identification and paternity testing in Rio Grande do Sul population. This paper follows the guidelines for publication of population data requested by the journal [12].

Acknowledgements

This work was supported by Laboratório de Investigação de Paternidade, CDCT/FEPPS. Covenant Tribunal de Justiça do Estado do Rio Grande do Sul.

References

[1]. [1]Marshall TC, Slate J, Kruuk LEB, Pemberton JM. Statistical confidence for likelihood-based paternity inference in natural populations. Mol. Ecol. 1998;7:639–655Available on the Internet at: http://www.fieldgenetics.com. MEDLINE | CrossRef

[2]. [2]Slate J, Marshall TC, Pemberton JM. A retrospective assessment of the accuracy of the paternity inference program CERVUS. Mol. Ecol. 2000;9:801–808. MEDLINE | CrossRef

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[6]. [6]Goés ACS, Silva DA, Gil EHF, Silva MTD, Pereira RW, Carvalho EF. Allele frequencies data and statistic parameters for 16 STR loci D19S433, D2S1338, CSF1PO, D16S539, D7S820, D21S11, D18S51, D13S317, D5S818, FGA, Penta E, TH01, vWA, D8S1179, TPOX, D3S1358 in the Rio de Janeiro population, Brazil. Forensic Sci. Int. 2004;140:131–132. Abstract | Full Text | Full-Text PDF (291 KB) | CrossRef

[7]. [7]Bydlowski SP, Moura-Neto RS, Soares RPS, Silva R, Debes-Bravo AA, Morganti L. Genetic data on 12 STRs (F13A01, F13B, FESFPS, LPL, CSF1PO, TPOX, TH01, vWA, D16S539, D7S820, D13S317, D5S818) from four ethnic groups of São Paulo, Brazil. Forensic Sci. Int. 2003;135:67–71. Abstract | Full Text | Full-Text PDF (74 KB) | CrossRef

[8]. [8]Rodrigues EMR, Palha TJBF, Santos SEB. Allele frequencies data and statistic parameters for 13 STR loci in a population of the Brazilian Amazon Region. Forensic Sci. Int. 2007;168:244–247. Abstract | Full Text | Full-Text PDF (228 KB) | CrossRef

[9]. [9]Velosa RG, Fernandes AT, Brehm A. Genetic profile of the Açores Archipelago population using the new PowerPlex 16 System Kit. Forensic Sci. Int. 2002;129:68–71. Abstract | Full Text | Full-Text PDF (62 KB) | CrossRef

[10]. [10]Andreini E, Frison S, Longhi E, Torelli R, De Fazio N, Poli F. Allele frequencies for nine STR loci (D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820) in the Italian population. Forensic Sci. Int. 2007;168:e13–316. Abstract | Full Text | Full-Text PDF (158 KB) | CrossRef

[11]. [11]Anslinger K, Rolf B, Keil W. Evaluation and application of the AmpFlSTR Profiler Plus PCR amplification kit in a Bavarian population sample. Int. J. Legal Med. 2001;114:278–280. MEDLINE | CrossRef

[12]. [12]Lincoln P, Carracedo A. Publication of population data of human polymorphism. Forensic Sci. Int. 2000;110:03–05.

a Laboratório de Investigação de Paternidade, Centro de Desenvolvimento Científico e Tecnológico (CDCT), Fundação Estadual de Produção e Pesquisa em Saúde (FEPPS), Av. Ipiranga, 5400, Bairro Jardim Botânico, CEP 90610-000 Porto Alegre, RS, Brazil

b Programa de Pós-graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Bairro Agronomia, CEP 91501-970 Porto Alegre, RS, Brazil

c Setor de Biologia Molecular, Laboratório de Perícias, Instituto Geral de Perícias, Setor de Biologia Molecular, Av. Azenha, 255, Azenha, CEP 90160-000 Porto Alegre, RS, Brazil

d Universidade Luterana do Brasil, Curso de Pós-graduação em Diagnóstico Genético Molecular, Curso de Pós-graduação Genética e Toxicologia Aplicada, Av. Farroupilha, 8001, Bairro São José, CEP 92425-900 Canoas, Rio Grande do Sul, Brazil

Corresponding author at: Fundação Estadual de Produção e Pesquisa em Saúde, Centro de Desenvolvimento Científico e Tecnológico, Laboratório de Investigação de Paternidade, Av. Ipiranga, 5400, Jardim Botânico, CEP 90610-000 Porto Alegre, Rio Grande do Sul, Brazil. Tel.: +55 51 33520336; fax: +55 51 33520336.

PII: S1872-4973(08)00084-7

doi:10.1016/j.fsigen.2008.05.006

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