Allele frequencies and haplotypes of 8 Y-chromosomal STRs in the Santa Catarina population of southern Brazil

Forensic Science International 148 (2005) 75–79

Announcement of population data

Allele frequencies and haplotypes of 8 Y-chromosomal STRs in the Santa Catarina population of southern Brazil Laura Caine´*, Francisco Corte-Real, Duarte N. Vieira, Mo´nica Carvalho, Armando Serra, Virgı´nia Lopes, Maria C. Vide National Institute Legal Medicine, 3000-213 Coimbra, Portugal Received 28 July 2003; received in revised form 16 April 2004; accepted 22 April 2004 Available online 24 June 2004

Abstract Allele frequencies and haplotypes of eight Y-chromosomal short tandem repeats (STRs), DYS19, DYS385, DYS389 I, DYS389 II, DYS390, DYS391, DYS392 and DYS393 were determined in a sample of 109 males from Santa Catarina. The origin of this southern Brazilian population is mainly from Portuguese people, namely from Azores archipelago. # 2004 Elsevier Ireland Ltd. All rights reserved. Keywords: Y-chromosomal; Short tandem repeats; Haplotype; Santa Catarina; DNA typing; Population genetics

1. Population

amplified in a thermocycler GeneAmp1 PCR System 9600 (Perkin-Elmer).

A total number of 109 unrelated, autochthonous healthy males from Santa Catarina (Brazil). 4. Typing 2. Extraction Blood stains were collected and air dried. DNA was extracted using the Chelex1 resin [1].

3. PCR Eight Y-chromosomal STRs were analyzed. The pentaplex amplification of DYS19, DYS389 I, DYS389 II, DYS390, and DYS393 loci was performed as described by Gusma˜o et al. [2]. The triplex amplification of DYS391, DYS392 and DYS393 was carried out according to Kloosterman et al. [3] and Jonkisz et al. [4]. The singleplex amplification of DYS385 was complied with the methodology described by Schneider et al. [5]. All loci were * Corresponding author. Tel.: þ351 239 85 42 30; fax: þ351 239 83 6470. E-mail address: [email protected] (L. Caine´).

By ABI PRISM1 377 DNA Sequencer (PE, Applied Biosystems). Fragment sizes were determined automatically using the ABI 377 GeneScan1 Analysis 2.1 Software with local southern method and by comparison with allelic ladders. Alleles were designated according to the published nomenclatures and in concordance with the International Society for Forensic Genetics (ISFG) guidelines for forensic STR analysis [6].

5. Results Table 1 shows the distribution of Y-chromosomal haplotypes obtained for 109 individuals. Table 2 shows the allele frequencies and gene diversity values for each loci.

6. Quality control Proficiency testing of the GEP-ISFG WG.

0379-0738/$ – see front matter # 2004 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.forsciint.2004.04.068

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Table 1 Distribution of Y-STR haplotypes in the Santa Catarina population (N ¼ 109). Ha

DYS19

DYS385

DYS389 I

DYS389 II

DYS390

DYS391

DYS392

DYS393

Nb

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57

12 13 13 13 13 13 13 13 13 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14

11, 10, 11, 12, 12, 13, 14, 15, 16, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 13, 13,

14 13 13 14 12 14 13 14 14 13 14 13 14 11 11 12 12 13 13 13 13 13 13 13 13 13 14 14 13 13 13 13 13 13 12 13 13 13 13 13 13 13 13 13 13 13 15 13 13 12 12 14 12 12 13 12 12

30 29 30 30 30 30 29 31 31 31 30 29 30 26 28 28 29 29 29 29 30 29 29 29 29 29 30 31 30 30 29 29 29 29 27 29 29 29 29 29 29 31 29 29 29 30 32 29 29 28 25 29 28 28 29 28 28

23 24 23 22 23 24 24 24 24 24 23 24 24 24 24 24 24 26 20 23 24 25 24 22 24 24 24 25 23 23 24 25 24 24 24 24 20 25 24 23 24 24 23 24 25 25 25 25 26 22 23 24 23 24 23 22 23

10 10 9 13 10 9 10 10 10 11 11 11 11 11 11 11 11 11 11 11 10 10 11 11 10 12 11 10 11 11 11 10 10 10 11 11 11 10 11 11 11 11 11 10 11 11 11 13 10 10 10 11 10 10 10 10 10

14 13 11 10 11 11 11 11 10 13 13 13 13 13 13 13 13 13 13 13 13 13 13 11 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 12 12 13 13 12 13 13 13 10 11 11 11 13 11 13 11 11 11

13 13 13 13 12 13 13 14 13 13 13 14 13 13 13 13 13 13 13 14 12 13 13 13 12 13 14 11 12 13 14 14 13 13 13 14 13 13 13 13 15 13 13 14 13 13 13 13 12 13 13 12 13 13 12 14 13

1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 1 2 1 1 1 4 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 3

13 13 16 15 18 14 17 17 19 11 10 12 12 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 14 14 14 11 12 13 14 14 14 14 14 14 14 14 14 14 14 14 14 15 12 13 13 13 14 15 15 13 14

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Table 1 (Continued ) Ha

DYS19

DYS385

DYS389 I

DYS389 II

DYS390

DYS391

DYS392

DYS393

Nb

58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95

14 14 14 14 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 16 16 16 16 16 16 16 16

13, 13, 14, 16, 9, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 14, 14, 14, 18, 10, 11, 12, 12, 14, 15, 15, 16,

12 14 14 13 13 13 13 13 13 13 12 12 13 13 13 13 12 12 13 13 13 13 13 14 12 13 12 14 13 13 13 14 14 13 12 12 13 14

29 31 31 30 29 29 29 29 29 28 29 29 29 31 30 29 29 26 29 30 29 29 30 31 28 29 29 32 31 31 30 31 29 30 28 29 29 31

21 23 23 24 25 23 24 24 24 24 24 25 24 25 24 22 23 24 23 24 23 23 22 22 25 24 22 23 23 24 24 25 23 23 21 22 23 21

10 10 10 10 11 11 11 10 11 10 11 11 11 11 11 10 10 11 9 11 11 10 10 10 10 10 11 10 10 10 11 11 10 11 11 9 10 10

11 11 11 11 11 13 13 13 15 13 13 11 13 11 11 11 11 13 11 11 13 12 11 11 11 13 11 12 11 11 13 11 11 11 11 12 12 11

14 12 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 14 12 13 12 14 15 14 12 12 14 16 14 13 13 13 13 13 14 12 15 15

1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1

a b

14 14 15 18 13 12 13 13 13 13 14 14 14 15 16 18 13 14 15 16 16 14 14 14 16 16 14 15 16 19 13 14 12 17 15 16 18 17

Haplotype. Number of individuals observed for each haplotype.

7. Analysis of data Allele frequencies were calculated through the gene counting method. Haplotype and gene diversities for the eight Y-chromosomal STRs were calculated according to Nei [7] using the Arlequin software package [8].

8. Other remarks In this population, a total of 95 different haplotypes were observed, 85 of them being unique. The most frequent haplotype, for the studied systems was 14, 10–13, 13, 29, 24, 11, 13, and 13. The haplotype diversity for all eight

Y-chromosomal STRs loci was 0.9968  0.0019. The data generated show that the eight loci haplotype (DYS19, DYS385, DYS389 I, DYS389, DYS390, DYS391, DYS392, and DYS393) is highly polymorphic and discriminative in Santa Catarina (Brazil) population. Since the origin of Santa Catarina population is mainly from Portuguese people, some comparisons with Portuguese samples were made: Azores and Central Portugal [9] and Madeira archipelago [10]. The gene diversity value did not show significant differences in the compared populations. The alleles 30, 31, 32 in DYS389 II, 20 in DSY390, 13 in DYS391 and 11 and 16 in DYS393 can be found in the Santa Catarina population but not in the Portuguese populations.

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Table 2 Allele/genotype frequencies and gene diversity value at nine Y-STR loci in the Santa Catarina population (N ¼ 109). Allele

DYS19

DYS389 I

DYS389 II

DYS390

DYS391

DYS392

DYS393

Genotype

DYS385

9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 – – – – – – – – – –

– – – 0.0092 0.0734 0.5780 0.2661 0.0734 – – – – – – – – – – – – – – – – – – – – – – – – – –

– – 0.0183 0.2202 0.5963 0.1560 0.0092 – – – – – – – – – – – – – – – – – – – – – – – – – – –

– – – – – – – – – – – – – – – – 0.0092 0.0183 0.0092 0.1193 0.5321 0.1651 0.1284 0.0183 – – – – – – – – – –

– – – – – – – – – – – 0.0275 0.0275 0.0917 0.2661 0.4404 0.1284 0.0183 – – – – – – – – – – – – – – – –

0.0367 0.4312 0.5046 0.0092 0.0183 – – – – – – – – – – – – – – – – – – – – – – – – – – – – –

– 0.0275 0.3853 0.0642 0.5046 0.0092 0.0092 – – – – – – – – – – – – – – – – – – – – – – – – – – –

– – 0.0092 0.1284 0.6606 0.1560 0.0367 0.0092 – – – – – – – – – – – – – – – – – – – – – – – – – –

8–11 9–13 10–10 10–12 10–13 10–14 11–11 11–12 11–13 11–14 11–15 11–16 11–18 12–12 12–13 12–14 12–15 12–16 12–17 12–18 13–13 13–14 13–16 14–14 14–15 14–16 14–17 15–16 15–17 15–18 16–17 16–18 16–19 18–19

0.0092 0.0092 0.0092 0.0275 0.2477 0.0275 0.0092 0.0092 0.0183 0.1835 0.0183 0.0183 0.0183 0.0183 0.0367 0.0183 0.0459 0.0183 0.0092 0.0092 0.0092 0.0826 0.0183 0.0092 0.0275 0.0183 0.0092 0.0092 0.0092 0.0092 0.0092 0.0092 0.0092 0.0092

0.5897

0.5765

0.6641

0.7151

0.5629

0.5973

0.5262

–

0.8962

ha a

Gene diversity value.

As this is the first study concerning data from these Ychromosomal STRs loci in Santa Catarina population, no other comparisons were made. The complete data set is available upon request. This paper follows the guidelines for publication data requested by the journal [11].

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