A GEP-ISFG collaborative study on the optimization of an X-STR decaplex: data on 15 Iberian and Latin American populations

Abstract

In a collaborative work carried out by the Spanish and Portuguese ISFG Working Group (GEP-ISFG), a polymerase chain reaction multiplex was optimized in order to type ten X-chromosome short tandem repeats (STRs) in a single reaction, including: DXS8378, DXS9902, DXS7132, DXS9898, DXS6809, DXS6789, DXS7133, GATA172D05, GATA31E08, and DXS7423. Using this X-decaplex, each 17 of the participating laboratories typed a population sample of approximately 200 unrelated individuals (100 males and 100 females). In this work, we report the allele frequencies for the ten X-STRs in 15 samples from Argentina (Buenos Aires, Córdoba, Río Negro, Entre Ríos, and Misiones), Brazil (São Paulo, Rio de Janeiro, Paraná, and Mato Grosso do Sul), Colombia (Antioquia), Costa Rica, Portugal (Northern and Central regions), and Spain (Galicia and Cantabria). Gene diversities were calculated for the ten markers in each population and all values were above 56%. The average diversity per locus varied between 66%, for DXS7133, and 82%, for DXS6809. For this set of STRs, a high discrimination power was obtained in all populations, both in males (≥1 in 5 × 105) and females (≥1 in 3 × 109), as well as high mean exclusion chance in father/daughter duos (≥99.953%) and in father/mother/daughter trios (≥99.999%). Genetic distance analysis showed no significant differences between northern and central Portugal or between the two Spanish samples from Galicia and Cantabria. Inside Brazil, significant differences were found between Rio de Janeiro and the other three populations, as well as between São Paulo and Paraná. For the five Argentinean samples, significant distances were only observed when comparing Misiones with Entre Ríos and with Río Negro, the only two samples that do not differ significantly from Costa Rica. Antioquia differed from all other samples, except the one from Río Negro.

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Acknowledgments

IPATIMUP is partially supported by Fundação para a Ciência e a Tecnologia, through POCI (Programa Operacional Ciência e Inovação 2010).

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Correspondence to Leonor Gusmão.

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GEP-ISFG (The Spanish-Portuguese Working Group of the International Society for Forensic Genetics)

Electronic supplementary material

Below is the link to the electronic supplementary material.

Fig. S1

DXS9898, DXS9902, and DXS7132 allelic ladders used in the present work (PDF 133 KB)

Fig. S2

Comparative results obtained when using GeneScan-500 LIZ and GeneScan-600 LIZ size standards (Applied Biosystems) in fragment size analysis of the DXS7132 sequenced allelic ladder (PDF 24.7 KB)

Table S1

X-STR marker profiles of the samples distributed with the annual proficiency testing of the GEP-ISFG Working Group (PDF 7.20 KB)

Table S2

List of male haplotypes and female genotypes in all population samples (114 KB)

Table S3

Allele frequency distribution in the studied population samples and forensic parameters; expected probability of exclusion in trios involving daughters (MECT), expected probability of exclusion in mother/son duos (MECD), power of discrimination in females (PDF) and power of discrimination in males (PDM). Observed (Ho) and expected (He) heterozygosity and p values for Hardy–Weinberg test (P-HW) in female samples (PDF 37.2 KB)

Table S4

Pairwise p values of linkage disequilibrium test in male samples for all pairs of loci (DXS or GATA were removed from the beginning of the STR names) (PDF 11.1 KB)

Table S5

Pairwise genetic distances (below the diagonal) and the corresponding p values (above the diagonal) between pairs of populations (PDF 16.0 KB)

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Gusmão, L., Sánchez-Diz, P., Alves, C. et al. A GEP-ISFG collaborative study on the optimization of an X-STR decaplex: data on 15 Iberian and Latin American populations. Int J Legal Med 123, 227–234 (2009). https://doi.org/10.1007/s00414-008-0309-4

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Keywords

  • X-chromosome
  • STRs
  • GEP-ISFG
  • Iberia
  • Latin America