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Development of two multiplex PCR systems for the analysis of 14 X-chromosomal STR loci in a southern Brazilian population sample

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Abstract

We developed two multiplex systems for the coamplification of X-chromosomal short tandem repeats (STRs). X-Multiplex 1 consisted of DXS6807, DXS6800, DXS7424, DXS101, GATA172D05 and HPRTB and X-Multiplex 2 consisted of DXS8378, DXS9898, DXS6801, DXS6809, DXS6789, DXS7133, DXS8377 and DXS7423. In addition, we present allele frequencies for these loci in a south Brazilian population comprising 124 females and 141 males and haplotype frequencies of linked markers for males. Hardy–Weinberg equilibrium (HWE) was tested in the female sample and no significant deviations were found after applying Bonferroni’s correction. Linkage disequilibrium (LD) tests were performed for all pairs of loci and three significant results, out of 91 pairwise comparisons, were obtained. We did not find any evidence of linkage disequilibrium between close or linked markers. The power of discrimination in females (PDF) varied between 0.832 for DXS6801 and 0.987 for DXS8377. DXS6801 was the least informative marker (PIC = 0.605), while DXS8377 was the most polymorphic (PIC = 0.911), followed by DXS101 (PIC = 0.872). Genetic distances were estimated for each STR marker applying the calculation of F ST between our total sample and other studies from Brazil, Europe, Asia and Africa. The most distant populations were Japan, Korea, China, Ghana and Uganda.

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References

  1. Asamura H, Sakai H, Kobayashi K, Ota M, Fukushima H (2006) MiniX–STR multiplex system population study in Japan and application to degraded DNA analysis. Int J Legal Med 120:174–181

    Article  PubMed  CAS  Google Scholar 

  2. Shin SH, Yu JS, Park SW, Min GS, Chung KW (2005) Genetic analysis of 18 X-linked short tandem repeat markers in Korean population. Forensic Sci Int 147:35–41

    Article  PubMed  CAS  Google Scholar 

  3. Pereira R, Gomes I, Amorim A, Gusmão L (2007) Genetic diversity of 10 X chromosome STRs in northern Portugal. Int J Legal Med 121:192–197

    Article  PubMed  Google Scholar 

  4. Turrina S, Atzei R, Filippini G, Leo DD (2007) Development and forensic validation of a new multiplex PCR assay with 12 X-chromosomal short tandem repeats. Forensic Sci Int Genet 1:201–204

    Article  PubMed  Google Scholar 

  5. Poetsch M, El-Mostaqim D, Tschentscher F, Browne ENL, Timmann C, Hortsmann RD, Wurmb-Schwark N (2009) Allele frequencies of 11 X-chromosomal loci in a population sample from Ghana. Int J legal Med 123:81–83

    Article  PubMed  Google Scholar 

  6. Desmarais D, Zhong Y, Chakraborty R, Perreault C, Busque L (1998) Development of a highly polymorphic STR marker for identity testing purposes at the human androgen receptor gene(HUMARA). J Forensic Sci 43:1046–1049

    PubMed  CAS  Google Scholar 

  7. Gomes I, Prinz M, Pereira R, Meyers C, Mikulasovich RS, Amorim A, Carracedo A, Gusmão L (2007) Genetic analysis of three US population groups using an X-chromosomal STR decaplex. Int J Legal Med 121:198–203

    Article  PubMed  Google Scholar 

  8. Hering S, Kuhlisch E, Szibor R (2001) Development of the X-linked tetrameric microsatellite marker HumDXS6789 for forensic purposes. Forensic Sci Int 119:42–46

    Article  PubMed  CAS  Google Scholar 

  9. Edelmann J, Hering S, Kuhlisch E, Szibor R (2002) Validation of the STR DXS7424 and the linkage situation on the X-chromosome. Forensic Sci Int 125:217–222

    Article  PubMed  CAS  Google Scholar 

  10. Rodrigues EMR, Leite FPN, Hutz MH, Palha TJBF, Santos AKCR, Santos SEB (2008) A multiplex PCR for 11 X chromosome STR markers and population data from a Brazilian Amazon Region. Forensic Sci Int Genet 2:154–158

    Article  Google Scholar 

  11. Edelmann J, Szibor R (1999) Validation of the HumDXS6807 short tandem repeat polymorphism for forensic application. Electrophoresis 20:2844–2846

    Article  PubMed  CAS  Google Scholar 

  12. Edelmann J, Deichsel D, Hering S, Plate I, Szibor R (2002) Sequence variation and allele nomenclature for the X-linked STRs DXS9895, DXS8378, DXS7132, DXS6800, DXS7133, GATA172D05, DXS7423 and DXS8377. Forensic Sci Int 129:99–103

    Article  PubMed  CAS  Google Scholar 

  13. Edelmann J, Szibor R (2001) DXS101: a highly polymorphic X-linked STR. Int J Legal Med 114:301–304

    Article  PubMed  CAS  Google Scholar 

  14. Poetsch M, Petersmann H, Repenning A, Lignitz E (2005) Development of two pentaplex systems with X-chromosomal STR loci and their allele frequencies in a northeast German population. Forensic Sci Int 155:71–76

    Article  PubMed  CAS  Google Scholar 

  15. Hering S, Szibor R (2000) Development of the X-linked tetrameric microsatellite marker DXS9898 for forensic purposes. J Forensic Sci 45:929–931

    PubMed  CAS  Google Scholar 

  16. Edelmann J, Szibor R (2005) Validation of the X-linked STR DXS6801. Forensic Sci Int 148:219–220

    Article  PubMed  CAS  Google Scholar 

  17. Robino C, Giolitti A, Gino S, Torre C (2006) Development of two multiplex PCR systems for the analysis of 12 X-chromosomal STR loci in a northwestern Italian population sample. Int J Legal Med 120:315–318

    Article  PubMed  CAS  Google Scholar 

  18. Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evol Bioinform Online 1:47–50

    CAS  Google Scholar 

  19. Abramson JH (2011) WINPEPI updated: computer programs for epidemiologists, and their teaching potential. Epidemiol Perspect Innov 8:1

    Article  PubMed  Google Scholar 

  20. Finner H (1990) Some new inequalities for the range distribution with application to the determination of optimum significance levels of multiple range tests. J Am Stat Assoc 85:191–194

    Google Scholar 

  21. Botstein D, White RI, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331

    PubMed  CAS  Google Scholar 

  22. Nei M, Roychoudhury AK (1974) Sampling variances of heterozygosity and genetic distance. Genetics 76:379–390

    PubMed  CAS  Google Scholar 

  23. Slatkin M (2008) Linkage disequilibrium — understanding the evolutionary past and mapping the medical future. Nat Rev Genet 9:477–485

    Article  PubMed  CAS  Google Scholar 

  24. Amorim CEG, Wang S, Marrero AR, Salzano FM, Ruiz-Linares A, Bortolini MC (2011) X-chromosomal genetic diversity and linkage disequilibrium patterns in Amerindians and Non-Amerindian populations. Am J Hum Biol 23:299–304

    Article  PubMed  Google Scholar 

  25. Tavares CC, Gusmão L, Domingues C, Domingues P, Silva DA, Aquino J, Peixe C, Amorim A, Carvalho EF (2008) Population data for six X-chromosome STR loci in a Rio de Janeiro (Brazil) sample: usefulness in forensic casework. Forensic Sci Int Genet Suppl Ser 1:164–166

    Article  Google Scholar 

  26. Kang L, Li S (2006) X-chromosome STR polymorphism of Luoba Ethnic Group living in Tibet (SW China). Forensic Sci Int 156:88–89

    Article  PubMed  CAS  Google Scholar 

  27. Aler M, Sánchez-Diz P, Gomes I, Gisbert M, Carracedo A, Amorim A, Gusmão L (2007) Genetic data of 10 X-STRs in a Spanish population sample. Forensic Sci Int 173:193–196

    Article  PubMed  CAS  Google Scholar 

  28. Gomes I, Pereira V, Gomes V, Prata MJ, Pinto N, Carracedo A, Amorim A, Gusmão L (2009) The Karimojong from Uganda: genetic characterization using an X-STR decaplex system. Forensic Sci Int Genet 3:127–128

    Article  Google Scholar 

  29. Martins JA, Costa JC, Paneto GG, Gusmão L, Sánchez-Diz P, Carracedo A, Cicarelli RMB (2009) Genetic data of 10 X-chromosomal loci in Vitória population (Espírito Santo State, Brazil). Forensic Sci Int Genet, in press

  30. Cainé LM, Zarrabeitia MT, Riancho JA, Pinheiro MF (2010) Genetic data of a Brazilian population sample (Santa Catarina) using an X-STR decaplex. J Forensic Leg Med 17:272–274

    Article  PubMed  Google Scholar 

  31. Martins JA, Costa JC, Paneto GG, Figueiredo RF, Gusmão L, Sánchez-Diz P, Carracedo A, Cicarelli RM (2010) Genetic profile characterization of 10 X-STRs in four populations of the southeastern region of Brazil. Int J Legal Med 124:427–432

    Article  PubMed  Google Scholar 

  32. Leite FPN, Santos SEB, Rodriguez EMR, Callegari-Jacques SM, Demarchi DA, Tsuneto LT, Petzl-Erler ML, Salzano FM, Hutz MH (2009) Linkage disequilibrium patterns and genetic structure of Amerindian and non-Amerindian Brazilian populations revealed by long-range X-STR markers. Am J Phys Anthropol 139:404–412

    Article  PubMed  Google Scholar 

  33. Ribeiro-Rodrigues EM, de Palha T J, Bittencourt EA, Ribeiro-Dos-Santos A, Santos S (2011) Extensive survey of 12 X-STRs reveals genetic heterogeneity among Brazilian populations. Int J Legal 125:445–452

    Article  Google Scholar 

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Acknowledgements

This work was supported by Fundo de Incentivo à Pesquisa e Eventos do Hospital de Clínicas de Porto Alegre (FIPE-HCPA) and the Brazilian Higher Education Training Program (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior [CAPES]). The authors would like to acknowledge Steven Read (Micropathology Ltd), Leonor Gusmão (Institute of Pathology and Molecular Immunology of the University of Porto, Portugal), Carlos Eduardo Guerra Amorim and Sidia Maria Callegari-Jacques (Department of Genetics and Department of Statistics, Federal University of Rio Grande do Sul).

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Authors and Affiliations

  1. Postgraduate Program in Medicine, Medical Sciences, School of Medicine, Federal University of Rio Grande do Sul, Porto Alegre, Brazil

    Larissa Siqueira Penna & Patricia Hartstein Salim

  2. Department of Immunology, Hospital de Clínicas, Porto Alegre, Brazil

    Fernanda Gamio Silva, Gisele Ewald, Mariana Jobim & Luiz Fernando Jobim

  3. Department of Gynecology and Obstetrics, Hospital de Clínicas, Porto Alegre, Brazil

    José Antônio de Azevedo Magalhães

  4. Department of Internal Medicine, Faculty of Medicine, Federal University of Rio Grande do Sul, Porto Alegre, Brazil

    Luiz Fernando Jobim

  5. Serviço de Imunologia, 2°andar, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, Bairro Bom Fim, CEP 90035-903, Porto Alegre, RS, Brazil

    Larissa Siqueira Penna & Luiz Fernando Jobim

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  1. Larissa Siqueira Penna
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  2. Fernanda Gamio Silva
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  3. Patricia Hartstein Salim
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  4. Gisele Ewald
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  5. Mariana Jobim
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  6. José Antônio de Azevedo Magalhães
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Correspondence to Larissa Siqueira Penna or Luiz Fernando Jobim.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary Table 1

Allele frequencies distribution of 14 X-STRs (n=265, 124 females, 141 males, 389 chromosomes) (DOC 376 kb)

Supplementary Table 2

Haplotype of linked markers DXS6801, DXS6809 and DXS6789 in 141 males from Rio Grande do Sul (DOC 109 kb)

Supplementary Table 3

Haplotype of linked markers DXS7424 and DXS101 in 141 males from Rio Grande do Sul (DOC 85 kb)

Supplementary Table 4

Haplotype of linked markers DXS8377 and DXS7423 in 141 males from Rio Grande do Sul (DOC 87 kb)

Supplementary Table 5

Statistical parameters for 14 X-STRs in Southern Brazilian Population (DOC 69 kb)

Supplementary Table 6

Genetic distances between our population and other Brazilian, European, Asian and African studies (F ST values) (DOC 130 kb)

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Penna, L.S., Silva, F.G., Salim, P.H. et al. Development of two multiplex PCR systems for the analysis of 14 X-chromosomal STR loci in a southern Brazilian population sample. Int J Legal Med 126, 327–330 (2012). https://doi.org/10.1007/s00414-011-0629-7

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  • DOI: https://doi.org/10.1007/s00414-011-0629-7

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