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Genetic characterization of 32 X-InDels in a population sample from São Paulo State (Brazil)

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Abstract

X-chromosomal markers can be useful in some forensic cases, where the analysis of the autosomal markers is not conclusive. In this study, a population sample of 500 unrelated individuals born in São Paulo State was characterized for 32 X-InDel markers. No deviations from the Hardy–Weinberg equilibrium were detected, except for MID1361. The 32 X-InDels showed an accumulated power of discrimination of 0.9999999999993 in females and 0.99999993 in males and an exclusion chance of 0.999996 in trios and 0.99995 in duos. São Paulo showed lower genetic distances to the Colombian admixed and European populations than to Native American, Asian, or African populations. Ancestry analysis revealed 41.8% European, 31.6% African, and 26.6% Native American contributions. Segregation analysis was performed in 101 trios, and the mutation rate was estimated to be low.

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References

  1. Gomes C, Magalhães M, Alves C, Amorim A, Pinto N, Gusmão L (2012) Comparative evaluation of alternative batteries of genetic markers to complement autosomal STRs in kinship investigations: autosomal indels vs. X-chromosome STRs. Int J Legal Med 126:917–921. https://doi.org/10.1007/s00414-012-0768-5

    Article  PubMed  Google Scholar 

  2. Pinto N, Magalhães M, Conde-Sousa E, Gomes C, Pereira R, Alves C, Gusmão L, Amorim A (2013) Assessing paternities with inconclusive STR results: the suitability of bi-allelic markers. Forensic Sci Int Genet 7:16–21. https://doi.org/10.1016/j.fsigen.2012.05.002

    Article  CAS  PubMed  Google Scholar 

  3. Szibor R, Krawczak M, Hering S, Edelmann J, Kuhlisch E, Krause D (2003) Use of X-linked markers for forensic purposes. Int J Legal Med 117:67–74. https://doi.org/10.1007/s00414-002-0352-5

    Article  CAS  PubMed  Google Scholar 

  4. Szibor R (2007) X-chromosomal markers: past, present and future. Forensic Sci Int Genet 1:93–99. https://doi.org/10.1016/j.fsigen.2007.03.003

    Article  PubMed  Google Scholar 

  5. Tillmar AO, Kling D, Butler JM, Parson W, Prinz M, Schneider PM, Egeland T, Gusmão L (2017) DNA Commission of the International Society for Forensic Genetics (ISFG): guidelines on the use of X-STRs in kinship analysis. Forensic Sci Int Genet 29:269–275. https://doi.org/10.1016/j.fsigen.2017.05.005

  6. Pinto N, Gusmão L, Amorim A (2011) X-chromosome markers in kinship testing: a generalisation of the IBD approach identifying situations where their contribution is crucial. Forensic Sci Int Genet 5:27–32. https://doi.org/10.1016/j.fsigen.2010.01.011

    Article  CAS  PubMed  Google Scholar 

  7. Freitas NSC, Resque RL, Ribeiro-Rodrigues EM, Guerreiro JF, Santos NPC, Ribeiro-dos-Santos Â, Santos S (2010) X-linked insertion/deletion polymorphisms: forensic applications of a 33-markers panel. Int J Legal Med 124:589–593. https://doi.org/10.1007/s00414-010-0441-9

    Article  PubMed  Google Scholar 

  8. Pereira R, Pereira V, Gomes I, Tomas C, Morling N, Amorim A, Prata MJ, Carracedo Á, Gusmão L (2012) A method for the analysis of 32 X chromosome insertion deletion polymorphisms in a single PCR. Int J Legal Med 126:97–105. https://doi.org/10.1007/s00414-011-0593-2

    Article  PubMed  Google Scholar 

  9. THE 1000 GENOMES PROJECT CONSORTIUM (2015) A global reference for human genetic variation. Nature 526:68–74. https://doi.org/10.1038/nature15393

    Article  Google Scholar 

  10. Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and windows. Mol Ecol Resour 10:564–567. https://doi.org/10.1111/j.1755-0998.2010.02847.x

    Article  PubMed  Google Scholar 

  11. Pinto JC, Prereira V, Marques SL, Amorim A, Alvarez L, Prata MJ (2015) Mirandese language and genetic differentiation in Iberia: a study using X chromosome markers. Ann Hum Biol 42:20–25. https://doi.org/10.3109/03014460.2014.944215

    Article  CAS  PubMed  Google Scholar 

  12. Edelmann J, Kohl M, Dressler J, Hoffmann A (2016) X-chromosomal 21-indel marker panel in German and Baltic populations. Int J Legal Med 130:357–360. https://doi.org/10.1007/s00414-015-1221-3

    Article  PubMed  Google Scholar 

  13. Ferragut JF, Bentayebi K, Pereira R, Castro JA, Amorim a, Ramon C, Picornell A (2017) Genetic portrait of Jewish populations based on three sets of X-chromosome markers: Indels, Alu insertions and STRs. Forensic Sci Int Genet 31:e5–e11. https://doi.org/10.1016/j.fsigen.2017.09.008

    Article  CAS  PubMed  Google Scholar 

  14. Ibarra A, Restrepo T, Rojas W, Castilho A, Amorim A, Martinez B, Burgos G, Ostos H, Álvarez K, Camacho M, Suarez Z, Pereira R Gusmão L (2014) A. et al. Evaluating the X chromosome-specific diversity of Colombian populations using insertion/deletion) polymorphisms. PLoS One 9:e87202. https://doi.org/10.1371/journal.pone.0087202

  15. Caputo M, Amador MA, Santos S, Corach D (2017) Potential forensic use of a 33 X-Indel panel in the Argentinean population. Int J Legal Med 131:107–112. https://doi.org/10.1007/s00414-016-1399-z

    Article  PubMed  Google Scholar 

  16. Pereira V, Tomas C, Sanchez JJ, Syndercombe-Court D, Amorim A, Gusmão L, Prata MJ, Morling N (2015) The peopling of Greenland: further insights from the analysis of genetic diversity using autosomal and X-chromosomal markers. Eur J Hum Genet 23:245–251. https://doi.org/10.1038/ejhg.2014.90

    Article  CAS  PubMed  Google Scholar 

  17. Resque RL, Freitas NS, Rodrigues EM, Guerreiro JF, Santos NP, Ribeiro dos Santos A, Zago MA Santos S (2010) Estimates of interethnic admixture in the Brazilian population using a panel of 24 X-linked insertion/deletion markers. Am J Hum Biol 22:849–852. https://doi.org/10.1002/ajhb.21089

    Article  PubMed  Google Scholar 

  18. Pereira V, Moncada E, Diez IE, Tomas C, Amorim A, Morling N, Gusmão L, Prata MJ (2011) Genetic characterization of Somali and Iraqi populations using a set of 33 X-chromosome Indels. Forensic Sci Int Genet 3:e137–e138. https://doi.org/10.1016/j.fsigss.2011.08.069

    Article  Google Scholar 

  19. Zarrabeitia MT, Alonso A, Martin J (2006) Study of six X-linked tetranucleotide microsatellites: population data from five Spanish regions. Int J Legal Med 120:147–150. https://doi.org/10.1007/s00414-005-0057-7

    Article  PubMed  Google Scholar 

  20. Ossa H, Aquino J, Sierra S, Ramírez A, Carvalho EF, Gusmão L (2015) Analysis of admixture in Native American populations from Colombia. Forensic Sci Int Genet, Supplement Series 5:e332–e333. https://doi.org/10.1016/j.fsigss.2015.09.132

    Article  Google Scholar 

  21. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Moura RR, Coelho AVC, Balbino VQ, Crovella S, Brandão LAC (2015) Meta-analysis of Brazilian genetic admixture and comparison with other Latin America countries. Am J Hum Biol 27:674–680. https://doi.org/10.1002/ajhb.22714

    Article  PubMed  Google Scholar 

  23. Wang S, Ray N, Rojas W, Parra MV, Bedoya G, Gallo C, Poletti G, Mazzotti G, Hill K, Hurtado AM, Camrena B, Nicolini H, Klitz W, Barrantes R, Molina JA, Freimer NB, Bortolini MC, Salzano FM, Petzl-Erler AL, Tsuneto LT, Dipierri JE, Alfaro EL, Bailliet G, Bianchi NO, Lop E, Rothhammer F, Excoffier L, Ruiz-Linares A (2008) Geographic patterns of genome admixture in Latin American Mestizos. PLoS Genet 4:e1000037. https://doi.org/10.1371/journal.pgen.1000037

    Article  PubMed  PubMed Central  Google Scholar 

  24. Aquino JG, Jannuzzi J, Carvalho EF, Gusmão L (2015) Assessing the suitability of different sets of indels in ancestry estimation. Forensic Sci Int 5:e34–e36. https://doi.org/10.1016/j.fsigss.2015.09.014

    Google Scholar 

  25. Campbell CD, Eichler EE (2013) Properties and rates of germline mutations in humans. Trends Genet 29:575–584. https://doi.org/10.1016/j.tig.2013.04.005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Sun JX, Helgason A, Masson G, Ebenesersdóttir SS, Li H, Mallick S, Gnerre S, Patterson N, Kong A, Reich D, Stefansson K (2012) A direct characterization of human mutation based on microsatellites. Nat Genet 44(10):1161–1165. 10.1038/ng.2398

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Authors and Affiliations

  1. Laboratory of Paternity Investigation, School of Pharmaceutical Sciences, São Paulo State University (UNESP), São Paulo, Brazil

    Juliana Martinez, Fernanda Silva Polverari, Flávia Alves de Jesus Silva, Danilo Faustino Braganholi & Regina Maria Barretto Cicarelli

  2. Research Centre for Biochemistry and Molecular Biology, Medical School of São José do Rio Preto (FAMERP), São Paulo, Brazil

    Joyce Aparecida Martins Lopes Ferraz

  3. DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil

    Leonor Gusmão

Authors
  1. Juliana Martinez
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  2. Fernanda Silva Polverari
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  3. Flávia Alves de Jesus Silva
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  7. Regina Maria Barretto Cicarelli
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Correspondence to Juliana Martinez.

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Martinez, J., Polverari, F.S., Silva, F.A. et al. Genetic characterization of 32 X-InDels in a population sample from São Paulo State (Brazil). Int J Legal Med 133, 1385–1388 (2019). https://doi.org/10.1007/s00414-018-01988-w

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