Estimation of the Y-chromosomal short tandem repeat (Y-STR) mutation rates in Turkey

Elif Mertoglu 1 , Gonul Filogluhttp://orcid.org/0000-0002-8807-317X 2 , Tolga Zorlu 2 ,  and Ozlem Bulbulhttp://orcid.org/0000-0003-2920-7614 2
  • 1 Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Istanbul, Turkey
  • 2 Institute of Forensic Sciences, Istanbul University, Istanbul, Turkey
Elif Mertoglu
  • Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Istanbul, Turkey
  • Search for other articles:
  • degruyter.comGoogle Scholar
, Gonul FilogluORCID iD: http://orcid.org/0000-0002-8807-317X, Tolga Zorlu and Ozlem BulbulORCID iD: http://orcid.org/0000-0003-2920-7614

Abstract

Background:

The Non-recombining region of the Y-chromosome (NRY) is transferred from father to son in an unchanged form without recombination in meiosis. Since Short tandem repeats on Y-chromosome (Y-STRs) in this region do not have any recombination, these regions are identical in all male individuals who are related to the father except for mutations. Therefore, these regions gain importance in identification for the forensic sciences or determination of paternity. In determination of paternity, if mismatches are observed between father and child, population-specific mutation rates should be used to determine whether it is a mutation or a true exclusion. Therefore in this study, we aim to determine the mutation rates of 17 Y-STR loci in Turkey.

Material and methods:

17 Y-STR loci were typed by using AmpFlSTR® Yfiler™ Kit in 90 volunteer father-son pairs. Mutation rates were calculated and compared with other populations.

Results:

The mutations were found between three father-son pairs at DYS439 and DYS458 loci. In addition, a duplication in DYS389 II loci* 30, 31 was observed. The average mutation rate was determined as 1.96×10−3 for Turkish population.

Conclusion:

This investigation will contribute to minimize the possibility of false exclusion of the father-son and kinship relations.

  • 1.

    Gusmao L, Sanchez-Diz P, Calafell F, Martin P, Alonso CA, Alvarez-Fernandez F, et al. Mutation rates at Y chromosome specific microsatellites. Hum Mutat 2005;26:520–8.

    • Crossref
    • PubMed
    • Export Citation
  • 2.

    McElreavey K, Krausz C. Male infertility and the Y chromosome. Am J Hum Genet 1999;64:928–33.

    • Crossref
    • Export Citation
  • 3.

    Gusmao L, Butler JM, Carracedo A, Gill P, Kayser M, Mayr WR, et al. DNA commission of the international society of forensic genetics (ISFG): an update of the recommendations on the use of Y-STRs in forensic analysis. Forensic Sci Int 2006;157:187–97.

    • Crossref
    • PubMed
    • Export Citation
  • 4.

    Jobling MA, Pandya A, TylerSmith C. The Y chromosome in forensic analysis and paternity testing. Int J Legal Med 1997;110:118–24.

    • Crossref
    • Export Citation
  • 5.

    Sibille I, Duverneuil C, de la Grandmaison GL, Guerrouache K, Teissiere F, Durigon M, et al. Y-STR DNA amplification as biological evidence in sexually assaulted female victims with no cytological detection of spermatozoa. Forensic Sci Int 2002;125:212–6.

    • Crossref
    • PubMed
    • Export Citation
  • 6.

    Caplinskiene M, Pauliukevicius A, Jankauskiene J, Bunokiene D, Kukiene J, Savanevskyte K, et al. Autosomal and Y-STR mutations in Lithuanian population. Forensic Sci Int Genet Suppl Ser 2008;1:237–8.

    • Crossref
    • Export Citation
  • 7.

    Vieira-Silva C, Dario P, Ribeiro T, Lucas I, Geada H, Espinheira R. Y-STR mutational rates determination in South Portugal Caucasian population. Forensic Sci Int Genet Suppl Ser 2009;2:60–1.

    • Crossref
    • Export Citation
  • 8.

    Brinkmann B, Klintschar M, Neuhuber F, Huhne J, Rolf B. Mutation rate in human microsatellites: influence of the structure and length of the tandem repeat. Am J Hum Genet 1998;62:1408–15.

    • Crossref
    • PubMed
    • Export Citation
  • 9.

    Jobling MA, Hurles ME, Tyler-Smith C. The diversity of the human genome. In: Human evolutionary genetics: origins, peoples & disease. New York: Garland Science, 2004:523.

  • 10.

    Burgarella C, Navascues M. Mutation rate estimates for 110 Y-chromosome STRs combining population and father-son pair data. Eur J Hum Genet 2011;19:70–5.

    • Crossref
    • PubMed
    • Export Citation
  • 11.

    YHRD: Y-Chromosome STR haplotype reference database. Available at: https://yhrd.org/pages/resources/mutation_rates. Accessed: May 2016.

  • 12.

    Balanovsky O. Toward a consensus on SNP and STR mutation rates on the human Y-chromosome. Hum Genet 2017;136:575–90.

    • Crossref
    • Export Citation
  • 13.

    Ballantyne KN, Keerl V, Wollstein A, Choi Y, Zuniga SB, Ralf A, et al. A new future of forensic Y-chromosome analysis: rapidly mutating Y-STRs for differentiating male relatives and paternal lineages. Forensic Sci Int-Gen 2012;6:208–18.

    • Crossref
    • Export Citation
  • 14.

    Ballantyne KN, Ralf A, Aboukhalid R, Achakzai NM, Anjos MJ, Ayub Q, et al. Toward male individualization with rapidly mutating Y-chromosomal short tandem repeats. Hum Mutat 2014;35:1021–32.

    • Crossref
    • PubMed
    • Export Citation
  • 15.

    Applied Biosystems. The AmpFlSTR® Y-filer™ PCR Amplification Kit, User’s Manual. Thermo Fisher Scientific Inc., California, USA, 2006.

  • 16.

    Exact Binomial and Poisson Confidence Intervals. Available at: http://statpages.org/confint.html. Accessed: April 2016.

  • 17.

    de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, et al. Initial sequencing and analysis of the human genome. Nature 2001;412:565–6.

    • Crossref
    • Export Citation
  • 18.

    Ballantyne KN, Goedbloed M, Fang R, Schaap O, Lao O, Wollstein A, et al. Mutability of Y-chromosomal microsatellites: rates, characteristics, molecular bases, and forensic implications. Am J Hum Genet 2010;87:341–53.

    • Crossref
    • PubMed
    • Export Citation
  • 19.

    Decker AE, Kline MC, Redman JW, Reid TM, Butler JM. Analysis of mutations in father-son pairs with 17 Y-STR loci. Forensic Sci Int-Gen 2008;2:E31–5.

    • Crossref
    • Export Citation
  • 20.

    Lee HY, Park MJ, Chung U, Lee HY, Yang WI, Cho SH, et al. Haplotypes and mutation analysis of 22 Y-chromosomal STRs in Korean father-son pairs. Int J Legal Med 2007;121:128–35.

    • Crossref
    • PubMed
    • Export Citation
  • 21.

    Sen Shi M, Tang JP, Bai RF, Yu XJ, Lv JY, Hu B. Haplotypes of 20 Y-chromosomal STRs in a population sample from southeast China (Chaoshan area). Int J Legal Med 2007;121:455–62.

    • Crossref
    • Export Citation
  • 22.

    Onofri V, Buscemi L, Tagliabracci A. Evaluating Y-chromosome STRs mutation rates: a collaborative study of the Ge.F.I.-ISFG Italian Group. Forensic Sci Int Genet Suppl Ser 2009;2:419–20.

    • Crossref
    • Export Citation
  • 23.

    Budowle B, Adamowicz M, Aranda XG, Barna C, Chakraborty R, Cheswick D, et al. Twelve short tandem repeat loci Y chromosome haplotypes: genetic analysis on populations residing in North America. Forensic Sci Int 2005;150:1–15.

    • Crossref
    • PubMed
    • Export Citation
  • 24.

    Hohoff C, Dewa K, Sibbing U, Hoppe K, Forster P, Brinkmann B. Y-chromosomal microsatellite mutation rates in a population sample from northwestern Germany. Int J Legal Med 2007;121:359–63.

    • Crossref
    • Export Citation
  • 25.

    Kurihara R, Yamamoto T, Uchihi R, Li SL, Yoshimoto T, Ohtaki H, et al. Mutations in 14 Y-STR loci among Japanese father-son haplotypes. Int J Legal Med 2004;118:125–31.

    • Crossref
    • PubMed
    • Export Citation
  • 26.

    Farfán MJ, Prieto V. Mutations at 17 Y-STR loci in father–son pairs from Southern Spain. Forensic Sci Int Genet Suppl Ser 2009;2:425–6.

    • Crossref
    • Export Citation
  • 27.

    Domingues PM, Gusmao L, da Silva DA, Amorim A, Pereira RW, de Carvalho EF. Sub-Saharan Africa descendents in Rio de Janeiro (Brazil): population and mutational data for 12 Y-STR loci. Int J Legal Med 2007;121:238–41.

    • Crossref
    • Export Citation
  • 28.

    Laouina A, Nadifi S, Boulouiz R, El Arji M, Talbi J, El Houate B, et al. Mutation rate at 17 Y-STR loci in “Father/Son” pairs from moroccan population. Legal Med 2013;15:269–71.

    • Crossref
    • Export Citation
  • 29.

    Rolf B, Keil W, Brinkmann B, Roewer L, Fimmers R. Paternity testing using Y-STR haplotypes: assigning a probability for paternity in cases of mutations. Int J Legal Med 2001;115:12–5.

    • Crossref
    • PubMed
    • Export Citation
  • 30.

    Butler JM, Decker AE, Kline MC, Vallone PM. Chromosomal duplications along the Y-chromosome and their potential impact on Y-STR interpretation. J Forensic Sci 2005;50:853–9.

    • PubMed
    • Export Citation
  • 31.

    Cakir AH, Celebioglu A, Yardimci E. Y-STR haplotypes in Central Anatolia region of turkey. Forensic Sci Int 2004;144:59–64.

    • Crossref
    • PubMed
    • Export Citation
  • 32.

    Kayser M, Roewer L, Hedman M, Henke L, Henke J, Brauer S, et al. Characteristics and frequency of germline mutations at microsatellite loci from the human Y chromosome, as revealed by direct observation in father/son pairs. Am J Hum Genet 2000;66:1580–8.

    • Crossref
    • PubMed
    • Export Citation
  • 33.

    Ge JY, Budowle B, Planz JV, Eisenberg AJ, Ballantyne J, Chakraborty R. US forensic Y-chromosome short tandem repeats database. Legal Med 2010;12:289–95.

    • Crossref
    • Export Citation
  • 34.

    Coble MD, Hill CR, Butler JM. Haplotype data for 23 Y-chromosome markers in four US population groups. Forensic Sci Int-Gen 2013;7:E66–8.

    • Crossref
    • Export Citation
  • 35.

    Wang Y, Zhang YJ, Zhang CC, Li R, Yang Y, Ou XL, et al. Genetic polymorphisms and mutation rates of 27 Y-chromosomal STRs in a Han population from Guangdong Province, Southern China. Forensic Sci Int-Gen 2016;21:5–9.

    • Crossref
    • Export Citation
Purchase article
Get instant unlimited access to the article.
$42.00
Log in
Already have access? Please log in.


or
Log in with your institution

Journal + Issues

Turkish Journal of Biochemistry (TJB), official journal of Turkish Biochemical Society, is issued electronically every 2 months. The main aim of the journal is to support the research and publishing culture by ensuring that every published manuscript has an added value and thus providing international acceptance of the “readability” of the manuscripts published in the journal.

Search