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Haplotype data for the 12 RM Y-STR loci in a Syrian population

  • Mustafa Ay
    Affiliations
    Cukurova University, Institute of Addiction and Forensic Sciences, Department of Forensic Sciences, Adana, Turkey
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  • Ayse Serin
    Correspondence
    Corresponding author at: Cukurova University, Faculty of Medicine, Department of Forensic Medicine, Adana, Turkey.
    Affiliations
    Cukurova University, Institute of Addiction and Forensic Sciences, Department of Forensic Sciences, Adana, Turkey

    Cukurova University, Faculty of Medicine, Department of Forensic Medicine, Adana, Turkey
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  • Husniye Canan
    Affiliations
    Cukurova University, Institute of Addiction and Forensic Sciences, Department of Forensic Sciences, Adana, Turkey
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  • Necmi Cekin
    Affiliations
    Cukurova University, Institute of Addiction and Forensic Sciences, Department of Forensic Sciences, Adana, Turkey

    Cukurova University, Faculty of Medicine, Department of Forensic Medicine, Adana, Turkey
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Published:September 30, 2019DOI:https://doi.org/10.1016/j.fsigss.2019.09.035

      Abstract

      Researches with RM Y-STRs have shown that these loci provide substantially higher haplotype diversity and haplotype discrimination capacity in worldwide populations when compared with the YSTRs commonly used in genetic forensics. The aim of this study was to develop an allelic frequency database for the Syrian population living in Turkey in order to obtain population data of 12 RM Y-STRs. A total of 80 unrelated males from the Syrian population living in Turkey were typed with 12 RM Y-STRs loci: DYF387S1, DYF399S1, DYF404S1, DYS449, DYS518, DYS526a/b, DYS547, DYS570, DYS576, DYS612, DYS626 and DYS627. The highest GD was observed for the locus DYF399S1 (0.91), followed by loci DYS449 (0.86) and DYS518 (0.83). RM Y-STR haplotype diversity was found 1.00 in these samples. Based on the results of this study, the RM YSTR loci showed remarkable haplotype resolution power in the Syrian population, high genetic diversity and, therefore, demonstrating their usefulness in forensic identification cases.

      Keywords

      1. Introduction

      Y-chromosomal Short Tandem Repeat (Y-STR) markers have been used for forensic purposes such as kinship analysis of male-linage and detection of a male DNA component in a mixture of male and female DNA. However, the Y-STRs generally used in forensic sciences show low haplotype diversity in some populations and cannot distinguish between closely or distantly related males [
      • Parson W.
      • Niederstätter H.
      • Brandstätter A.
      • Berger B.
      Improved specificity of YSTR typing in DNA mixture samples.
      ,
      • Prinz M.
      • Boll K.
      • Baum H.
      • Shaler B.
      Multiplexing of Y chromosome specific STRs and performance for mixed samples.
      ]. A recently identified set of 13 rapidly mutating (RM) Y-STRs (DYF387S1, DYF399S1, DYF403S1, DYF404S1, DYS449, DYS518, DYS526, DYS547, DYS570, DYS576, DYS612, DYS626, and DYS627) provides a substantially higher discrimination between haplotypes than other commercially available Y-STR sets and enables differentiation between closely and distantly related males [
      • Ballantyne K.N.
      • Ralf A.
      • Aboukhalid R.
      • Achakzai N.M.
      • Anjos M.J.
      • et al.
      Towards male individualization with rapidly mutating Y-chromosomal STRs.
      ,
      • Alghafri R.
      • Goodwin W.
      • Ralf A.
      • Kayser M.
      • Hadi S.
      A novel multiplex assay for simultaneously analyzing 13 rapidly mutating Y-STRs.
      ,
      • Serin A.
      • Ay M.
      • Sevay H.
      • Gürkan C.
      • Canan H.
      Genetic characterisation of 13 rapidly mutating Y-STR loci in 100 father and son pairs from South and East Turkey.
      ].
      The aim of this study was to develop an allelic frequency database for the Syrian population living in Turkey in order to obtain population data of 12 RM Y-STRs.

      2. Materials and methods

      Genomic DNA was extracted from 80 unrelated Syrian males using either silica (Qiagen, Hilden, Germany) or chelex-based (InstaGene Matrix; Bio-Rad, Hercules, CA) method.
      PCR amplification of the 12 RM Y-STR loci (DYF387S1, DYF399S1, DYF404S1, DYS449, DYS518, DYS526a/b, DYS547, DYS570, DYS576, DYS612, DYS626, and DYS627) and electrophoresis were carried out as previously described elsewhere [
      • Serin A.
      • Ay M.
      • Sevay H.
      • Gürkan C.
      • Canan H.
      Genetic characterisation of 13 rapidly mutating Y-STR loci in 100 father and son pairs from South and East Turkey.
      ].
      Allele frequency calculations were carried out according to Ballantyne et al. Haplotype and gene diversity values were calculated based on Nei [
      • Nei M.
      • Tajima F.
      DNA polymorphism detectable by restriction endonucleases.
      ]. To investigate pairwise genetic distances among RM-YSTR population dataset, an allele frequency based approach was taken whereby Nei’s DA distances were computed and visualized using Neighbour-Joining phylogenetic tree from POPTREE software [
      • Takezaki N.
      • Nei M.
      • Tamura K.
      POPTREE2: software for constructing population trees from allele frequency data and computing other population statistics with windows interface.
      ].

      3. Results and discussion

      A total of 80 different haplotypes were identified from 80 unrelated male individuals. Since all the 80 haplotypes were unique, HD and DC values were both calculated as one.
      A total of 128 alleles were detected at 12 RM Y-STR loci. The number of alleles at each locus ranged from 7 for DYF576 to 19 for DYS399. DYF387S1, DYF399S1, and DYF404S1 often show multiple alleles and are therefore categorized as multi copy loci. As expected, the RM Y-STR loci showed high genetic diversity (GD) values. The average gene diversity was high in Syrian population (0.88). The highest GD was observed for the locus DYF399S1 (0.91), followed by loci DYS449 (0.86) and DYS518 (0.83) (Table 1) in Supplementary material.
      Allele frequencies of this population were compared to relatively geographically close populations previously reported (Turkey, Greece, Czech Republic, Hungary, Slovenia, Bosnia, Croatia, Ukraine) were compared for the genetic distances [
      • Ballantyne K.N.
      • Ralf A.
      • Aboukhalid R.
      • Achakzai N.M.
      • Anjos M.J.
      • et al.
      Towards male individualization with rapidly mutating Y-chromosomal STRs.
      ,
      • Serin A.
      • Ay M.
      • Sevay H.
      • Gürkan C.
      • Canan H.
      Genetic characterisation of 13 rapidly mutating Y-STR loci in 100 father and son pairs from South and East Turkey.
      ]. Nei’s DA genetic distances between ten populations data were estimated and visualized using Neighbor-Joining phylogenetic tree on the POPTREE software and shown at the bottom figure [
      • Takezaki N.
      • Nei M.
      • Tamura K.
      POPTREE2: software for constructing population trees from allele frequency data and computing other population statistics with windows interface.
      ]. For these set of markers, the comparison with published data showed that the population in this study had low genetics distances values with Turkish and Greek populations that are geographically close. This figure also showed that as the geographical distance between countries increases, genetic differences also increases (Fig. 1).
      Fig. 1
      Fig. 1Neighbor joining tree based on the population pairwise genetic distances between 10 population’s data (Syria, Turkey-1 and 2, Greece, Czech Republic 1 and 2, Hungary, Bosnia, Croatia, Ukraine), generated using the POPTREE2 software.

      4. Conclusion

      New RM-YSTR multiplex assay tested in this study functioned well and efficiently generated genotyping data for all 80 Syrian donors. Based on the results of this study, the RM Y-STR loci showed remarkable haplotype resolution power in the population of Syrian living in Turkey, high genetic diversity and, therefore, demonstrating their usefulness in forensic identification and parentage cases.

      Funding

      This work was supported by a grant from the Cukurova University Scientific Research Project Support Unit ( TSA-2018-7850 ).

      Declaration of Competing Interest

      None.

      Acknowledgement

      We are grateful to all the volunteers who donated samples that made this research possible.

      Appendix A. Supplementary data

      The following is Supplementary data to this article:

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