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Forensic and population genetic analysis of Serbian population using 21 STR loci of GlobalFiler™ PCR amplification kit

  • Dragana Zgonjanin
    Correspondence
    Corresponding author at: Institute of Forensic Medicine, Clinical Center of Vojvodina, Novi Sad, Serbia.
    Affiliations
    Institute of Forensic Medicine, Clinical Center of Vojvodina, Novi Sad, Serbia

    Faculty of Medicine, University of Novi Sad, Novi Sad, Serbia
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  • Reem Almheiri
    Affiliations
    General Department of Forensic Sciences and Criminology, Dubai Police G.H.Q., Dubai, United Arab Emirates
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  • Rashed Alghafri
    Affiliations
    General Department of Forensic Sciences and Criminology, Dubai Police G.H.Q., Dubai, United Arab Emirates

    College of Science, Biology Department, United Arab Emirates University, United Arab Emirates
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  • Dalibor Nedić
    Affiliations
    Institute of Forensic Medicine of Republic of Srpska, Banja Luka, Bosnia and Herzegovina

    Medical Faculty, University of Banja Luka, Banja Luka, Republic of Srpska, Bosnia and Herzegovina
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  • Goran Stojiljković
    Affiliations
    Institute of Forensic Medicine, Clinical Center of Vojvodina, Novi Sad, Serbia

    Faculty of Medicine, University of Novi Sad, Novi Sad, Serbia
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Published:September 23, 2019DOI:https://doi.org/10.1016/j.fsigss.2019.09.020

      Abstract

      Autosomal short tandem repeats (STRs) have been widely used in forensic investigations. Prior to the application of any DNA based identification method, it is essential to estimate the allele frequencies and forensic statistical parameters of targeted STR loci in each population in order to provide a more precise reference database for forensic investigation. The GlobalFiler™ Kit is a multiplex assay that combines the 13 original CODIS loci with 7 non-overlapping loci from the expanded European Standard Set (ESS), as well as the highly discriminating SE33 locus, two Y-based loci and the sex determining maker, Amelogenin. The full complement of loci in the GlobalFiler™ Kit are: D13S317, D7S820, D5S818, CSF1PO, D1S1656, D12S391, D2S441, D10S1248, D18S51, FGA, D21S11, D8S1179, vWA, D16S539, TH01, D3S1358, AMEL, D2S1338, D19S433, DYS391, TPOX, D22S1045, SE33 and a Y-specific insertion/deletion locus (Yindel). The 6-dye GlobalFiler™ PCR Amplification kit (ThermoFisher Scientific) comprises 21 autosomal STRs have already been proven to be able to provide reliable DNA profiling results and enhance the power of discrimination between individuals. In this study, we are presenting an analysis of GlobalFiler STR loci on 209 unrelated individuals from Serbia.

      Keywords

      1. Introduction

      Evaluating STR allelic frequencies is an essential prerequisite to start applying such analysis in the forensic casework, as it has been shown before that, each population will have its own composition of alleles distribution and therefore, it will facilitate the correct calculations of weigth of evidence. By utilizing one of the most powerful commercially available STR amplification kits (GloblaFiler™) can aid development of allelic frequency database to enhance knowledge about patterns of genetic diversity and to have further understanding about population genetic structure [
      • Buckleton J.
      • Curran J.
      • Goudet J.
      • Taylor D.
      • Thiery A.
      • Weir B.S.
      Population-specific FST values for forensic STR markers: a worldwide survey.
      ].

      2. Materials and methods

      Total of 209 DNA samples was extracted and purified from blood stains or buccal swabs by using the Chelex 100 extraction method [
      • Walsh P.S.
      • Metzger D.A.
      • Higuchi R.
      Chelex 100 as a medium for simple extraction of DNA for PCR-based typing for forensic material.
      ] from unrelated individuals from Serbia, following informed consent. DNA was amplified using the GlobalFiler™ Kit (ThermoFisher Scientific) in a thermal cycler GeneAmp 9700 PCR system (Applied Biosystems), according to manufacturer’s recommendations, but reducing the PCR final volume to half (12.5 μl) of the recommended quantity. The electrophoresis was carried out on 3500 Genetic Analyzer (Applied Biosystems, USA) and the fragment analysis was performed with GeneMapper ID-X v.1.4 software (Applied Biosystems). Arlequin version 3.5 [
      • Excoffier L.
      • Lischer H.E.
      Arlequin suite ver 3. 5: a new series of programs to perform population genetics analyses under Linux and Windows.
      ] was used to calculate allele frequencies, expected heterozygosity (He), observed heterozygosity (Ho), probability value of the Hardy-Weinberg equilibrium (HWE) exact test. Population genetics statistical parameters were calculated using PowerStats version 1.2.

      3. Results

      Allele frequencies and resulting statistical parameters are given in Table 1. No significant deviations from Hardy–Weinberg equilibrium and linkage disequilibrium were detected within and between the 21 STR loci. Locus SE33 has shown the greatest power of discrimination in Serbia population, whereas TPOX has was the lowest. The combined power of discrimination was found to be 0.99999999999999999999999989954, whereas the random match probability was found to be 4.2 × 10−26 and the combined power of exclusion was 0.999999990605.
      Table 1Allele frequencies and statistical parameters of 21 autosomal STRs loci in a population sample from Serbia (N = 209).
      Allele/

      Locus
      D3S1358vWAD16S539CSF1POTPOXD8S1179D21S11D18S51D2S441D19S433TH01FGAD22S1045D5S818D13S317D7S820SE33D10S1248D1S1656D12S391D2S1338
      60.002
      6.20.251
      70.0100.1530.026
      80.0140.0020.5550.0120.0020.0930.1390.175
      90.1360.0310.0790.0120.1960.1960.0430.0550.179
      9.30.285
      100.0670.2850.0570.0550.0070.3350.0190.0690.0620.282
      110.2920.2970.2800.0740.0050.0670.0140.0020.1480.3330.3610.1770.0070.112
      120.3010.3250.0170.1440.1340.0530.0960.0220.3800.2680.1290.0050.0220.132
      130.0050.1480.0530.3230.1360.0260.2320.0310.1600.0890.0240.0100.2560.081
      13.20.012
      140.0930.1120.0330.0070.2250.1910.2680.3210.3880.0070.0260.0070.0240.2660.0720.005
      14.20.0380.002
      14.30.002
      150.2420.1000.0070.1390.1390.0450.1650.2850.0070.0550.2340.1340.0650.002
      15.20.0020.038
      15.30.041
      160.2680.2220.0170.1390.0070.0430.1000.0630.1750.1410.0260.053
      16.20.031
      16.30.053
      170.2060.2780.1120.0020.0240.0770.0290.0550.1000.234
      17.20.005
      17.30.1000.002
      180.1670.1870.0740.0220.0020.0770.0100.0020.1990.093
      18.20.0020.002
      18.30.0600.033
      190.0190.0810.0330.1080.1480.0600.0020.1290.086
      19.20.0020.002
      19.30.0140.014
      200.0170.0140.1050.0720.1340.146
      20.20.0020.010
      20.30.002
      210.0020.0100.1770.0240.0930.029
      21.20.0050.002
      220.0020.1840.0070.1050.017
      22.20.0100.041
      230.1440.0650.110
      23.20.0020.048
      240.1200.0120.105
      24.20.029
      250.0530.0170.100
      25.20.0050.048
      260.0050.0500.0020.012
      26.20.0020.043
      270.0360.0070.007
      27.20.058
      280.1670.002
      28.20.087
      290.196
      29.20.046
      300.208
      30.20.0410.046
      310.0550.002
      31.20.1200.019
      320.007
      32.20.1170.019
      33.20.0430.010
      340.002
      34.20.0050.005
      350.002
      PD0.9220.9360.9140.8750.7910.9310.9410.9650.8760.8980.8430.9640.8870.8620.8980.9320.9900.9150.9610.9650.965
      PE0.6150.5710.5800.4260.2450.5970.6150.7170.4410.5370.4340.6520.4960.4110.4720.5880.7850.4880.7850.7850.597
      PI2.6132.3222.3751.6591.1362.4882.6133.6031.7132.1331.6852.9031.9351.6081.8332.4304.7501.9004.7504.0192.824
      Ho0.8090.7850.7900.6990.6990.7990.8090.8610.7080.7660.7030.8280.7420.6890.7270.7940.8950.7370.8950.8760.823
      PD – power of discrimination, PE – power of exclusion, PI –paternity index, Ho – observed heterozygosity.
      Relative to the power of discrimination (PD), the values range between 0.7911 and 0.9899, being the highest and the lowest values given, respectively, by SE33 and TPOX markers. The most informative marker is SE33, which present the highest polymorphic information content (PIC) of 0.941. All of the other markers have PIC values above 0.547. Moreover, the power of exclusion (PE) is 0.2454 for TPOX marker (minimum value) and 0.7847 for SE33 (maximum value). Paternity Index (PI) is situated between 1.1358 (TPOX) and 4.75 (SE33).

      4. Discussion

      In sum, among the 21 markers presents in the commercial kit GlobalFiler™ the most polymorphic, informative and powerful locus in forensic identification was found to be SE33. This marker has the highest PIC, PD, PE, PI and the lowest MP and homozygosity frequency. These results are concordant to others studies, that showed that TPOX is the molecular marker, present in CODIS, that revealed lowest variation among individuals [
      • Thanakiatkrai P.
      • Kitpipit T.
      Current STR-based techniques in forensic science.
      ].

      5. Conclusion

      This study represents the first report of frequencies for the GlobalFiler™ markers set in a population of Serbia. Power of discrimination, gene diversity and alleles frequencies presented in this study suggest that the 21 STR loci have great value in forensic casework analysis as well as in kinship analysis.

      Declaration of Competing Interest

      No conflicts of interest.

      Acknowledgements

      The project was supported by Vojvodine Government , by the Grant No. 142-451-2704/2018-01/02 of the Provincial Secretariat for higher education and scientific research of the Vojvodina Province.

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