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Correspondence| Volume 25, e12-e13, November 2016

Typing concordance between PowerPlex® Fusion and GlobalFiler® based on 1501 Japanese individuals and the causes of typing discrepancies

  • Koji Fujii
    Correspondence
    Corresponding author at: First Department of Forensic Science, National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
    Affiliations
    First Department of Forensic Science, National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan

    Identification Center, National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
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  • Haruhiko Watahiki
    Affiliations
    First Department of Forensic Science, National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
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  • Yusuke Mita
    Affiliations
    First Department of Forensic Science, National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
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  • Yasuki Iwashima
    Affiliations
    First Department of Forensic Science, National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan

    Forensic Science Laboratory, Kyoto Prefectural Police HQ, 85-3, 85-4, Shimodachiuri-dori, Kamanza-higashiiru, Yabunouchi-cho, Kamigyo-ku, Kyoto 602-8550, Japan
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  • Tetsushi Kitayama
    Affiliations
    First Department of Forensic Science, National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan

    Identification Center, National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
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  • Hiroaki Nakahara
    Affiliations
    First Department of Forensic Science, National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
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  • Natsuko Mizuno
    Affiliations
    First Department of Forensic Science, National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
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  • Kazumasa Sekiguchi
    Affiliations
    First Department of Forensic Science, National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
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Published:August 01, 2016DOI:https://doi.org/10.1016/j.fsigen.2016.07.023
Typing concordance between PowerPlex® Fusion and GlobalFiler® based on 1501 Japanese individuals and the causes of typing discrepancies
Previous ArticlePopulation genetic data for 20 autosomal STR loci in an Iraqi Arab population: Application to the identification of human remains
Next ArticleGenetic diversity of 21 autosomal STR loci in the Han Chinese population from Hainan Province in South China
      Typing discrepancies have been reported in concordance studies in which population samples were genotyped using different short tandem repeat (STR) kits [
      • Budowle B.
      • Masibay A.
      • Anderson S.J.
      • Barna C.
      • Biega L.
      • Brenneke S.
      • et al.
      STR primer concordance study.
      Forensic Sci. Int. 2001; 124: 47-54
      ,
      • Budowle B.
      • Sprecher C.J.
      Concordance study on population database samples using the PowerPlex™ 16 kit and AmpFℓSTR® Profiler Plus™ kit and AmpFℓSTR® COfiler™ kit.
      J. Forensic Sci. 2001; 46: 637-641
      ,
      • Hill C.R.
      • Kline M.C.
      • Mulero J.J.
      • Lagacé R.E.
      • Chang C.-W.
      • Hennessy L.K.
      • et al.
      Concordance study between the AmpFℓSTR® MiniFiler™ PCR amplification kit and conventional STR typing kits.
      J. Forensic Sci. 2007; 52: 870-873
      ,
      • Hill C.R.
      • Duewer D.L.
      • Kline M.C.
      • Sprecher C.J.
      • McLaren R.S.
      • Rabbach D.R.
      • et al.
      Concordance and population studies along with stutter and peak height ratio analysis for the PowerPlex® ESX 17 and ESI 17 systems.
      Forensic Sci. Int. Genet. 2011; 5: 269-275
      ,
      • Welch L.A.
      • Gill P.
      • Phillips C.
      • Ansell R.
      • Morling N.
      • Parson W.
      • et al.
      European network of forensic science institutes (ENFSI): evaluation of new commercial STR multiplexes that include the european standard set (ESS) of markers.
      Forensic Sci. Int. Genet. 2012; 6: 819-826
      ,
      • Westen A.A.
      • Kraaijenbrink T.
      • Robles de Medina E.A.
      • Harteveld J.
      • Willemse P.
      • Zuniga S.B.
      • et al.
      Comparing six commercial autosomal STR kits in a large Dutch population sample.
      Forensic Sci. Int. Genet. 2014; 10: 55-63
      ,
      • Park H.-C.
      • Kim K.
      • Nam Y.
      • Park J.
      • Lee J.
      • Lee H.
      • et al.
      Population genetic study for 24 STR loci and Y indel (GlobalFiler™ PCR amplification kit and PowerPlex® Fusion system) in 1000 Korean individuals.
      Legal Med. (Tokyo). 2016; 21: 53-57
      ]. However, as far as we know, no comprehensive concordance studies have examined typing results for the Japanese population. Previously, we genotyped 1501 Japanese samples using PowerPlex® Fusion [
      • Fujii K.
      • Iwashima Y.
      • Kitayama T.
      • Nakahara H.
      • Mizuno N.
      • Sekiguchi K.
      Allele frequencies for 22 autosomal short tandem repeat loci obtained by PowerPlex Fusion in a sample of 1501 individuals from the Japanese population.
      Legal Med. (Tokyo). 2014; 16: 234-237
      ] and GlobalFiler® [
      • Fujii K.
      • Watahiki H.
      • Mita Y.
      • Iwashima Y.
      • Kitayama T.
      • Nakahara H.
      • et al.
      Allele frequencies for 21 autosomal short tandem repeat loci obtained using GlobalFiler in a sample of 1501 individuals from the Japanese population.
      Legal Med. (Tokyo). 2015; 17: 306-308
      ]. Of the 1501 samples, one heterozygous sample showed a discrepancy at the D5S818 locus (designated 9.3, 12 using PowerPlex® Fusion, but 10, 12 using GlobalFiler®), which was attributed to a single nucleotide deletion in the primer biding site [
      • Fujii K.
      • Iwashima Y.
      • Watahiki H.
      • Mita Y.
      • Kitayama T.
      • Nakahara H.
      • et al.
      D5S818 typing discrepancy between PowerPlex® Fusion and other STR kits including GlobalFiler® caused by a one-base deletion in 31 nucleotides upstream of the repeat region.
      J. Forensic Sci. 2016; 61: 752-758
      ]. Herein, we examined the typing concordance between the two STR kits and confirmed the presence of silent alleles in the additional discordant samples by a sequencing analysis. In addition, for the D2S441 and D22S1045 loci, the positions of the 5′ ends of the GlobalFiler® forward primers were also estimated using our method [
      • Mizuno N.
      • Inokuchi S.
      • Kitayama T.
      • Fujii K.
      • Kasai K.
      • Sekiguchi K.
      A method to determine the 5′ end of the binding site of primers included in a commercially available forensic human identification kit.
      Forensic Sci. Int. Genet. 2014; 9: 76-80
      ] in order to examine the causes of the discordant results.
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      References

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        • Masibay A.
        • Anderson S.J.
        • Barna C.
        • Biega L.
        • Brenneke S.
        • et al.
        STR primer concordance study.
        Forensic Sci. Int. 2001; 124: 47-54
        View in Article
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        Concordance study on population database samples using the PowerPlex™ 16 kit and AmpFℓSTR® Profiler Plus™ kit and AmpFℓSTR® COfiler™ kit.
        J. Forensic Sci. 2001; 46: 637-641
        View in Article
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        • Lagacé R.E.
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        Concordance study between the AmpFℓSTR® MiniFiler™ PCR amplification kit and conventional STR typing kits.
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        View in Article
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        Concordance and population studies along with stutter and peak height ratio analysis for the PowerPlex® ESX 17 and ESI 17 systems.
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        View in Article
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        View in Article
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        Population genetic study for 24 STR loci and Y indel (GlobalFiler™ PCR amplification kit and PowerPlex® Fusion system) in 1000 Korean individuals.
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        View in Article
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        View in Article
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        D5S818 typing discrepancy between PowerPlex® Fusion and other STR kits including GlobalFiler® caused by a one-base deletion in 31 nucleotides upstream of the repeat region.
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        View in Article
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      Article info

      Publication history

      Published online: August 01, 2016
      Accepted: July 30, 2016
      Received in revised form: July 27, 2016
      Received: May 22, 2016

      Identification

      DOI: https://doi.org/10.1016/j.fsigen.2016.07.023

      Copyright

      © 2016 Elsevier Ireland Ltd. All rights reserved.

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