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Off-ladder alleles due to a single nucleotide polymorphism in the flanking region at DYS481 detected by the PowerPlex® Y23 System

  • Eun Young Lee
    Affiliations
    Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea
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  • Hwan Young Lee
    Affiliations
    Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea
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  • Kyoung-Jin Shin
    Correspondence
    Corresponding author at: Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea.
    Affiliations
    Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea

    Brain Korea 21 PLUS Project for Medical Science, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea
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      Several commercial kits are available for Y-chromosome short tandem repeat (STR) haplotyping for forensic purposes. The PowerPlex® Y23 System (Promega Corp., Madison, MI, USA) was recently released and has been used worldwide in several populations [
      • Purps J.
      • Siegert S.
      • Willuweit S.
      • Nagy M.
      • et al.
      A global analysis of Y-chromosomal haplotype diversity for 23 STR loci.
      ]. To accumulate South Asian haplotype data, we analyzed 270 DNA samples from Pakistani Pathans using the PowerPlex® Y23 System, which was previously used to type 22 Y-STRs (17 STRs of AmpFlSTR Yfiler™, DYS388, DYS446, DYS447, DYS449, and DYS464) [
      • Lee E.Y.
      • Shin K.J.
      • Rakha A.
      • Sim J.E.
      • Park M.J.
      • Kim N.Y.
      • Yang W.I.
      • Lee H.Y.
      Analysis of 22 Y chromosomal STR haplotypes and Y haplogroup distribution in Pathans of Pakistan.
      ]. The full haplotypes for the PowerPlex® Y23 STRs are available on the Y-chromosome haplotype reference database (http://yhrd.org) under the accession number YA003846. While genotyping the 23 Y-STRs, off-ladder alleles were observed at DYS481 in 20 of the 270 Pathan samples (Table 1). In the meantime, microvariant alleles designated as a one nucleotide intermediate allele at DYS481 were reported in only 26 of the 19,630 samples from the PowerPlex® Y23 analysis [
      • Purps J.
      • Siegert S.
      • Willuweit S.
      • Nagy M.
      • et al.
      A global analysis of Y-chromosomal haplotype diversity for 23 STR loci.
      ].
      Table 1Frequency of the off-ladder alleles at DYS481 observed in 270 Pakistani Pathan samples.
      Allele Allele No. of samples Frequency
      by PowerPlex® Y23 by sequencing
      All samples reported as off-ladder alleles at DYS481 by the PowerPlex® Y23 System contained the L266 mutation.
      18.1 18 1 0.004
      23.1 23 1 0.004
      24.1 24 7 0.026
      25.1 25 7 0.026
      26.1 26 3 0.011
      27.1 27 1 0.004
      Total 20 0.074
      a All samples reported as off-ladder alleles at DYS481 by the PowerPlex® Y23 System contained the L266 mutation.
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