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Updated: Feb 14, 2026

The ITS2 Database
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Kit-dependent discrepancy in D16S539 and general considerations for database matches.

Barbara Karolina Zajac1, Richard Zehner2, Stefanie Scheiper2

  • 1Institute of Forensic Medicine and Traffic Medicine, Department for Forensic Genetics, University Hospital Heidelberg, Germany.

Forensic Science International. Genetics
|February 27, 2018
PubMed
Summary

Multiplex PCR kits for forensic STR typing can yield different results due to primer binding site mutations. These sequence variations, like the 16-nucleotide deletion at D16S539, can hinder database matches.

Keywords:
D16S539Database matchesIndelsSTR-kit dependent allele discrepancies

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Area of Science:

  • Forensic Science
  • Genetics
  • Molecular Biology

Background:

  • Multiplex PCR kits are widely used for forensic short tandem repeat (STR) typing.
  • Variations in STR profiles can occur when using different commercial STR kits.

Observation:

  • Primer binding site mutations, insertions, or deletions in flanking regions of STR loci can cause genotype discrepancies.
  • A 16-nucleotide deletion near the primer binding site downstream of the D16S539 repeat sequence was identified.

Findings:

  • This deletion resulted in different genotypes at the D16S539 locus when analyzed with various STR kits.
  • Sequence variations in STR flanking regions represent a common and significant challenge in forensic STR typing.

Implications:

  • Undetected sequence variations can lead to a failure in matching STR profiles in national databases.
  • These discrepancies have far-reaching consequences for forensic investigations and identification processes.
  • The study highlights the need to consider and address sequence variations in STR flanking regions for accurate forensic analysis.