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Updated: Mar 6, 2026

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Non-reproducible sequence artifacts in FFPE tissue: an experience report.

Richard Ofner1, Cathrin Ritter1,2, Selma Ugurel3

  • 1Department of General Dermatology, Medical University Graz, Graz, Austria.

Journal of Cancer Research and Clinical Oncology
|March 19, 2017
PubMed
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Formalin-fixed paraffin-embedded (FFPE) DNA fragmentation and deamination cause sequence artifacts, hindering accurate cancer mutation detection. Implementing workflow measures is crucial for reliable genomic analysis in clinical practice.

Area of Science:

  • Genomic medicine
  • Molecular oncology
  • Cancer genomics

Background:

  • Genomic analyses are integral to molecularly targeted cancer therapy.
  • Accurate detection of actionable mutations aids diagnosis and treatment selection.
  • Formalin-fixed paraffin-embedded (FFPE) tissue DNA presents significant challenges for genetic testing.

Purpose of the Study:

  • To share experiences with FFPE DNA challenges in PCR-based sequencing.
  • To investigate DNA fragmentation and hydrolytic deamination as sources of sequence artifacts.
  • To propose strategies for improving the detection of targetable mutations.

Main Methods:

  • Isolation of genomic DNA from FFPE tumor samples.
  • PCR amplification and Sanger sequencing of target genes.
Keywords:
ERBB4FFPEMelanomaSanger sequencingSequencing artifacts

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  • Statistical analysis of sequencing data.

    • Main Results:

    • Identified 46 ERBB4 mutations in 27 of 96 FFPE samples.
    • Discovered 11 mutations at three novel mutational hotspots.
    • Failed to confirm hotspot mutations, indicating sequence artifacts likely from FFPE DNA lesions.

    Conclusions:

    • FFPE DNA is the primary source for mutational analyses.
    • Sequence artifacts from FFPE DNA damage can compromise accuracy.
    • Workflow adjustments are necessary to assess DNA damage and ensure reliable mutation detection.