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Using FFPEsig to Remove Formalin-Induced Artifacts and Characterize Mutational Signatures in Cancer.

Qingli Guo1,2, Ann-Marie Baker3, Ville Mustonen4

  • 1Genomics and Evolutionary Dynamics Laboratory, Centre for Evolution and Cancer, Institute of Cancer Research, London, UK. qingli.guo@icr.ac.uk.

Methods in Molecular Biology (Clifton, N.J.)
|August 8, 2025
PubMed
Summary

Our FFPEsig algorithm removes artifactual mutations from formalin-fixed, paraffin-embedded cancer biopsies. This enables accurate inference of true biological mutational signatures for cancer genomics research.

Keywords:
Biological mutation signalDe-noisingFFPE samplesMutational processesSignature analysis

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Area of Science:

  • Oncology
  • Genomics
  • Bioinformatics

Background:

  • Formally fixed, paraffin-embedded (FFPE) cancer biopsies are a valuable resource for genomic research.
  • Formalin fixation introduces artifactual mutations that can interfere with accurate mutational analysis.
  • Existing methods struggle to distinguish true biological mutations from FFPE-induced artifacts.

Purpose of the Study:

  • To provide practical guidance on using the FFPEsig algorithm for de-noising FFPE cancer biopsy data.
  • To enable researchers to confidently identify true biological mutational signatures.
  • To improve the reliability of cancer genomics research using FFPE samples.

Main Methods:

  • Development and application of the FFPEsig de-noising algorithm.
  • Detailed protocols for wet-lab experimental procedures with FFPE samples.
  • Bioinformatics analysis pipelines for processing FFPE data with FFPEsig.

Main Results:

  • FFPEsig effectively removes formalin-induced artifactual mutations.
  • The algorithm enables accurate inference of biological mutational signatures.
  • User guidance facilitates robust and significant results in cancer genomics.

Conclusions:

  • FFPEsig is a crucial tool for accurate cancer genomics research using FFPE samples.
  • The algorithm enhances the utility of archival FFPE biopsy collections.
  • Researchers can achieve reliable mutational signature analysis with FFPEsig.