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FFixR: a machine learning framework for accurate somatic mutation calling from FFPE RNA-seq data in cancer.

Bioinformatics (Oxford, England) - 2 Jul 2026

Livne Or, Yizhak Keren

Abstract excerpt

MOTIVATION: Formalin-fixed paraffin-embedded (FFPE) tissues are widely used in clinical and research settings, yet their use for detecting somatic mutations from RNA sequencing (RNA-seq) is hindered by artefactual mutations introduced by cytosine deamination and strand-specific damage. Existing FFPE noise-filtering tools are tailored to DNA sequencing (DNA-seq) and rely on strand bias, rendering them unsuitable...

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Formaldehyde
Machine Learning
Melanoma
Neoplasms
Paraffin Embedding
RNA-Seq

Methodology Data sources Editorial policy Privacy About Contact Helena Bioinformatics

Sequence Analysis, RNA

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PMID: 42340671
DOI: 10.1093/bioinformatics/btag405
PMCID: PMC13335478

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PubMed metadata and Literature Corpus relationships. Corpus snapshot updated 31 Aug 2026.

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