ArticleNature communications2022
The mutational signatures of formalin fixation on the human genome.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 81 papers.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
81 citing papers in PubMed, 100 citations in OpenAlex.
- Mutational Signature-Based Biomarker for Phase II Trial of Olaparib Maintenance in Advanced High-Grade Ovarian Cancer.Cancer science · 2026Trial
- DNA Repair gene alterations and efficacy from gemcitabine and nab-paclitaxel with/without durvalumab and tremelimumab in metastatic pancreatic ductal adenocarcinoma.Nature communications · 2026Trial
- FFPE-CUTAC: A Single Assay, Multiple Layers.bioRxiv : the preprint server for biology · 2026Article
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- A Practical Workflow for Correcting Kit-Specific Effects in Whole-Exome Sequencing Data.Methods and protocols · 2026Article
- Molecular characterization of mismatch repair deficient tumors in young Jordanian patients.Discover oncology · 2026Article
- Article
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- FFixR: a machine learning framework for accurate somatic mutation calling from FFPE RNA-seq data in cancer.Bioinformatics (Oxford, England) · 2026Article
- Impact of Genomic Mutations on the Transcriptional Pathways and Tumor Microenvironment Landscape of Localized Early Prostate Cancer.The Prostate · 2026Article
- Effects of ethanol and acetaldehyde on multi-organ genomic mutation landscapes.Cell biology and toxicology · 2026Article
- DREAM repressive activity links somatic mutation, lifespan and disease.Nature aging · 2026Article
- Mutational signature-based classification uncovers emerging oral cancer subtypes with distinct molecular patterns.International journal of oral science · 2026Article
- The Molecular Landscape of CASTLE: A Rare Thymus-like Head and Neck Cancer.International journal of molecular sciences · 2026Article
- Clinical validation of a high-performance somatic exome sequencing assay: from target-enrichment strategy to variant calling.NPJ genomic medicine · 2026Article
- Investigating the contribution of rare non-coding variants in BRCA1, BRCA2 and PALB2 to hereditary breast cancer.NPJ breast cancer · 2026Article
- Single-cell and spatial profiling in cancer biology and clinical oncology.Nature cancer · 2026Review
- Integrating breast tumour homologous recombination deficiency status to aid germline BRCA1 and BRCA2 variant classification.EBioMedicine · 2026Article
- Development and Performance Validation of a Comprehensive Liquid Biopsy Genotyping Panel for Pan-cancer Analysis.Annals of laboratory medicine · 2026Article
- Microbiome-Genome Crosstalk in Colorectal Cancer: Colibactin Signatures andInternational journal of molecular sciences · 2026Review
21 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 3 countries.
Funding
Abstract
Clinical archives of patient material near-exclusively consist of formalin-fixed and paraffin-embedded (FFPE) blocks. The ability to precisely characterise mutational signatures from FFPE-derived DNA has tremendous translational potential. However, sequencing of DNA derived from FFPE material is known to be riddled with artefacts. Here we derive genome-wide mutational signatures caused by formalin fixation. We show that the FFPE-signature is highly similar to signature 30 (the signature of Base Excision Repair deficiency due to NTHL1 mutations), and chemical repair of DNA lesions leads to a signature highly similar to signature 1 (clock-like signature due to spontaneous deamination of methylcytosine). We demonstrate that using uncorrected mutational catalogues of FFPE samples leads to major mis-assignment of signature activities. To correct for this, we introduce FFPEsig, a computational algorithm to rectify the formalin-induced artefacts in the mutational catalogue. We demonstrate that FFPEsig enables accurate mutational signature analysis both in simulated and whole-genome sequenced FFPE cancer samples. FFPEsig thus provides an opportunity to unlock additional clinical potential of archival patient tissues.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.