Evidence map›Paper›PMID 40779107›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2025

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

Qingli Guo, Ann-Marie Baker, Ville Mustonen, Trevor A Graham

Abstract read
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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

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.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors.

Qingli GuoGenomics and Evolutionary Dynamics Laboratory, Centre for Evolution and Cancer, Institute of Cancer Research, London, UK. qingli.guo@icr.ac.uk.
Ann-Marie BakerGenomics and Evolutionary Dynamics Laboratory, Centre for Evolution and Cancer, Institute of Cancer Research, London, UK.
Ville MustonenOrganismal and Evolutionary Biology Research Programme, Department of Computer Science, University of Helsinki, Helsinki, Finland.
Trevor A GrahamGenomics and Evolutionary Dynamics Laboratory, Centre for Evolution and Cancer, Institute of Cancer Research, London, UK.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The wealth of routinely processed formalin-fixed and paraffin-embedded (FFPE) cancer biopsies is potentially a tremendous resource for cancer genomics research. However, the presence of formalin-induced artifactual mutations in FFPE material can confound mutational analyses. Our de-noising algorithm, FFPEsig, removes FFPE-related artifactual mutations enabling the inference of biological mutational signatures. In this chapter, we focus on the practical use of FFPEsig, offering a detailed guidance from both the wet-lab experimental and bioinformatics analysis perspectives. Our aim is to assist users to generate robust and significant results using FFPEsig.

Indexed as

ArtifactsFormaldehydeMutationNeoplasmsParaffin EmbeddingTissue FixationAlgorithmsComputational BiologyDNA Mutational AnalysisHumansFormaldehydeBiological mutation signalDe-noisingFFPE samplesMutational processesSignature analysis

Identifiers

PMID40779107

What OpenQuestion holds

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Registered trials

None linked

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.