Discover Community Create You

Loading publication...

Noodle always counts identifier-free feature events for service operation. With your permission, Google Analytics can also estimate audience and engagement. Search text, publication identifiers, cookies, IP addresses and browser fingerprints are never included in Noodle's first-party event counters.

Privacy details

Article

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

Methods in molecular biology (Clifton, N.J.) - 1 Jan 2025

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

Abstract excerpt

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...

Read the complete abstract on PubMed

Topics

Share this publication in a Topic to start or enrich a Post.

Share to Algorithms
Share to Artifacts
Share to Computational Biology

Methodology Data sources Editorial policy Privacy About Contact Helena Bioinformatics

Share to DNA Mutational Analysis

Share to Formaldehyde

Share to Neoplasms

Share to Paraffin Embedding

Share to Tissue Fixation

Source

Identifiers

PMID: 40779107
DOI: 10.1007/978-1-0716-4566-6_6

Provenance

PubMed metadata and Literature Corpus relationships. Corpus snapshot updated 3 Sept 2026.

Related research

Semantic proximity does not establish scientific evidence.

Research trail→

Click a neighbor to travelStep 1 · 12 closest

Using FFPEsig to Remove Formalin-Induced Artifacts and Characterize Mutational Signatures in Cancer.PMID 40779107Read ↗

The mutational signatures of formalin fixation on the human genomeSemantic proximity Read ↗

The mutational signatures of formalin fixation on the human genome.Semantic proximity Read ↗

Large-scale analysis of whole genome sequencing data from formalin-fixed paraffin-embedded cancer specimens demonstrates preservation of clinical utility.Semantic proximity Read ↗

Excerno: Using Mutational Signatures in Sequencing Data to Filter False Variants Caused by Clinical Archival.Semantic proximity Read ↗

Correction of the cytosine deamination artifacts in FFPE-based sequencing experimentsSemantic proximity Read ↗

Why Formalin-fixed, Paraffin-embedded Biospecimens Must Be Used in Genomic Medicine: An Evidence-based Review and Conclusion.Semantic proximity Read ↗

Accurate somatic variant detection from formalin fixed, paraffin embedded tissue (FFPE) derived WES and WGS by DeepOmicsFFPE-PLUS, a sequence context-based transformerSemantic proximity Read ↗

Sequence Artifacts in DNA from Formalin-Fixed Tissues: Causes and Strategies for MinimizationSemantic proximity Read ↗

FFixR: A Machine Learning Framework for Accurate Somatic Mutation Calling from FFPE RNA-Seq Data in CancerSemantic proximity Read ↗

Comparison of Accuracy of Whole-Exome Sequencing with Formalin-Fixed Paraffin-Embedded and Fresh Frozen Tissue SamplesSemantic proximity Read ↗

Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics.Semantic proximity Read ↗

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

⌁Select a neighboring publication to make it the new centre.