ArticleNature communications2024
Large-scale analysis of whole genome sequencing data from formalin-fixed paraffin-embedded cancer specimens demonstrates preservation of clinical utility.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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
20 citing papers in PubMed.
- Mutational Signature-Based Biomarker for Phase II Trial of Olaparib Maintenance in Advanced High-Grade Ovarian Cancer.Cancer science · 2026Trial
- Highly Sensitive Spatial Host-Microbiome Transcriptomics in FFPE Tissues via Iterative Hydrogel Expansion.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Capillary-Driven Microfluidic Electrical Screening of Influenza H3N2-Infected A549 Cells Using AgNP-Decorated Laser-Patterned Villous Microstructures.Biosensors · 2026Article
- Effects of ethanol and acetaldehyde on multi-organ genomic mutation landscapes.Cell biology and toxicology · 2026Article
- Long-read sequencing technologies and bioinformatics: a new perspective for decoding DNA methylation modifications.Journal of translational medicine · 2026Review
- Implementing whole genome and transcriptome sequencing for cancer patients in routine healthcare: a comprehensive guide to costing.British journal of cancer · 2026Article
- Pre-Analytical and Analytical Challenges in Whole-Exome Sequencing of Formalin-Fixed Paraffin-Embedded Breast and Prostate Cancer Tissue: A Real-World Multicenter Study.Diagnostics (Basel, Switzerland) · 2026Article
- ctDNA monitoring using tumor-informed copy number analysis.EMBO molecular medicine · 2026Article
- Haplotype-aware segmentation with HapASeg increases accuracy of detecting homolog-specific somatic copy number alterations.Genome biology · 2026Article
- Comparative evaluation of HTG and TempO Seq targeted transcriptome profiling methods.Scientific reports · 2026Article
- Evaluation of ensilication technology for ambient DNA preservation.NAR molecular medicine · 2026Article
- Enabling whole genome sequencing analysis from FFPE specimens in clinical oncology.Nature communications · 2025Article
- Cryopreserved Tissue Biospecimens Offer Superior Quality for Whole-Genome Sequencing of Various Cancers Compared to Paired Formalin-Fixed Paraffin-Embedded Tissues.International journal of molecular sciences · 2025Article
- Article
- Next-Generation Sequencing: A Review of Its Transformative Impact on Cancer Diagnosis, Treatment, and Resistance Management.Diagnostics (Basel, Switzerland) · 2025Review
- Genome-scale multi-organ analysis of mutagenic effects of ethanol and acetaldehyde in Sprague Dawley rats.bioRxiv : the preprint server for biology · 2025Article
- Benchmarking copy number variation detection with low-coverage whole-genome sequencing.Briefings in bioinformatics · 2025Article
- Optimization of methylation capture sequencing workflow in formalin fixed tissue from oral squamous cell carcinoma patients.Oral oncology · 2025Article
- Whole genome sequencing improves tissue-of-origin diagnosis and treatment options for cancer of unknown primary.Nature communications · 2025Article
- A cost-effective and scalable approach for DNA extraction from FFPE tissues.Biology methods & protocols · 2025Article
Corrections and comments
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Authors and funding
23 authors.
Funding
Abstract
Whole genome sequencing (WGS) provides comprehensive, individualised cancer genomic information. However, routine tumour biopsies are formalin-fixed and paraffin-embedded (FFPE), damaging DNA, historically limiting their use in WGS. Here we analyse FFPE cancer WGS datasets from England's 100,000 Genomes Project, comparing 578 FFPE samples with 11,014 fresh frozen (FF) samples across multiple tumour types. We use an approach that characterises rather than discards artefacts. We identify three artefactual signatures, including one known (SBS57) and two previously uncharacterised (SBS FFPE, ID FFPE), and develop an "FFPEImpact" score that quantifies sample artefacts. Despite inferior sequencing quality, FFPE-derived data identifies clinically-actionable variants, mutational signatures and permits algorithmic stratification. Matched FF/FFPE validation cohorts shows good concordance while acknowledging SBS, ID and copy-number artefacts. While FF-derived WGS data remains the gold standard, FFPE-samples can be used for WGS if required, using analytical advancements developed here, potentially democratising whole cancer genomics to many.
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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.