ArticleThe journal of histochemistry and cytochemistry : official journal of the Histochemistry Society2020
Why Formalin-fixed, Paraffin-embedded Biospecimens Must Be Used in Genomic Medicine: An Evidence-based Review and Conclusion.
Article in The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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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
43 citing papers in PubMed, 74 citations in OpenAlex.
- Cytology smears from endobronchial ultrasound-guided transbronchial needle aspiration as a source of nucleic acids with adequate yield for next-generation sequencing.Journal of thoracic disease · 2026Article
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- Sequencing of Fibroblast Growth Factor Receptor Inhibitors in Cholangiocarcinoma: A Review of Published Cases.JCO precision oncology · 2026Review
- Single-cell analysis of matched FFPE and frozen tissue samples reveals comparable resolution of intratumoural heterogeneity.Frontiers in genetics · 2026Article
- Tumor Genomic and Transcriptomic Analysis Integrated With Liquid Biopsy ctDNA Monitoring: Analytical Validation and Clinical Insights.Cancer medicine · 2025Article
- Unveiling roles of non-coding RNAs in cancer through advanced technologies.Quantitative biology (Beijing, China) · 2025Article
- Enabling whole genome sequencing analysis from FFPE specimens in clinical oncology.Nature communications · 2025Article
- AI-augmented intraoperative decision-making workflows in diffuse midline glioma biopsy using cryosection pathology.Nature communications · 2025Article
- Evaluation of the HumanMethylationEPIC v2.0 Bead Chip Using Low Quality and Quantity DNA Samples.Biological procedures online · 2025Article
- Optimization of methylation capture sequencing workflow in formalin fixed tissue from oral squamous cell carcinoma patients.Oral oncology · 2025Article
- Spatial transcriptomic and morpho-functional information derived from single mouse FFPE slides allows in-depth fingerprinting of lung fibrosis.Respiratory research · 2025Article
- Assessing the suitability of formalin-fixed paraffin-embedded (FFPE) tissue for genome-wide association studies (GWAS).BMC research notes · 2025Article
- Multicenter In-House Evaluation of an Amplicon-Based Next-Generation Sequencing Panel for Comprehensive Molecular Profiling.Molecular diagnosis & therapy · 2025Article
- Genetic Uncertainties Fueling Cholangiocarcinoma Progression.Current genomics · 2025Review
- Article
- Cryo-X-Ray Phase Contrast Imaging Enables Combined 3D Structural Quantification and Nucleic Acid Analysis of Myocardial Biopsies.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- From Genomic Exploration to Personalized Treatment: Next-Generation Sequencing in Oncology.Current issues in molecular biology · 2024Review
- Large-scale analysis of whole genome sequencing data from formalin-fixed paraffin-embedded cancer specimens demonstrates preservation of clinical utility.Nature communications · 2024Article
- Review
- Biomarker development for PD-(L)1 axis inhibition: a consensus view from the SITC Biomarkers Committee.Journal for immunotherapy of cancer · 2024Review
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Fresh-frozen tissue is the "gold standard" biospecimen type for next-generation sequencing (NGS). However, collecting frozen tissue is usually not feasible because clinical workflows deliver formalin-fixed, paraffin-embedded (FFPE) tissue blocks. Some clinicians and researchers are reticent to embrace the use of FFPE tissue for NGS because FFPE tissue can yield low quantities of degraded DNA, containing formalin-induced mutations. We describe the process by which formalin-induced deamination can lead to artifactual cytosine (C) to thymine (T) and guanine (G) to adenine (A) (C:G > T:A) mutation calls and perform a literature review of 17 publications that compare NGS data from patient-matched fresh-frozen and FFPE tissue blocks. We conclude that although it is indeed true that sequencing data from FFPE tissue can be poorer than those from frozen tissue, any differences occur at an inconsequential magnitude, and FFPE biospecimens can be used in genomic medicine with confidence.
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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.