ArticlePloS one2017
A Comparison of RNA-Seq Results from Paired Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Glioblastoma Tissue Samples.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers, 1 of them a synthesis that pooled it.
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Who cites it
76 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Molecular analysis of H&E- and Papanicolau-stained samples-systematic review.Histochemistry and cell biology · 2020Pooled it
- Safety and efficacy of depatuxizumab mafodotin in Japanese patients with malignant glioma: A nonrandomized, phase 1/2 trial.Cancer science · 2021Trial
- The association between MGMT expression and outcome in H3 G34-mutant diffuse hemispheric glioma is robust to adjustment for pre-analytic and technical variables.Acta neuropathologica · 2026Article
- Extracellular Particles Isolated from Leftover Discarded Formalin-Fixed Tissues Exhibit Atypical Extracellular RNA Profiles.Biomolecules · 2026Article
- National Tissue Freezing Protocol is Essential for Modern Cancer Care and Research.Trends in medicine · 2026Article
- iCLAP: an innovative method for integrable co-detection of low-abundance antigens with high-plex immunostaining.Nature communications · 2026Article
- Article
- Determining the Biological Features of Aggressive Meningioma Growth with Transcriptomic Profiling.Cancers · 2025Article
- Spatial transcriptomic and morpho-functional information derived from single mouse FFPE slides allows in-depth fingerprinting of lung fibrosis.Respiratory research · 2025Article
- Clinical and analytical validation of a combined RNA and DNA exome assay across a large tumor cohort.Communications medicine · 2025Article
- Transcriptomics and epigenomics datasets of primary brain cancers in formalin-fixed paraffin embedded format.Scientific data · 2025Article
- Classification of non-TCGA cancer samples to TCGA molecular subtypes using compact feature sets.Cancer cell · 2025Article
- The Potential of Single-Transcription Factor Gene Expression by RT-qPCR for Subtyping Small Cell Lung Cancer.International journal of molecular sciences · 2025Article
- Impact of commercial RNA extraction methods on the recovery of human RNA sequence data from archival fixed tissues.BioTechniques · 2025Article
- Reliable RNA-seq analysis from FFPE specimens as a means to accelerate cancer-related health disparities research.PloS one · 2025Article
- A consensus molecular subtypes classification strategy for clinical colorectal cancer tissues.Life science alliance · 2024Article
- Article
- ChromogenicNon-coding RNA research · 2024Article
- Optimization of FFPE preparation and identification of gene attributes associated with RNA degradation.NAR genomics and bioinformatics · 2024Article
- Comparison of LIRADS 5 Image Guided Core Biopsy Derived From Formalin Fixed and Frozen Tissue Cores for Radiogenomics and Radioproteomics Analysis in Well, Moderate and Poorly Differentiated Hepatocellular Carcinoma.Global medicine and therapeutics · 2024Article
16 more citing papers are in PubMed but not listed here.
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19 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The molecular classification of glioblastoma (GBM) based on gene expression might better explain outcome and response to treatment than clinical factors. Whole transcriptome sequencing using next-generation sequencing platforms is rapidly becoming accepted as a tool for measuring gene expression for both research and clinical use. Fresh frozen (FF) tissue specimens of GBM are difficult to obtain since tumor tissue obtained at surgery is often scarce and necrotic and diagnosis is prioritized over freezing. After diagnosis, leftover tissue is usually stored as formalin-fixed paraffin-embedded (FFPE) tissue. However, RNA from FFPE tissues is usually degraded, which could hamper gene expression analysis. We compared RNA-Seq data obtained from matched pairs of FF and FFPE GBM specimens. Only three FFPE out of eleven FFPE-FF matched samples yielded informative results. Several quality-control measurements showed that RNA from FFPE samples was highly degraded but maintained transcriptomic similarities to RNA from FF samples. Certain issues regarding mutation analysis and subtype prediction were detected. Nevertheless, our results suggest that RNA-Seq of FFPE GBM specimens provides reliable gene expression data that can be used in molecular studies of GBM if the RNA is sufficiently preserved.
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