ArticlePloS one2023
Comparison of whole transcriptome sequencing of fresh, frozen, and formalin-fixed, paraffin-embedded cardiac tissue.
Article in PloS one, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers, 1 of them a synthesis that pooled it.
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Who cites it
35 citing papers in PubMed, 1 synthesis or guideline pooled it, 56 citations in OpenAlex.
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- Therapeutic Target Mapping to Advance Drug Repurposing for Cardiovascular Disease: A Perspective from an Explanted Heart Biobank.Journal of personalized medicine · 2026Review
- Perspectives From an Expert-Guided Discussion on Maximizing the Research Potential of Small Biopsy Tissue.JCO precision oncology · 2026Article
- Transcriptome predictors of second breast events in ductal carcinoma in situ: a case‒control study including Black and White women.Breast cancer research : BCR · 2026Article
- Pre-analytical Best Practices for RNA Sequencing from Small Biopsies and Cytologic Specimens.Molecular diagnosis & therapy · 2026Review
- Integrated epidemiological and molecular data inform the relationship between precancer and cancer states of esophageal adenocarcinoma.Nature medicine · 2026Article
- National Tissue Freezing Protocol is Essential for Modern Cancer Care and Research.Trends in medicine · 2026Article
- Application of RNA markers in forensic body fluid analysis: from specificity and stability to polymorphism.International journal of legal medicine · 2026Review
- The actionable transcriptome: a framework for incorporating RNA sequencing into precision oncology.Nature reviews. Clinical oncology · 2026Review
- Systematic evaluation of long- and short-read RNA-seq for human peripheral blood.NAR molecular medicine · 2026Article
- 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
- Identification of palmitoylation-related lncRNAs as prognostic biomarkers and immune modulators in HCC.Discover oncology · 2025Article
- Generative and integrative modeling for transcriptomics with formalin fixed paraffin embedded material.Journal of translational medicine · 2025Article
- Article
- Current Role and Future Frontiers of Spatial Transcriptomics in Genitourinary Cancers.Cancers · 2025Review
- Comparative analysis of library preparation approaches for FFPE gene expression profiling and related recommendations.Scientific reports · 2025Article
- Leveraging RNA from DNA Extraction Lysate to Rescue "Insufficient" Samples for More Comprehensive Genomic Profiling in Patients with Scant Tumor Specimens.The Journal of molecular diagnostics : JMD · 2025Article
- Spatial transcriptomic and morpho-functional information derived from single mouse FFPE slides allows in-depth fingerprinting of lung fibrosis.Respiratory research · 2025Article
- Cyclosporine A Accelerates Neurorecovery Transcriptional Trajectory in a Swine Model of Diffuse Traumatic Brain Injury.International journal of molecular sciences · 2025Article
- Blood-based detection of MMP11 as a marker of prostate cancer progression regulated by the ALDH1A1-TGF-β1 signaling mechanism.Journal of experimental & clinical cancer research : CR · 2025Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The use of fresh tissue for molecular studies is preferred but often impossible. Instead, frozen or formalin-fixed, paraffin-embedded (FFPE) tissues are widely used and constitute valuable resources for retrospective studies. We assessed the utility of cardiac tissue stored in different ways for gene expression analyses by whole transcriptome sequencing of paired fresh, frozen, and FFPE tissues. RNA extracted from FFPE was highly degraded. Sequencing of RNA from FFPE tissues yielded higher proportions of intronic and intergenic reads compared to RNA from fresh and frozen tissues. The global gene expression profiles varied with the storage conditions, particularly mitochondrial and long non-coding RNAs. However, we observed high correlations among protein-coding transcripts (ρ > 0.94) with the various storage conditions. We did not observe any significant storage effect on the allele-specific gene expression. However, FFPE had statistically significantly (p < 0.05) more discordant variant calls compared to fresh and frozen tissue. In conclusion, we found that frozen and FFPE tissues can be used for reliable gene expression analyses, provided that proper quality control is performed and caution regarding the technical variability is withheld.
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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.