ArticleToxicological sciences : an official journal of the Society of Toxicology2019
Enhanced Quality Metrics for Assessing RNA Derived From Archival Formalin-Fixed Paraffin-Embedded Tissue Samples.
Article in Toxicological sciences : an official journal of the Society of Toxicology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 25 citations in OpenAlex.
- FFPE-CUTAC: A Single Assay, Multiple Layers.bioRxiv : the preprint server for biology · 2026Article
- Article
- Assessing the Effects of a 3-Dimensional (3D) Pathology Tissue-Processing Workflow on Downstream Molecular Analyses.Laboratory investigation; a journal of technical methods and pathology · 2026Article
- Exploring the human brain: spatial transcriptomics challenges and approaches in post-mortem analysis.Brain : a journal of neurology · 2026Review
- Advancement in the Methods for Isolating High Quality RNA From Mouse and Rat Intervertebral Disc.JOR spine · 2026Article
- Impact of commercial RNA extraction methods on the recovery of human RNA sequence data from archival fixed tissues.BioTechniques · 2025Article
- Effective Preparation of FFPE Tissue Samples for Preserving Appropriate Nucleic Acid Quality for Genomic Analysis in Thyroid Carcinoma.Endocrine pathology · 2024Article
- Comparative Analysis of Gene Expression Analysis Methods for RNA in Situ Hybridization Images.The Journal of molecular diagnostics : JMD · 2024Article
- Effect of formalin-fixation and paraffin-embedded tissue storage times on RNAscope in situ hybridization signal amplification.Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc · 2024Article
- Areas of Crush Nuclear Streaming Should Be Included as Tumor Content in the Era of Molecular Diagnostics.Cancers · 2023Article
- Comprehensive Development and Implementation of Good Laboratory Practice for NGS Based Targeted Panel on Solid Tumor FFPE Tissues in Diagnostics.Diagnostics (Basel, Switzerland) · 2022Article
- Genome-wide spatial expression profiling in formalin-fixed tissues.Cell genomics · 2021Article
- Transcriptomic analysis to identify genes associated with selective hippocampal vulnerability in Alzheimer's disease.Nature communications · 2021Article
- Large scale, robust, and accurate whole transcriptome profiling from clinical formalin-fixed paraffin-embedded samples.Scientific reports · 2020Article
- A Novel HPLC-Based Method to Investigate on RNA after Fixation.International journal of molecular sciences · 2020Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues provide an important resource for toxicogenomic research. However, variability in the integrity or quality of RNA obtained from archival FFPE specimens can lead to unreliable data and wasted resources, and standard protocols for measuring RNA integrity do not adequately assess the suitability of FFPE RNA. The main goal of this study was to identify improved methods for evaluating FFPE RNA quality for whole-genome sequencing. We examined RNA quality metrics conducted prior to RNA-sequencing in paired frozen and FFPE samples with varying levels of quality based on age in block and time in formalin. RNA quality was measured by the RNA integrity number (RIN), a modified RIN called the paraffin-embedded RNA metric, the percentage of RNA fragments >100-300 nucleotides in size (DV100-300), and 2 quantitative PCR-based methods. This information was correlated to sequencing read quality, mapping, and gene detection. Among fragmentation-based methods, DV and PCR-based metrics were more informative than RIN or paraffin-embedded RNA metric in determining sequencing success. Across low- and high-quality FFPE samples, a minimum of 80% of RNA fragments >100 nucleotides (DV100 > 80) provided the best indication of gene diversity and read counts upon sequencing. The PCR-based methods further showed quantitative reductions in amplifiable RNA of target genes related to sample age and time in formalin that inform input quantity of FFPE RNA for sequencing. These results should aid in screening and prioritizing archival FFPE samples for retrospective analyses of gene expression.
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