ArticleScientific reports2020
Large scale, robust, and accurate whole transcriptome profiling from clinical formalin-fixed paraffin-embedded samples.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 50 citations in OpenAlex.
- Pre-analytical Best Practices for RNA Sequencing from Small Biopsies and Cytologic Specimens.Molecular diagnosis & therapy · 2026Review
- Identification and prioritisation of tumour antigen candidates from 79 glioblastoma transcriptomes.Cancer immunology, immunotherapy : CII · 2026Article
- HPV Integration in Head and Neck Cancer: Downstream Splicing Events and Expression Ratios Linked with Poor Outcomes.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026Article
- Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues.Nature communications · 2025Article
- Comprehensive molecular characterization of craniopharyngiomas using whole transcriptome and spatial transcriptomics approaches.Brain tumor pathology · 2025Article
- Comparative analysis of library preparation approaches for FFPE gene expression profiling and related recommendations.Scientific reports · 2025Article
- Spatial transcriptomic and morpho-functional information derived from single mouse FFPE slides allows in-depth fingerprinting of lung fibrosis.Respiratory research · 2025Article
- Identification of HER2-positive breast cancer molecular subtypes with potential clinical implications in the ALTTO clinical trial.Nature communications · 2024Article
- Article
- RNA Sequencing in Disease Diagnosis.Annual review of genomics and human genetics · 2024Review
- LINCATRA: Two-cycle method to amplify RNA for transcriptome analysis from formalin-fixed paraffin-embedded tissue.Heliyon · 2024Article
- Article
- Procrustes is a machine-learning approach that removes cross-platform batch effects from clinical RNA sequencing data.Communications biology · 2024Article
- Review of Molecular Technologies for Investigating Canine Cancer.Animals : an open access journal from MDPI · 2024Review
- Archival skin biopsy specimens as a tool for miRNA-based diagnosis: Technical and post-analytical considerations.Molecular therapy. Methods & clinical development · 2023Article
- A Genomic Analysis of Esophageal Squamous Cell Carcinoma in Eastern Africa.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2023Article
- Cost-Efficient Detection ofInternational journal of molecular sciences · 2023Article
- Inferred Immune-Cell Activity Is an Independent Predictor of HER2-Negative Breast Cancer Prognosis and Response to Paclitaxel-Based Therapy in the GeparSepto Trial.Clinical cancer research : an official journal of the American Association for Cancer Research · 2023Article
- Test of the FlashFREEZE unit in tissue samples freezing for biobanking purposes.Cell and tissue banking · 2023Article
- Comparison of whole transcriptome sequencing of fresh, frozen, and formalin-fixed, paraffin-embedded cardiac tissue.PloS one · 2023Article
Corrections and comments
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Authors and funding
10 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcriptome profiling can provide information of great value in clinical decision-making, yet RNA from readily available formalin-fixed paraffin-embedded (FFPE) tissue is often too degraded for quality sequencing. To assess the clinical utility of FFPE-derived RNA, we performed ribo-deplete RNA extractions on > 3200 FFPE slide samples; 25 of these had direct FFPE vs. fresh frozen (FF) replicates, 57 were sequenced in 2 different labs, 87 underwent multiple library analyses, and 16 had direct microdissected vs. macrodissected replicates. Poly-A versus ribo-depletion RNA extraction methods were compared using transcriptomes of TCGA cohort and 3116 FFPE samples. Compared to FF, FFPE transcripts coding for nuclear/cytoplasmic proteins involved in DNA packaging, replication, and protein synthesis were detected at lower rates and zinc finger family transcripts were of poorer quality. The greatest difference in extraction methods was in histone transcripts which typically lack poly-A tails. Encouragingly, the overall sequencing success rate was 81%. Exome coverage was highly concordant in direct FFPE and FF replicates, with 98% agreement in coding exon coverage and a median correlation of whole transcriptome profiles of 0.95. We provide strong rationale for clinical use of FFPE-derived RNA based on the robustness, reproducibility, and consistency of whole transcriptome profiling.
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