ArticleBMC bioinformatics2020
Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: comparison of gene expression profiling approaches.
Article in BMC bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
37 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of gene expression disease signatures in colonic biopsy tissue from patients with ulcerative colitis.Scientific reports · 2021Pooled it
- Immunoregulatory and lipid presentation pathways are upregulated in human face transplant rejection.The Journal of clinical investigation · 2021Trial
- Detection ofInternational journal of molecular sciences · 2026Article
- A guide to transcriptomic deconvolution in cancer.Nature reviews. Cancer · 2026Review
- Molecular mosaic of colorectal cancer: Why one classification system is no longer enough?World journal of gastrointestinal oncology · 2026Article
- Single-cell analysis of matched FFPE and frozen tissue samples reveals comparable resolution of intratumoural heterogeneity.Frontiers in genetics · 2026Article
- Comprehensive molecular characterization of craniopharyngiomas using whole transcriptome and spatial transcriptomics approaches.Brain tumor pathology · 2025Article
- MammOnc-DB, an integrative breast cancer data analysis platform for target discovery.NPJ breast cancer · 2025Article
- Exploring the influence of pre-analytical variables on gene expression measurements and relative expression orderings in cancer research.Scientific reports · 2025Article
- TempO-seq and RNA-seq gene expression levels are highly correlated for most genes: A comparison using 39 human cell lines.PloS one · 2025Article
- Strong correlation of gene counts and differentially expressed genes between a 3' RNA-Seq and an RNA hybridization platform in transcriptome analyses from canine archival tissues.Frontiers in veterinary science · 2025Article
- Proof of Concept Study: Comparison of Semi-Automated RNA Isolation Methods from Archived Formalin-Fixed, Paraffin-Embedded Tissues with Clinical Routine RNA Isolation Methods.Methods and protocols · 2024Article
- Drug Repurposing for Cancer Treatment: A Comprehensive Review.International journal of molecular sciences · 2024Review
- snPATHO-seq, a versatile FFPE single-nucleus RNA sequencing method to unlock pathology archives.Communications biology · 2024Article
- Identification of Tumor Budding-Associated Genes in Breast Cancer through Transcriptomic Profiling and Network Diffusion Analysis.Biomolecules · 2024Article
- PI3Kγ inhibition circumvents inflammation and vascular leak in SARS-CoV-2 and other infections.Science translational medicine · 2024Article
- LINCATRA: Two-cycle method to amplify RNA for transcriptome analysis from formalin-fixed paraffin-embedded tissue.Heliyon · 2024Article
- A High-Throughput PIXUL-Matrix-Based Toolbox to Profile Frozen and Formalin-Fixed Paraffin-Embedded Tissues Multiomes.Laboratory investigation; a journal of technical methods and pathology · 2024Article
- Mucosal expression of PI3, ANXA1, and VDR discriminates Crohn's disease from ulcerative colitis.Scientific reports · 2023Article
- RNA-seq RNAaccess identified as the preferred method for gene expression analysis of low quality FFPE samples.PloS one · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
18 authors.
Funding
Abstract
backgroundHigh-throughput transcriptomics has matured into a very well established and widely utilised research tool over the last two decades. Clinical datasets generated on a range of different platforms continue to be deposited in public repositories provide an ever-growing, valuable resource for reanalysis. Cost and tissue availability normally preclude processing samples across multiple technologies, making it challenging to directly evaluate performance and whether data from different platforms can be reliably compared or integrated.
methodsThis study describes our experiences of nine new and established mRNA profiling techniques including Lexogen QuantSeq, Qiagen QiaSeq, BioSpyder TempO-Seq, Ion AmpliSeq, Nanostring, Affymetrix Clariom S or U133A, Illumina BeadChip and RNA-seq of formalin-fixed paraffin embedded (FFPE) and fresh frozen (FF) sequential patient-matched breast tumour samples.
resultsThe number of genes represented and reliability varied between the platforms, but overall all methods provided data which were largely comparable. Crucially we found that it is possible to integrate data for combined analyses across FFPE/FF and platforms using established batch correction methods as required to increase cohort sizes. However, some platforms appear to be better suited to FFPE samples, particularly archival material.
conclusionsOverall, we illustrate that technology selection is a balance between required resolution, sample quality, availability and cost.
Indexed as
Identifiers
What OpenQuestion holds
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.