ArticleScientific reports2019
Deleterious effects of formalin-fixation and delays to fixation on RNA and miRNA-Seq profiles.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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
40 citing papers in PubMed.
- Perspectives From an Expert-Guided Discussion on Maximizing the Research Potential of Small Biopsy Tissue.JCO precision oncology · 2026Article
- Patterns of miRNA Expression in Primary and Metastatic Wilms Tumor.Medical science monitor : international medical journal of experimental and clinical research · 2026Article
- Pre-analytical Best Practices for RNA Sequencing from Small Biopsies and Cytologic Specimens.Molecular diagnosis & therapy · 2026Review
- A Field-Friendly, Non-Toxic Fixative for Integrated Morphological and Molecular Research in Non-Model Invertebrates.Ecology and evolution · 2026Article
- Use of Automated BaseScope Assay on the Leica BOND RX.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Genomic innovations in cancer prevention, diagnosis, prognosis and precision therapeutics.Frontiers in genetics · 2026Review
- Integration of phospho-signaling and transcriptomics in single cells reveals distinct Th17 cell fates.Cell reports · 2025Article
- Cannabinoid Receptors in the Horse Lateral Nucleus of the Amygdala: A Potential Target for Ameliorating Pain Perception, Stress and Anxiety in Horses.International journal of molecular sciences · 2025Article
- An ancient influenza genome from Switzerland allows deeper insights into host adaptation during the 1918 flu pandemic in Europe.BMC biology · 2025Article
- Silver Nanoparticles as a Novel Tissue Preservative: A Comparative Study with 10% Neutral Buffered Formalin.International journal of molecular sciences · 2025Article
- Article
- Microarray integrated spatial transcriptomics (MIST) for affordable and robust digital pathology.NPJ systems biology and applications · 2024Article
- Spatial oncology: Translating contextual biology to the clinic.Cancer cell · 2024Review
- Optimization of FFPE preparation and identification of gene attributes associated with RNA degradation.NAR genomics and bioinformatics · 2024Article
- Article
- Canine urothelial carcinoma: a pilot study of microRNA detection in formalin-fixed, paraffin-embedded tissue samples and in normal urine.Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc · 2024Article
- Transitioning single-cell genomics into the clinic.Nature reviews. Genetics · 2023Review
- Formalin Fixation, Delay to Fixation, and Time in Fixative Adversely Impact Copy Number Variation Analysis by aCGH.Biopreservation and biobanking · 2023Article
- Alterations of miRNA Expression in Diffuse Hyperplastic Perilobar Nephroblastomatosis: Mapping the Way to Understanding Wilms' Tumor Development and Differential Diagnosis.International journal of molecular sciences · 2023Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The National Cancer Institute conducted the Biospecimen Pre-analytical Variables (BPV) study to determine the effects of formalin fixation and delay to fixation (DTF) on the analysis of nucleic acids. By performing whole transcriptome sequencing and small RNA profiling on matched snap-frozen and FFPE specimens exposed to different delays to fixation, this study aimed to determine acceptable delays to fixation and proper workflow for accurate and reliable Next-Generation Sequencing (NGS) analysis of FFPE specimens. In comparison to snap-freezing, formalin fixation changed the relative proportions of intronic/exonic/untranslated RNA captured by RNA-seq for most genes. The effects of DTF on NGS analysis were negligible. In 80% of specimens, a subset of RNAs was found to differ between snap-frozen and FFPE specimens in a consistent manner across tissue groups; this subset was unaffected in the remaining 20% of specimens. In contrast, miRNA expression was generally stable across various formalin fixation protocols, but displayed increased variability following a 12 h delay to fixation.
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.