ArticleThe Journal of molecular diagnostics : JMD2010
Quantitative expression profiling in formalin-fixed paraffin-embedded samples by affymetrix microarrays.
Article in The Journal of molecular diagnostics : JMD, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers, 2 of them syntheses that pooled it.
What it found
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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
59 citing papers in PubMed, 2 syntheses or guidelines pooled it, 90 citations in OpenAlex.
- Analysis of a Biopsy-Based Genomic Classifier in High-Risk Prostate Cancer: Meta-Analysis of the NRG Oncology/Radiation Therapy Oncology Group 9202, 9413, and 9902 Phase 3 Randomized Trials.International journal of radiation oncology, biology, physics · 2023Pooled it
- Expression profiling of archival tumors for long-term health studies.Clinical cancer research : an official journal of the American Association for Cancer Research · 2012Pooled it
- Biopsy-based Basal-luminal Subtyping Classifier in High-risk Prostate Cancer: A Combined Analysis of the NRG Oncology/RTOG 9202, 9413, and 9902 Phase 3 Trials.European urology oncology · 2026Trial
- Predicting dose response to prostate cancer radiotherapy: validation of a radiation signature in the randomized phase III NRG/RTOG 0126 and SAKK 09/10 trials.Annals of oncology : official journal of the European Society for Medical Oncology · 2025Trial
- Genomic Classifier Performance in Intermediate-Risk Prostate Cancer: Results From NRG Oncology/RTOG 0126 Randomized Phase 3 Trial.International journal of radiation oncology, biology, physics · 2023Trial
- Insulin-like Growth Factor 2 Gene Expression Molecularly Differentiates Pleuropulmonary Blastoma and Embryonal Rhabdomyosarcoma.Journal of pediatric hematology/oncology · 2015Trial
- Genomic signatures for predicting survival and adjuvant chemotherapy benefit in patients with non-small-cell lung cancer.BMC medical genomics · 2012Trial
- SPRINTR: Swedish PRecision medicine Initiative for Novel Treatments and Research-towards efficient recruitment to clinical trials for prostate cancer.Acta oncologica (Stockholm, Sweden) · 2026Article
- Downregulation of ANPEP Is Associated with Aggressive Prostate Cancer and Poor Disease-specific Outcomes.European urology open science · 2026Article
- Expression patterns of miR-221, miR-214, and miR-375 in odontogenic keratocysts versus dentigerous cysts: an in vitro comparison.BMC oral health · 2025Article
- Precision diagnostics in transplanted organs using microarray-assessed gene expression: concepts and technical methods of the Molecular Microscope® Diagnostic System (MMDx).Clinical science (London, England : 1979) · 2024Review
- PA200-Mediated Proteasomal Protein Degradation and Regulation of Cellular Senescence.International journal of molecular sciences · 2024Review
- The Proteasome Activator PA200/PSME4: An Emerging New Player in Health and Disease.Biomolecules · 2022Review
- Pre-analytical processing protocol of breast biopsies affects multigene panel results.International journal of experimental pathology · 2022Article
- PRMT3 interacts with ALDH1A1 and regulates gene-expression by inhibiting retinoic acid signaling.Communications biology · 2021Article
- Characterization of the Cellular Microenvironment and Novel Specific Biomarkers in Pterygia Using RNA Sequencing.Frontiers in medicine · 2021Article
- Integrated bioinformatic analysis identifies COL4A3, COL4A4, and KCNJ1 as key biomarkers in Wilms tumor.International journal of clinical and experimental pathology · 2021Article
- Large scale, robust, and accurate whole transcriptome profiling from clinical formalin-fixed paraffin-embedded samples.Scientific reports · 2020Article
- Transcriptional characterization of conjunctival melanoma identifies the cellular tumor microenvironment and prognostic gene signatures.Scientific reports · 2020Article
- 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
5 authors at 3 institutions in 2 countries.
Funding
Abstract
To date, few studies have systematically characterized microarray gene expression signal performance with degraded RNA from fixed (FFPE) in comparison with intact RNA from unfixed fresh-frozen (FF) specimens. RNA was extracted and isolated from paired tumor and normal samples from both FFPE and FF kidney, lung, and colon tissue specimens and microarray signal dynamics on both the raw probe and probeset level were evaluated. A contrast metric was developed to directly compare microarray signal derived from RNA extracted from matched FFPE and FF specimens. Gene-level summaries were then compared to determine the degree of overlap in expression profiles. RNA extracted from FFPE material was more degraded and fragmented than FF, resulting in a reduced dynamic range of expression signal. In addition, probe performance was not affected uniformly and declined sharply toward 5' end of genes. The most significant differences in FFPE versus FF signal were consistent across three tissue types and enriched with ribosomal genes. Our results show that archived FFPE samples can be used to profile for expression signatures and assess differential expression similar to unfixed tissue sources. This study provides guidelines for application of these methods in the discovery, validation, and clinical application of microarray expression profiling with FFPE material.
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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.