ArticleThe Journal of molecular diagnostics : JMD2015
Comparing Platforms for Messenger RNA Expression Profiling of Archival Formalin-Fixed, Paraffin-Embedded Tissues.
Article in The Journal of molecular diagnostics : JMD, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers, 1 of them a synthesis that pooled it.
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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.
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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.
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Who cites it
21 citing papers in PubMed, 1 synthesis or guideline pooled it, 26 citations in OpenAlex.
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- Methylation profiling in neuropathological tumors diagnosis: a comprehensive review.Frontiers in oncology · 2025Review
- Intratumoral vitamin D signaling and lethal prostate cancer.Carcinogenesis · 2024Article
- LINCATRA: Two-cycle method to amplify RNA for transcriptome analysis from formalin-fixed paraffin-embedded tissue.Heliyon · 2024Article
- Prognostic significance of EGFR, AREG and EREG amplification and gene expression in muscle invasive bladder cancer.Frontiers in oncology · 2024Article
- Transcriptomes of Prostate Cancer with TMPRSS2:ERG and Other ETS Fusions.Molecular cancer research : MCR · 2023Article
- Identification of Novel Diagnostic Markers for Malignant Pleural Mesothelioma Using a Reverse Translational Approach Based on a Rare Synchronous Tumor.Diagnostics (Basel, Switzerland) · 2022Article
- Gene Expression Pathways in Prostate Tissue Associated with Vigorous Physical Activity in Prostate Cancer.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2021Article
- ARHGEF38 as a novel biomarker to predict aggressive prostate cancer.Genes & diseases · 2020Article
- Clinical relevance of gene expression in localized and metastatic prostate cancer exemplified by FABP5.World journal of urology · 2020Article
- Extensive Changes in Transcriptomic "Fingerprints" and Immunological Cells in the Large Organs of Patients Dying of Acute Septic Shock and Multiple Organ Failure Caused byFrontiers in cellular and infection microbiology · 2020Article
- Single-nucleotide polymorphisms in DNMT3B gene and DNMT3B mRNA expression in association with prostate cancer mortality.Prostate cancer and prostatic diseases · 2019Article
- Expression Concordance of 325 Novel RNA Biomarkers between Data Generated by NanoString nCounter and Affymetrix GeneChip.Disease markers · 2019Article
- Differential Gene Expression in Prostate Tissue According to Ejaculation Frequency.European urology · 2018Observational
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- Prognostic Utility of a New mRNA Expression Signature of Gleason Score.Clinical cancer research : an official journal of the American Association for Cancer Research · 2017Article
- Early Molecular Stratification of High-risk Primary Biliary Cholangitis.EBioMedicine · 2016Article
- Stress-Related Signaling Pathways in Lethal and Nonlethal Prostate Cancer.Clinical cancer research : an official journal of the American Association for Cancer Research · 2016Article
Corrections and comments
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Authors and funding
13 authors at 7 institutions in 2 countries.
Funding
Abstract
Archival formalin-fixed, paraffin-embedded (FFPE) tissue specimens represent a readily available but largely untapped resource for gene expression profiling-based biomarker discovery. Several technologies have been proposed to cope with the bias from RNA cross-linking and degradation associated with archival specimens to generate data comparable with RNA from fresh-frozen materials. Direct comparison studies of these RNA expression platforms remain rare. We compared two commercially available platforms for RNA expression profiling of archival FFPE specimens from clinical studies of prostate and ovarian cancer: the Affymetrix Human Gene 1.0ST Array following whole-transcriptome amplification using the NuGen WT-Ovation FFPE System V2, and the NanoString nCounter without amplification. For each assay, we profiled 7 prostate and 11 ovarian cancer specimens, with a block age of 4 to 21 years. Both platforms produced gene expression profiles with high sensitivity and reproducibility through technical repeats from FFPE materials. Sensitivity and reproducibility remained high across block age within each cohort. A strong concordance was shown for the transcript expression values for genes detected by both platforms. We showed the biological validity of specific gene signatures generated by both platforms for both cohorts. Our study supports the feasibility of gene expression profiling and large-scale signature validation on archival prostate and ovarian tumor specimens using commercial platforms. These approaches have the potential to aid precision medicine with biomarker discovery and validation.
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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.