ArticleThe American journal of pathology2004
Measurement of gene expression in archival paraffin-embedded tissues: development and performance of a 92-gene reverse transcriptase-polymerase chain reaction assay.
Article in The American journal of pathology, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 200 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
200 citing papers in PubMed, 565 citations in OpenAlex.
- The impact of Oncotype DX testing on breast cancer management and chemotherapy prescribing patterns in a tertiary referral centre.European journal of cancer (Oxford, England : 1990) · 2014Trial
- Molecular risk assessment of BIG 1-98 participants by expression profiling using RNA from archival tissue.BMC cancer · 2010Trial
- Subtype-Dependent Expression Patterns of Core Hippo Pathway Components in Thymic Epithelial Tumors (TETs): An RT-qPCR Study.Biomedicines · 2026Article
- Ki-67 and 21-gene recurrence score assay in decision making for adjuvant chemotherapy in breast cancer patients.Discover oncology · 2025Review
- Challenges and barriers for the adoption of personalized medicine in Europe: the case of Oncotype DX Breast Recurrence ScoreDiagnosis (Berlin, Germany) · 2025Review
- Impact of commercial RNA extraction methods on the recovery of human RNA sequence data from archival fixed tissues.BioTechniques · 2025Article
- RETRACTED: Genotyping strategies for tissues fixed with various embalming fluids for human identification, databasing, and traceability.Journal of forensic sciences · 2025Article
- Evaluating the potential of anti-dsRNA antibodies as an alternative viral sensing tool in encephalitides of different species.Frontiers in veterinary science · 2025Article
- Prognostic value of the 21-Gene Breast Recurrence Score® assay for hormone receptor-positive/human epidermal growth factor 2-negative advanced breast cancer: subanalysis from Japan Breast Cancer Research Group-M07 (FUTURE trial).Breast cancer research and treatment · 2024Article
- Evaluation of Hi-C Sequencing for Detection of Gene Fusions in Hematologic and Solid Tumor Pediatric Cancer Samples.Cancers · 2024Article
- RNA-Seq Analysis in Non-Small Cell Lung Cancer: What Is the Best Sample from Clinical Practice?Journal of personalized medicine · 2024Article
- A Diagnostic Algorithm for Detection of Leishmania spp. in Human Fresh and Fixed Tissue Samples.The American journal of tropical medicine and hygiene · 2024Article
- Utility of bronchoscopically obtained frozen cytology pellets for next-generation sequencing.BMC cancer · 2024Article
- Unveiling the HER2-low phenomenon: exploring immunohistochemistry and gene expression to characterise HR-positive HER2-negative early breast cancer.Breast cancer research and treatment · 2024Article
- Circulating miRNAs as Noninvasive Biomarkers for PDAC Diagnosis and Prognosis in Mexico.International journal of molecular sciences · 2023Article
- Quality Assessment of Proteins and RNA Following Storage in Archival Formalin-Fixed Paraffin-Embedded Human Breast Cancer Tissue Microarray Sections.Biopreservation and biobanking · 2023Article
- Using Machine Vision of Glycolytic Elements to Predict Breast Cancer Recurrences: Design and Implementation.Metabolites · 2022Review
- Article
- Improved Bladder Tumor RNA Isolation from Archived Tissues Using Methylene Blue for Normalization, Multiplex RNA Hybridization, Sequencing and Subtyping.International journal of molecular sciences · 2022Article
- Refining risk stratification in HR-positive/HER2-negative early breast cancer: how to select patients for treatment escalation?Breast cancer research and treatment · 2022Review
140 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Throughout the last decade many laboratories have shown that mRNA levels in formalin-fixed and paraffin-embedded (FPE) tissue specimens can be quantified by reverse transcriptase-polymerase chain reaction (RT-PCR) techniques despite the extensive RNA fragmentation that occurs in tissues so preserved. We have developed RT-PCR methods that are sensitive, precise, and that have multianalyte capability for potential wide use in clinical research and diagnostic assays. Here it is shown that the extent of fragmentation of extracted FPE tissue RNA significantly increases with archive storage time. Probe and primer sets for RT-PCR assays based on amplicons that are both short and homogeneous in length enable effective reference gene-based data normalization for cross comparison of specimens that differ substantially in age. A 48-gene assay used to compare gene expression profiles from the same breast cancer tissue that had been either frozen or FPE showed very similar profiles after reference gene-based normalization. A 92-gene assay, using RNA extracted from three 10- micro m FPE sections of archival breast cancer specimens (dating from 1985 to 2001) yielded analyzable data for these genes in all 62 tested specimens. The results were substantially concordant when estrogen receptor, progesterone receptor, and HER2 receptor status determined by RT-PCR was compared with immunohistochemistry assays for these receptors. Furthermore, the results highlight the advantages of RT-PCR over immunohistochemistry with respect to quantitation and dynamic range. These findings support the development of RT-PCR analysis of FPE tissue RNA as a platform for multianalyte clinical diagnostic tests.
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.