ArticleBMC medical genomics2008
Expression profiling with RNA from formalin-fixed, paraffin-embedded material.
Article in BMC medical genomics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
What it found
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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.
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Who cites it
25 citing papers in PubMed.
- Molecular risk assessment of BIG 1-98 participants by expression profiling using RNA from archival tissue.BMC cancer · 2010Trial
- Molecular characterization of breast cancer cell pools with normal or reduced ability to respond to progesterone: a study based on RNA-seq.Journal, genetic engineering & biotechnology · 2023Article
- Functional and molecular characterization of PD1Oncoimmunology · 2022Article
- Glyoxal fixation facilitates transcriptome analysis after antigen staining and cell sorting by flow cytometry.PloS one · 2021Article
- Characterization of molecular scores and gene expression signatures in primary breast cancer, local recurrences and brain metastases.BMC cancer · 2019Article
- National Cancer Institute Biospecimen Evidence-Based Practices: Harmonizing Procedures for Nucleic Acid Extraction from Formalin-Fixed, Paraffin-Embedded Tissue.Biopreservation and biobanking · 2018Article
- TREM-1 promotes intestinal tumorigenesis.Scientific reports · 2017Article
- TREM-1 links dyslipidemia to inflammation and lipid deposition in atherosclerosis.Nature communications · 2016Article
- Article
- DNA and RNA analysis of blood and muscle from bodies with variable postmortem intervals.Forensic science, medicine, and pathology · 2014Article
- An optimized workflow for improved gene expression profiling for formalin-fixed, paraffin-embedded tumor samples.Journal of clinical bioinformatics · 2013Article
- MicroRNA-29b is involved in the Src-ID1 signaling pathway and is dysregulated in human lung adenocarcinoma.Oncogene · 2012Article
- Testing an aflatoxin B1 gene signature in rat archival tissues.Chemical research in toxicology · 2012Article
- Prognostic significance of miR-205 in endometrial cancer.PloS one · 2012Article
- Performance and clinical evaluation of the 92-gene real-time PCR assay for tumor classification.The Journal of molecular diagnostics : JMD · 2011Article
- The homeobox gene HLXB9 is upregulated in a morphological subset of poorly differentiated hepatocellular carcinoma.Virchows Archiv : an international journal of pathology · 2011Article
- Reliable gene expression measurements from fine needle aspirates of pancreatic tumors: effect of amplicon length and quality assessment.The Journal of molecular diagnostics : JMD · 2010Article
- Quantitative expression profiling in formalin-fixed paraffin-embedded samples by affymetrix microarrays.The Journal of molecular diagnostics : JMD · 2010Article
- High-throughput quantification of splicing isoforms.RNA (New York, N.Y.) · 2010Article
- Genomic markers for decision making: what is preventing us from using markers?Nature reviews. Clinical oncology · 2010Review
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMolecular characterization of breast and other cancers by gene expression profiling has corroborated existing classifications and revealed novel subtypes. Most profiling studies are based on fresh frozen (FF) tumor material which is available only for a limited number of samples while thousands of tumor samples exist as formalin-fixed, paraffin-embedded (FFPE) blocks. Unfortunately, RNA derived of FFPE material is fragmented and chemically modified impairing expression measurements by standard procedures. Robust protocols for isolation of RNA from FFPE material suitable for stable and reproducible measurement of gene expression (e.g. by quantitative reverse transcriptase PCR, QPCR) remain a major challenge.
resultsWe present a simple procedure for RNA isolation from FFPE material of diagnostic samples. The RNA is suitable for expression measurement by QPCR when used in combination with an optimized cDNA synthesis protocol and TaqMan assays specific for short amplicons. The FFPE derived RNA was compared to intact RNA isolated from the same tumors. Preliminary scores were computed from genes related to the ER response, HER2 signaling and proliferation. Correlation coefficients between intact and partially fragmented RNA from FFPE material were 0.83 to 0.97.
conclusionWe developed a simple and robust method for isolating RNA from FFPE material. The RNA can be used for gene expression profiling. Expression measurements from several genes can be combined to robust scores representing the hormonal or the proliferation status of the tumor.
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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.