ArticleBritish journal of cancer2011
Exon-array profiling unlocks clinically and biologically relevant gene signatures from formalin-fixed paraffin-embedded tumour samples.
Article in British journal of cancer, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers, 1 of them a synthesis that pooled it.
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Who cites it
18 citing papers in PubMed, 1 synthesis or guideline pooled it, 28 citations in OpenAlex.
- 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
- Intrinsic molecular subtypes of glioma are prognostic and predict benefit from adjuvant procarbazine, lomustine, and vincristine chemotherapy in combination with other prognostic factors in anaplastic oligodendroglial brain tumors: a report from EORTC study 26951.Journal of clinical oncology : official journal of the American Society of Clinical Oncology · 2013Trial
- 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
- Genome-wide analysis of canine oral malignant melanoma metastasis-associated gene expression.Scientific reports · 2019Article
- A novel rapid quantitative method reveals stathmin-1 as a promising marker for esophageal squamous cell carcinoma.Cancer medicine · 2018Article
- Robust transcriptional tumor signatures applicable to both formalin-fixed paraffin-embedded and fresh-frozen samples.Oncotarget · 2017Article
- Whole Transcriptome Analysis of Pre-invasive and Invasive Early Squamous Lung Carcinoma in Archival Laser Microdissected Samples.Respiratory research · 2017Article
- Article
- Comparing Platforms for Messenger RNA Expression Profiling of Archival Formalin-Fixed, Paraffin-Embedded Tissues.The Journal of molecular diagnostics : JMD · 2015Article
- Transcriptome instability as a molecular pan-cancer characteristic of carcinomas.BMC genomics · 2014Article
- Article
- Development of a robust protocol for gene expression analysis using formalin-fixed, paraffin-embedded liver transplant biopsy specimens.Journal of clinical pathology · 2013Article
- Enhanced stability of microRNA expression facilitates classification of FFPE tumour samples exhibiting near total mRNA degradation.British journal of cancer · 2012Article
- Testing an aflatoxin B1 gene signature in rat archival tissues.Chemical research in toxicology · 2012Article
- Gene expression profiles of gliomas in formalin-fixed paraffin-embedded material.British journal of cancer · 2012Article
- Transcriptome-wide detection of differentially expressed coding and non-coding transcripts and their clinical significance in prostate cancer.Journal of oncology · 2012Article
- Quality control parameters on a large dataset of regionally dissected human control brains for whole genome expression studies.Journal of neurochemistry · 2011Article
- Impact of collection and storage of lung tumor tissue on whole genome expression profiling.The Journal of molecular diagnostics : JMDArticle
Corrections and comments
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Authors and funding
11 authors at 4 institutions in 1 country.
Funding
Abstract
backgroundDegradation and chemical modification of RNA in formalin-fixed paraffin-embedded (FFPE) samples hamper their use in expression profiling studies. This study aimed to show that useful information can be obtained by Exon-array profiling archival FFPE tumour samples.
methodsNineteen cervical squamous cell carcinoma (SCC) and 9 adenocarcinoma (AC) FFPE samples (10-16-year-old) were profiled using Affymetrix Exon arrays. The gene signature derived was tested on a fresh-frozen non-small cell lung cancer (NSCLC) series. Exploration of biological networks involved gene set enrichment analysis (GSEA). Differential gene expression was confirmed using Quantigene, a multiplex bead-based alternative to qRT-PCR.
resultsIn all, 1062 genes were higher in SCC vs AC, and 155 genes higher in AC. The 1217-gene signature correctly separated 58 NSCLC into SCC and AC. A gene network centered on hepatic nuclear factor and GATA6 was identified in AC, suggesting a role in glandular cell differentiation of the cervix. Quantigene analysis of the top 26 differentially expressed genes correctly partitioned cervix samples as SCC or AC.
conclusionFFPE samples can be profiled using Exon arrays to derive gene expression signatures that are sufficiently robust to be applied to independent data sets, identify novel biology and design assays for independent platform validation.
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