ArticleThe journal of histochemistry and cytochemistry : official journal of the Histochemistry Society2011
Genome-wide gene expression profiling of formalin-fixed paraffin-embedded breast cancer core biopsies using microarrays.
Article in The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers, 2 of them syntheses that pooled it.
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Who cites it
17 citing papers in PubMed, 2 syntheses or guidelines pooled it, 34 citations in OpenAlex.
- Mining the Archives: A Cross-Platform Analysis of Gene Expression Profiles in Archival Formalin-Fixed Paraffin-Embedded Tissues.Toxicological sciences : an official journal of the Society of Toxicology · 2015Pooled 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
- Decision Theory versus Conventional Statistics for Personalized Therapy of Breast Cancer.Journal of personalized medicine · 2022Article
- Decision theory for precision therapy of breast cancer.Scientific reports · 2021Article
- Formalin-fixed paraffin-embedded renal biopsy tissues: an underexploited biospecimen resource for gene expression profiling in IgA nephropathy.Scientific reports · 2020Article
- Feasibility of developing reliable gene expression modules from FFPE derived RNA profiled on Affymetrix arrays.PloS one · 2018Article
- Gene expression information improves reliability of receptor status in breast cancer patients.Oncotarget · 2017Article
- Gene-expression analysis of a colorectal cancer-specific discriminatory transcript set on formalin-fixed, paraffin-embedded (FFPE) tissue samples.Diagnostic pathology · 2015Article
- Prognostic stromal gene signatures in breast cancer.Breast cancer research : BCR · 2015Article
- Use of formalin-fixed paraffin-embedded samples for gene expression studies in breast cancer patients.PloS one · 2015Article
- New network topology approaches reveal differential correlation patterns in breast cancer.BMC systems biology · 2013Article
- Isolation of microarray-quality RNA from primary human cells after intracellular immunostaining and fluorescence-activated cell sorting.Journal of immunological methods · 2013Article
- Transcriptomic profiling of human peritumoral neocortex tissues revealed genes possibly involved in tumor-induced epilepsy.PloS one · 2013Article
- Grainyhead-like 2 (GRHL2) inhibits keratinocyte differentiation through epigenetic mechanism.Cell death & disease · 2012Article
- The application of gene co-expression network reconstruction based on CNVs and gene expression microarray data in breast cancer.Molecular biology reports · 2012Article
- Quality assurance of RNA expression profiling in clinical laboratories.The Journal of molecular diagnostics : JMD · 2012Review
- Clinical implementation of RNA signatures for pharmacogenomic decision-making.Pharmacogenomics and personalized medicine · 2011Article
Corrections and comments
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Authors and funding
10 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The routine workflow for invasive cancer diagnostics includes biopsy processing by formalin fixation and paraffin embedding. It has been shown only recently that this kind of sample can be used for gene expression analysis with microarrays. To support this view, the authors conducted a microarray study using formalin-fixed paraffin-embedded (FFPE) core needle biopsies from breast cancers. Typically, for the 3'-biased chip type that was used, the probe sets interrogate sequences near the poly-A-tail of the transcripts, and this kind of probe turned out to be suitable to measure RNA levels in FFPE biopsies. For ER and HER2, the authors observed strong correlations between RNA levels and protein expression (p = 0.000003 and p = 0.0022). ER and HER2 classification of the biopsies by the RNA levels was feasible with high sensitivity and specificity (AUROC = 0.93 and AUROC = 0.96). Furthermore, a signature of 346 genes was identified that correlated with ER and a signature of 528 genes that correlated with HER2 protein status. Many of these genes (ER: 63%) could be confirmed by analysis of gene expression data from frozen tissues. The findings support the notion that clinically relevant information can be gained from microarray analyses of FFPE cancer biopsies. This opens new opportunities for biomarker detection studies and the integration of microarrays into the workflow of cancer diagnostics.
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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.