ArticleJournal of clinical bioinformatics2013
An optimized workflow for improved gene expression profiling for formalin-fixed, paraffin-embedded tumor samples.
Article in Journal of clinical bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- A qualitative transcriptional signature for predicting the biochemical recurrence risk of prostate cancer patients after radical prostatectomy.The Prostate · 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
- Feasibility of developing reliable gene expression modules from FFPE derived RNA profiled on Affymetrix arrays.PloS one · 2018Article
- Robust transcriptional tumor signatures applicable to both formalin-fixed paraffin-embedded and fresh-frozen samples.Oncotarget · 2017Article
- Optimization of gene expression microarray protocol for formalin-fixed paraffin-embedded tissues.Genomics data · 2016Article
- Gene-expression analysis of a colorectal cancer-specific discriminatory transcript set on formalin-fixed, paraffin-embedded (FFPE) tissue samples.Diagnostic pathology · 2015Article
- Comparing Platforms for Messenger RNA Expression Profiling of Archival Formalin-Fixed, Paraffin-Embedded Tissues.The Journal of molecular diagnostics : JMD · 2015Article
- Prognostic stromal gene signatures in breast cancer.Breast cancer research : BCR · 2015Article
- Article
- Use of formalin-fixed paraffin-embedded samples for gene expression studies in breast cancer patients.PloS one · 2015Article
- The tissue is the issue: improved methylome analysis from paraffin-embedded tissues by application of the HOPE technique.Laboratory investigation; a journal of technical methods and pathology · 2014Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWhole genome microarray gene expression profiling is the 'gold standard' for the discovery of prognostic and predictive genetic markers for human cancers. However, suitable research material is lacking as most diagnostic samples are preserved as formalin-fixed, paraffin-embedded tissue (FFPET). We tested a new workflow and data analysis method optimized for use with FFPET samples.
methodsSixteen breast tumor samples were split into matched pairs and preserved as FFPET or fresh-frozen (FF). Total RNA was extracted and tested for yield and purity. RNA from FFPET samples was amplified using three different commercially available kits in parallel, and hybridized to Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays. The array probe set was optimized in silico to exclude misdesigned and misannotated probes.
resultsFFPET samples processed using the WT-Ovation™ FFPE System V2 (NuGEN) provided 80% specificity and 97% sensitivity compared with FF samples (assuming values of 100%). In addition, in silico probe set redesign improved sequence detection sensitivity and, thus, may rescue potentially significant small-magnitude gene expression changes that could otherwise be diluted by the overall probe set background.
conclusionIn conclusion, our FFPET-optimized workflow enables the detection of more genes than previous, nonoptimized approaches, opening new possibilities for the discovery, validation, and clinical application of mRNA biomarkers in human diseases.
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