title: Evaluation and selection of a non-PCR based technology for improved gene expression profiling from clinical formalin-fixed, paraffin-embedded samples.
abstract: OBJECTIVE
  Formalin-fixed, paraffin-embedded (FFPE) clinical tissue samples have the potential to provide valuable gene-expression data for the development of cancer biomarkers. However, FFPE RNA is extensively fragmented, presenting a significant challenge for reliably detecting gene expression using traditional qPCR methods.
  
  
  RESULTS
  We evaluated three novel methodologies along with the traditional qPCR method for their ability to detect Notch pathway gene expression in colorectal cancer FFPE tissue RNAs. We found that quantitative nuclease protection assay-detected gene expression in high-quality RNAs as sensitively as qPCR, and consistently detected mRNAs in highly fragmented FFPE tissue RNAs.
  
  
  CONCLUSIONS
  Quantitative nuclease protection assay represents an improved methodology for detecting gene expression in FFPE tissue and has the potential to advance the development of cancer biomarkers.
authors.affiliation: Clinical Translational Technologies & Operations, Bristol-Myers Squibb, Route 206 & Province Line Road, Princeton, NJ 08543, USA.
authors.forename: Zhenhao
authors.initials: Z
authors.lastname: Qi
authors.affiliation: Clinical Translational Technologies & Operations, Bristol-Myers Squibb, Route 206 & Province Line Road, Princeton, NJ 08543, USA.
authors.forename: Lisu
authors.initials: L
authors.lastname: Wang
authors.affiliation: Genetically Defined Diseases & Genomics, Bristol-Myers Squibb, Route 206 & Province Line Road, Princeton, NJ 08543, USA.
authors.forename: Aiqing
authors.initials: A
authors.lastname: He
authors.affiliation: Genetically Defined Diseases & Genomics, Bristol-Myers Squibb, Route 206 & Province Line Road, Princeton, NJ 08543, USA.
authors.forename: Manling
authors.initials: M
authors.lastname: Ma-Edmonds
authors.affiliation: Clinical Translational Technologies & Operations, Bristol-Myers Squibb, Route 206 & Province Line Road, Princeton, NJ 08543, USA.
authors.forename: John
authors.initials: J
authors.lastname: Cogswell
keywords: FFPE tissue; Notch pathway; RNA; biomarkers; colorectal cancer; gene expression; qPCR; quantitative nuclease protection assay