Comparing Platforms for Messenger RNA Expression Profiling of Archival Formalin-Fixed, Paraffin-Embedded Tissues

Publication date: Available online 30 April 2015 Source:The Journal of Molecular Diagnostics Author(s): Svitlana Tyekucheva , Neil E. Martin , Edward C. Stack , Wei Wei , Vinod Vathipadiekal , Levi Waldron , Michelangelo Fiorentino , Rosina T. Lis , Meir J. Stampfer , Massimo Loda , Giovanni Parmigiani , Lorelei A. Mucci , Michael Birrer Archival formalin-fixed, paraffin-embedded (FFPE) tissue specimens represent a readily available but largely untapped resource for gene expression profiling–based biomarker discovery. Several technologies have been proposed to cope with the bias from RNA cross-linking and degradation associated with archival specimens to generate data comparable with RNA from fresh-frozen materials. Direct comparison studies of these RNA expression platforms remain rare. We compared two commercially available platforms for RNA expression profiling of archival FFPE specimens from clinical studies of prostate and ovarian cancer: the Affymetrix Human Gene 1.0ST Array following whole-transcriptome amplification using the NuGen WT-Ovation FFPE System V2, and the NanoString nCounter without amplification. For each assay, we profiled 7 prostate and 11 ovarian cancer specimens, with a block age of 4 to 21 years. Both platforms produced gene expression profiles with high sensitivity and reproducibility through technical repeats from FFPE materials. Sensitivity and reproducibility remained high across block age within each cohort. A strong concordanc...
Source: The Journal of Molecular Diagnostics - Category: Pathology Source Type: research