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

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.

Source: Journal of Molecular Diagnostics - April 29, 2015 Category: Pathology Authors: 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 Tags: Regular Article Source Type: research