Feasibility of developing reliable gene expression modules from FFPE derived RNA profiled on Affymetrix arrays
Vinu Jose, Debora Fumagalli, Francoise Rothe, Samira Majjaj, Sherene Loi, Stefan Michiels, Christos Sotiriou
PLOS ONE | PUBLIC LIBRARY SCIENCE | Published : 2018
The reliability of differential gene expression analysis on formalin-fixed, paraffin-embedded (FFPE) expression profiles generated using Affymetrix arrays is questionable, due to the high range of percent-present values reported in studies which profiled FFPE samples using this technology. Moreover, the validity of gene-modules derived from external datasets in FFPE microarray expression profiles is unknown. By generating matched gene expression profiles using RNAs derived from fresh-frozen (FF) and FFPE preserved breast tumors with Affymetrix arrays and FF/FFPE RNA specific amplification-and-labeling kits, the reliability of differential expression analysis and the validity of gene modules ..View full abstract
VJ received funding from a grant F.R.S-FNRS "Fonds de la Recherche Scientifique" - Televie (Belgium), for this work. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.