Gene expression profiling of FFPE breast cancer samples [Affymetrix platform]

The use of Affymetrix U133 2.0 Plus chips on FFPE samples when coupled with a qPCR-based sample pre-assessment step, yielded satisfactory results from the point of view of biological reliability. When compared with the Illumina DASL WG platform, specifically designed for degraded RNA, the data generated with the Affymetrix platform showed a wider interquartile range (IQR 1.32 vs 0.57, p<2.2x10-16) suggesting a superior discriminatory power within samples as indicated by the good agreement with the immunohistiochemically derived ER status. FFPE primary breast cancer samples profiled using Affymetrix HG-U133 Plus 2.0 microarray platform after RNA amplification with the Nugen WT-Ovation FFPE System The following criteria were considered for a direct comparison of 12 GEPs obtained from Affymetrix and DASL platforms: gene variability as defined by IQR, ESR1 expression in ER status subgroups defined by IHC, distribution of fold changes for predefined ER related genes when comparing ER positive and negative samples.