A novel method of amplification of FFPET derived-RNA enables accurate disease classification with microarrays

A new method for amplification and labeling of RNA is assessed that permits gene expression microarray analysis of formalin-fixed paraffin embedded tissue (i.e. FFPET) samples. Valid biological data was obtained using gene expression microarrays of diffuse large B-cell lymphoma (i.e. DLBCL) FFPET samples. We examined 59 matched DLBCL patient samples, FFPET and fresh/frozen. The samples contained both prognostic subgroups of DLBCL: germinal center B-cell (i.e. GCB) and activated B-cell (ABC). Fresh/frozen (i.e. FF) samples were amplified by both the traditional Eberwine oligo-dT method and a new method described herein. The matching FFPET samples were also amplified using the new method. This study is a collaboration among Roche Molecular Diagnostics, British Columbia Cancer Agency, National Cancer Institute and Nugen Technologies (the maker of the WT-Ovation FFPET reagents).