RNA-seq from archival FFPE Breast Cancer samples: Molecular Pathway Fidelity and Novel Discovery

Archival Formalin-Fixed Paraffin Embedded (FFPE) tissue represents an abundant and more easily transferable source of patient tissue than live specimens. Furthermore cancer FFPE tissue deposited at major cancer research institutes is often paired with survival data increasing the value of biomarker and prediction based research from these samples. However the known fragility of RNA and artifacts introduced through the processes of tissue preservation and storage introduce the possibility of unfaithful RNA expression signatures from these sources. To evaluate this we established an RNA isolation, library prepration and data analysis pipeline at Oregon Health and Science University to evaluate the fidelity of RNA expression profiles from FFPE tissues utilizing gene and pathway expression comparisons between ER positive and ER negative samples in archival FFPE specimens compared to those obtained from public available data sets of fresh specimens. Overall design: Two Breast Cancer ER+ FFPE samples prepared by two different RNA expression library methodologies (Illumina-Access, and Nugen-Ovation) and sequenced in triplicate. 3 ER positive and 3 ER negative FFPE derived Breast Cancer specimens prepared by Illumina Access RNA Expression library and sequenced in singlet on HiSeq2000, with four samples per lane permitting approximately 70 million reads per sample.