Abstract 3563: New tools for RNA-sequencing of FFPE tumor samples

Abstract

Abstract Next generation RNA sequencing is an ideal platform to leverage archival formalin-fixed paraffin-embedded (FFPE) tissue samples for cancer research, as it offers extensive functional genomic information including transcriptome expression profiling, differential expression analysis and fusion detection. However, both RNA degradation from the formalin fixation process as well as limited sample material, pose major challenges for RNA sequencing of FFPE samples. Here we describe a novel method for generating whole-transcriptome RNA sequencing libraries from moderate to poor quality FFPE samples starting with as low as 20ng total RNA. This approach provides increased transcriptome coverage and robust measurement of gene expression levels compared to currently available FFPE RNA sequencing methods. Furthermore, we demonstrate that we can detect both known and novel gene fusions in clinical tumor samples that are potential drivers of disease. We anticipate this new technology will enable functional genomic studies on numerous FFPE tumor samples that would not previously be possible, providing invaluable information for developing cancer diagnostics and therapeutics. Citation Format: Lisa Watson, Smita Pathak, Stephen Gross, Irina Khrebtukova, Gary Schroth. New tools for RNA-sequencing of FFPE tumor samples. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3563. doi:10.1158/1538-7445.AM2014-3563