Evaluation of RNA Purification Protocols for Targeted Deep Sequencing of RNA from FFPE Tumors Poster
Part # PS233
Abstract
Geoff Otto1, Kristina Brennan1, Jie He1, Geneva Young1, Doug Horejsh2, Doron Lipson1, Jeff S Ross1,3, Phil Stephens1, Alex Parker1
1Foundation Medicine Inc., Cambridge, MA (USA); 2Promega Corporation, Madison WI; 3Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, NY (USA)
A single assay capable of characterizing both the genome and the transcriptome of diverse tumor types using targeted, deep sequencing will improve the application of personalized medicine to cancer. Integrating RNA-seq into our clinical FFPE DNA-seq test, which is highly sensitive to many types of genomic alterations in over 200 cancer related genes, will enable a comparison of changes in gene copy number with digital gene expression levels, facilitate validation of both recurrent and novel gene rearrangements and reveal changes exclusive to the transcriptome such as alternative splicing. Tumor samples are commonly stored as formalin fixed paraffin embedded (FFPE) blocks which degrades nucleic acids and requires careful processing to extract sufficient quantity and quality of DNA and RNA to enable comprehensive molecular profiling. Quantitative recovery of high purity RNA from FFPE tissues is essential to implementation of a targeted RNA-seq cancer assay.
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