Extensive archives of formalin-fixed, paraffin-embedded (FFPE) cancer tissues and next generation sequencing (NGS) capabilities provide rich resources for identifying and validating new cancer biomarkers. However, the ability to conduct FFPE-NGS studies has been limited by poor nucleic acid purification methods that are generally difficult and cumbersome to perform, particularly with RNA. FormaPure DNA was recently launched to provide a simplified workflow to extract DNA from FFPE curls. Its nucleic acid binding chemistry employs Beckman Coulter's proprietary SPRI (solid phase reversible immobilization) technology, which purifies nucleic acids without centrifugation or vacuum manifold. The SPRI technology ensures stronger binding and higher quality purification than other silica-coated bead methods that typically lead to lower quality results due to instances of nucleic acid shearing. Here, we present a modified FormaPure DNA workflow to purify RNA from FFPE samples, offering the flexibility to examine both genomic and transcriptomic roles in cancer biomarkers studies. We show that our extractions yield significantly more RNA (up to 2.5 µg per FFPE curl) and take a fraction of the time to perform compared to other benchmarks. Furthermore, we demonstrate that purified RNA can be used to generate high quality NGS data. Lastly, our extraction method can be automated on a variety of Beckman Coulter’s Biomek liquid handling workstations to offer an integrated solution for high-throughput FFPE-RNA-NGS experiments: RNA from 96 FFPE samples can be purified for NGS in less than 5 hours with minimal hands-on time.

Citation Format: Jung H. Doh. A simple yet powerful method to purify NGS compatible RNA from formalin fixed paraffin embedded tissues using FormaPure DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5351. doi:10.1158/1538-7445.AM2017-5351