Abstract B179: Targeted next generation sequencing for somatic mutations in human cancer.

Abstract

Abstract Objective: We have replaced single gene PCR-based methods for the detection of BRAF, KRAS and EGFR variants in routine clinical practice with next generation sequencing assays for the Ion Torrent AmpliSeq Cancer Hotspot Panel v2 (50 genes) and the Illumina TruSeq Amplicon Cancer panel (48 genes). Implementation of these panels requires constant optimization of technical and analytical procedures as reagents and software continue to be developed. In this study we describe somatic mutation findings from our clinical laboratory service. Methods: DNA was extracted from 90 formalin fixed, paraffin embedded tissue specimens that included 50 lung cancer, 24 colon cancer and 16 other cancers. Barcoded libraries were prepared from up to 10ng of extracted DNA and multiplexed on single 318 chips. Data analysis was performed using Golden Helix SVS for the Ion Torrent panel and Variant Studio for the Illumina panel. Variants that remained after the analysis pipeline were individually interrogated using the Integrative Genomics Viewer (IGV). Results: Of the 90 cancer cases sequenced, each panel returned on average 20 variants. Of these, there was 100% concordance between the two panels with respect to the clinically actionable mutations identified. Conclusions: We have implemented next generation sequencing technologies for the detection of somatic mutations in human cancers. Two platforms, the Ion Torrent PGM and the Illumina MiSeq, have been used for the routine analysis of FFPE cancer tissues in a clinical setting with actionable and non-actionable variants reported and archived. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):B179. Citation Format: Jason D. Peterson, Francine de Abreu, Torrey L. Gallagher, Paul R. Burchard, Christopher I. Amos, Wendy A. Wells, J. Marc Pipas, Marc S. Ernstoff, Camilo E. Fadul, James R. Rigas, Gregory J. Tsongalis. Targeted next generation sequencing for somatic mutations in human cancer. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr B179.