Abstract 4666: Revolutionizing clinical care using prospective, institution-wide tumor sequencing

Identification of predictive and prognostic biomarkers is central to clinical oncology. Use of targeted next generation sequencing (NGS) is increasing in molecular diagnostics labs, however the feasibility and impact of its routine application across all tumor types is largely untested. We launched an institution-wide effort to generate targeted NGS data (Oncopanel) for invasive tumors of all consenting patients. We hypothesized that this approach could replace traditional targeted testing, generate robust data on copy number alterations and structural variants, and provide novel patient-specific observations to facilitate clinical trial enrollment. Illumina NGS was performed on libraries prepared with Agilent SureSelect custom-designed hybrid capture of 4430 exons from 275 genes plus selected introns of 30 genes. Results were analyzed by an internally-developed computational pipeline for mutations, small insertions/deletions, copy number variation and rearrangements. Variants were characterized according to predictive, prognostic, or diagnostic actionability. Data is available for the first 4291 cases sequenced. Oncopanel succeeded in 96% of specimens with adequate DNA. In a subset analysis performed on the first 1000 cases, assay success ranged from 83-100% according to tumor type; breast carcinoma was most prone to failure (p Citation Format: Lynette M. Sholl, Elizabeth Garcia, Yonghui Jia, Matthew Ducar, Bernard Fendler, Priyanka Shivdasani, Frank C. Kuo, Azra H. Ligon, Barrett J. Rollins, Neal I. Lindeman, Laura E. MacConaill. Revolutionizing clinical care using prospective, institution-wide tumor sequencing. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4666. doi:10.1158/1538-7445.AM2015-4666