Abstract 624: Evaluation and comparison of two commercially available targeted NGS platforms to assist oncology decision making
Authors: Glen J. Weiss, Brandi R. Hoff, Robert P. Whitehead, Ashish Sangal, Susan A. Gingrich, Vivek Khemka
Journal: Cancer Research (2015)

Abstract Background: It is widely acknowledged that there is value in examining cancers for genomic aberrations via Next-Generation Sequencing (NGS) on formalin-fixed paraffin-embedded (FFPE) tumor tissue. How commercially available NGS platforms compare with each other and the clinical utility of the reported actionable results is not well known. During the course of the study, the Foundation One (F1) test generated data on a combination of somatic mutations, indels, chromosomal abnormalities, and DNA copy number changes at ∼250X coverage, while the PCDx test generated the same type of data at &amp;gt;5,000X coverage plus provided mRNA expression levels. We sought to compare and evaluate paired FFPE tumor using these two platforms. Methods: Paired FFPE blocks from patients were submitted to both vendors for NGS analysis. Samples were from patients with advanced solid tumors. Patients either had a cancer type for which no standard of care exists or had progression on &amp;gt;1 line of systemic therapy. Turnaround time (TAT) was calculated (calendar days between the date sample received at the vendor to time of first NGS report). A biomarker was considered actionable if it has a published association with treatment response in humans. The assay report was assigned the highest of the following categories based on the list of actionable biomarker(s): commercially available drug (CA) (highest), clinical trial drug (CT), or neither option (NO) (lowest). Results: There were 10M:11F; median age was 56 (range 35-65). The most common cancer types were 7 thoracic, 4 GI, and 3 GU. Paired F1 and PCDx results for 21 unique patient tumors submitted between 3/2014 and 9/2014 were available. Due to insufficient archival tissue from the same collection period, 1 case used samples from different collections. PCDx reported first results faster than F1 in 20 cases. When received at both vendors on the same day, PCDX reported first results for 14 of 15 cases, with a median TAT of 9 days earlier than F1 (range -7 to 14 days). PCDx and F1 reported a CA 6 and 5 times, CT 4 and 4 times, and NO 11 and 12 times; respectively. PCDx provided higher ranking actionable targets for 5 cases vs. 3 cases for F1; the rest had equivalent ranking. Conclusions: In this analysis, commercially available NGS platforms provided clinically relevant actionable targets (CA or CT) in ∼45% of diverse cancer types. PCDx outperformed F1 in TAT and clinically relevant higher ranking of actionable targets. Citation Format: Glen J. Weiss, Brandi R. Hoff, Robert P. Whitehead, Ashish Sangal, Susan A. Gingrich, Vivek Khemka. Evaluation and comparison of two commercially available targeted NGS platforms to assist oncology decision making. [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 624. doi:10.1158/1538-7445.AM2015-624