Clinical and analytic validation of FoundationOne CDx (TM) for NTRK fusion-positive solid tumors in patients treated with entrectinib

Introduction: Patients whose tumors harbor NTRK gene fusions represent an extremely small proportion of the overall cancer population (i.e., ~0.32-1%). While adult and pediatric cancer patients with NTRK fusion-positive solid tumors are rare, they comprise a patient population with a targetable alteration for whom there is currently no accepted standard of care. Comprehensive genomic profiling assays are a critical component in the identification of this sub-population, and herein we describe the clinical validation and analytic performance of FoundationOne CDx™ (F1CDx) as the companion diagnostic for entrectinib, a potent inhibitor of ROS1 and TRK A/B/C kinases. F1CDx and entrectinib were approved in Japan for the respective diagnosis and treatment of adult and pediatric patients with NTRK fusion-positive advanced recurrent solid tumors. Methods: Analytical concordance was determined by comparing F1CDx to a validated RNA NGS fusion panel using 28 NTRK fusion-positive and 53 NTRK fusion-negative samples. Concordance was defined as the overall percent agreement (OPA) between the two assays. Positive and negative percent agreement (PPA, NPA) were calculated using the RNA assay as the reference. Analytical sensitivity was calculated from representative gene fusions based on the 95% probability of detection, and intermediate precision was assessed from NTRK-positive samples run at and slightly above the platform limit of detection. Clinical validation for F1CDx as a companion diagnostic for entrectinib in Japan was estimated based upon patients in the primary efficacy population who had samples remaining for F1CDx testing using multiple imputation and sensitivity analysis of the concordance of F1CDx to the various enrollment assays. Results: OPA between F1CDx and an orthogonally validated RNA NGS fusion panel was 92.6% (95% CI: 84.6-97.2%). PPA and NPA values were 85.7% (95% CI: 67.3-96.0%) and 96.2% (95% CI: 87.0-99.5%), respectively. Platform sensitivity for rearrangements was between 6.4-11.3% tumor purity. Repeatability for NTRK fusions was 100% (95% CI: 73.5-100.0%) and reproducibility was 100% (95% CI: 90.3-100.0%). OPA, PPA and NPA values comparing F1CDx to the multiple enrollment assays utilized for the STARTRK-2 trial were 95.7% (95% CI: 87.8-99.1%), 84.2% (95% CI: 60.4-96.6%), and 100.0% (95% CI: 92.9-100.0%), respectively. The previously reported overall response rate (ORR) for the primary efficacy population in the STARTRK-2 trial was 57.4% (95% CI: 42.3-70.7%)1. Bridging analysis estimated that the ORR for the F1CDx NTRK-positive population was 50.0% (95% CI: 24.7-75.4%), with acceptable balance between co-variates in the F1CDx evaluable and non-evaluable populations. Conclusions: The DNA-based F1CDx assay demonstrated strong concordance compared to an externally validated RNA NGS fusion panel (92.6% OPA) for the detection of NTRK fusions. Furthermore, an analysis of the clinical efficacy demonstrated comparable results between F1CDx NTRK-positive patients (ORR of 50%; 95% CI: 24.7-75.4%) and the overall NTRK fusion-positive population (ORR of 57%; 95% CI: 42.3-70.7%) from the STARTRK-2 clinical trial evaluating entrectinib in patients with solid tumors. 1. ESMO [https://www.esmo.org/Oncology-News/Entrectinib-NTRK-Fusion-Positive-Tumours-Demetri] Citation Format: David Fabrizio, Coren Milbury, Wai-Ki Yip, Bahar Yilmazel, Xiaobo Bai, Juan Liao, David Smith, Christine Burns, Christine Vietz. Clinical and analytic validation of FoundationOne CDx™ for NTRK fusion-positive solid tumors in patients treated with entrectinib [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr A028. doi:10.1158/1535-7163.TARG-19-A028