Abstract 3630: Validation of the Archer FusionPlex solid tumor panel in the JAX cancer treatment profileTM
Authors: Helm Samantha , Ras Aleksandra , Spotlow Vanessa , Kelly Kevin , Mockus Susan , Statz Cara , Ananda Guruprasad , Malcolm Joan , Tsongalis Gregory J. 
Published: July 2016

Abstract
Introduction: A comprehensive somatic tumor profile with associated treatment selection options requires the detection of gene fusions. After evaluating the clinical utility of multiple methods of gene fusion detection, it was determined that the Archer FusionPlex Solid Tumor Panel (AFPSTP) best compliments the JAX Cancer Treatment ProfileTM (JAX-CTPTM) clinical test in terms of workflow, specimen requirements and turnaround time. Here we describe our analytical validation process for the AFPSTP assay.
Methods: AFPSTP was validated using 24 samples: 5 JAX Patient Derived Xenograft (PDX) cases, 4 translocation positive controls, 2 FFPE cancer samples, 1 normal tissue sample, and 12 cell lines. Nine of the cell lines were previously identified as positive for fusion transcripts and 3 lacked detectable fusion events. The validation was executed in 5 phases: (1) confirm that AFPSTP was able to detect known fusion or lack of fusion events in characterized specimens; (2) determine inter-assay concordance; (3) determine intra-assay concordance; (4) LOD and (5) sensitivity.
Results: The fusion detection results for this validation are listed in Table 1. All but one of these fusion events was previously identified. The one novel fusion was confirmed using TaqMan RT-PCR. In addition to the expected fusions, 4 false positive events were detected, 2 due to mispriming and 2 determined to be WT read through transcripts. The fusion detection inter and intra-assay concordance was found to be 100% and the sensitivity was calculated to be 91.67% at a LOD of 5%.
Conclusion: This analysis outlines the clinical validation of the incorporation of AFPSTP into the JAX-CTPTM test system. Once incorporated, the AFPSTP assay will accomplish the goal of making JAX-CTPTM a more comprehensive somatic tumor profiling assay without affecting the current acceptable turnaround time or required input material. List of 15 samples that were found to be fusion positive and the corresponding detected fusion.HorizonDx EML4/ALK PositiveEML4 → ALK variant 1HorizonDx RET PositiveCCDC6 → RETHorizonDx ROS PositiveSLC34A2 → ROS1HorizonDx Triple PositiveEML4 → ALK variant 3bHorizonDx Triple PositiveSLC34A2 → ROS1HorizonDx Triple PositiveCCDC6 → RETA673 Cell LineEWSR1 → FLI1VCaP Cell LineTMPRSS2 → ERGKM-12 Cell LineTPM3 → NTRK1RPMI-2650 Cell LineBRD4 → NUTM1NCI-H716 Cell LineFGFR2 → COL14A1OCI-AML2 Cell LineMBNL1 → RAF1REH Cell LineETV6 → RUNX1MDA-MB-175-VII Cell LineTENM4 → NRG1ASPS-1 Cell LineTFE3 → ASPSCR1ASPS-1 Cell LineASPSCR1 → TFE3PDX1EML4 → ALK 3bPDX2SYN2 → PPARG
Citation Format: Samantha Helm, Aleksandra Ras, Vanessa Spotlow, Kevin Kelly, Susan Mockus, Cara Statz, Guruprasad Ananda, Joan Malcolm, Gregory J. Tsongalis. Validation of the Archer FusionPlex solid tumor panel in the JAX cancer treatment profileTM. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3630.