Abstract 4581: Feasibility of an amplicon-based liquid biopsy for ALK and ROS1 fusions in advanced non-small cell lung cancer (NSCLC) patients
Authors: Mezquita Laura , Hu Yuebi , Howarth Karen , Jovelet Cecile , Planchard David , Lacroix Ludovic , Swalduz Aurelie , Ortiz-Cuaran Sandra , Avrillon Virginie , Plagnol Vincent , Beeler John , Baker-Neblett Katherine , Jones Greg , Rosenfeld Nitzan , Morris Clive , Green Emma , Kim Edward S. , Perol Maurice , Saintigny Pierre , Liu Stephen V. , Oxnard Geoff R. , Besse Benjamin 
Published: August 2018

Abstract
INTRODUCTION Circulating tumor DNA (ctDNA) is a surrogate material for somatic mutation detection, such as EGFR, BRAF or KRAS mutations in NSCLC patients, however the applicability of this technique for ALK and ROS1 fusion detection is poorly described. The aim of this combined analysis was to evaluate an amplicon-based ctDNA technology in a cohort of ALK and ROS1 positive NSCLC patients. METHODS ALK and ROS1 positive NSCLC patients were prospectively enrolled or retrospective specimens selected, to be included across 6 international centres. ALK/ROS1 positive status was determined by standard of care (FISH/IHC or NGS). The analysis of EML4-ALK fusions (variant 1,2,3) and ROS1 fusions (with partner genes CD74, SLC34A2, SDC4 and EZR) was performed using the InVision™ platform. RESULTS Patients included (n=65; 59 ALK, 6 ROS1): 35 (55%) females, 40 (63%) non-smokers, median age of 59 years, stage IV disease (88%) adenocarcinoma (97%). All patients were ALK/ROS positive by IHC (32), FISH (45) and/or tissue NGS (10). Samples (n=98) were collected across multiple timepoints. In total, 31 patients were fusion positive (25 ALK, 6 ROS1). Among treatment-naïve patients, sensitivity was 78% for ALK and 100% for ROS1. In contrast, fusions were detected in minority of samples (7/57) in patients responding to treatment. In patients with ctDNA positive ALK fusion (n=25): 8 patients (32%) presented the EML4-ALK variant 1; 2 (8%) the variant 2 and 15 (60%) the variant 3. In the ROS1 population (n=6), rearrangement with chromosome 5, resulting in CD74-ROS1 was seen in 4 of cases and translocation with chromosome 4 to generate SLC34A2-ROS1 occurred in 2 of cases. All patients had unique DNA fusion junctions identified and will be described, providing an insight at the DNA level of the molecular mechanisms leading to ALK and ROS1 driven lung cancers. Breakpoint microhomology was observed at the fusion junction in 50% of cases, ranging from 1 to 7bp. A 4bp insertion of non-templated DNA was seen in one case, with the remaining 47% of cases most likely the result of non-homologous end joining. Evidence for enrichment of microhomologous sequences and clustering of breaks within the introns will be investigated and reported at the conference. CONCLUSION The detection of ALK and ROS1 fusions using the amplicon-based NGS Invision liquid biopsy platform is feasible in routine clinical practice. Good sensitivity for clinically actionable ALK and ROS structural rearrangements in untreated advanced NSCLC patients was demonstrated.
Citation Format: Laura Mezquita, Yuebi Hu, Karen Howarth, Cecile Jovelet, David Planchard, Ludovic Lacroix, Aurelie Swalduz, Sandra Ortiz-Cuaran, Virginie Avrillon, Vincent Plagnol, John Beeler, Katherine Baker-Neblett, Greg Jones, Nitzan Rosenfeld, Clive Morris, Emma Green, Edward S. Kim, Maurice Perol, Pierre Saintigny, Stephen V. Liu, Geoff R. Oxnard, Benjamin Besse. Feasibility of an amplicon-based liquid biopsy for ALK and ROS1 fusions in advanced non-small cell lung cancer (NSCLC) patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4581.