Molecular Analysis of Driver Negative Lung Cancer for Rearrangements and Fusions Using a New HiC Sequencing Assay

Reference:

Ricketts, et al.

2025 World Conference on Lung Cancer - Barcelona, Spain

Abstract:

Introduction: Molecular testing in lung cancer has led to the identification of driver mutations that can be effectively targeted by new therapeutics. In addition to single point mutations that activate signaling proteins such as EGFR and KRAS, the presence of various fusion proteins that lead to protein overexpression and activation of key pathways have become prominent drug targets. Detection of these fusion proteins by FISH or sequencing is possible but may be limited due to changes in breakpoint regions, the panel may not target the fusion partner, or RNA expression may be affected by sample fixation or processing. This study aims to improve detection rate of targetable fusions and rearrangements in non-small cell lung cancer (NSCLC) using a new method called FusionPlus sequencing.​Methods: FusionPlus sequencing is a novel whole genome DNA-sequencing assay for detection of structural variation based on Hi-C chemistry method leveraging the sequencing of linked pairs of reads which occur nearby one another in 3-dimensional and linear space, from FFPE samples. Linking reads amplifies the rearrangement signal giving it much higher sensitivity. In previous studies, FusionPlus has been shown to detect gene fusions and rearrangements in many different tumor types missed by other clinical testing modalities such as FISH and RNA sequencing. ​Results: In a pilot set of NSCLC samples, FusionPlus sequencing demonstrated 100% concordance with FISH and/or RNA sequencing results (10/10, including 4 ALK, 2 MET, 2 ROS, 1 NTRK, and 1 RET fusions). In this current study, we have examined 100 NSCLC FFPE specimens (25 complete, to date), which were previously determined by DNA and RNA sequencing to be negative for drivers such as EGFR and KRAS mutations and fusions of ALK, MET, NTRK, RET, and ROS.  In the first 25 samples, we have detected eleven total rearrangements in FGFR1 (7), RAD51B (2), ERBB2 (1) and FGFR4 (1). We have also detected two amplifications, one MET and one KRAS.  The other 75 samples have been sequenced and are currently being analyzed.   ​Conclusions: Encouraging results from this study suggest that FusionPlus sequencing may be a valuable tool in the molecular classification of lung cancers and could lead to improvement in patient care. FusionPlus can detect gene fusions and rearrangements that are known to drive cancer and may be used for therapy selection, including in cases which were negative by standard genetic testing.