Abstract A013: Hi-C DNA Sequencing of Solid Tumors for Rearrangements and Fusions Detects Targetable Biomarkers Missed by RNA Sequencing

Abstract Introduction: Molecular testing in lung and other solid tumors 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 location, the panel may not target the specific exons or fusion partner, or RNA quality may be affected by sample fixation or processing. This study aims to improve detection rate of targetable fusions and rearrangements in solid tumors using a new method called Hi-C sequencing. Methods: Hi-C sequencing is a novel whole genome DNA-sequencing assay for detection of structural variation based on unique Hi-C chemistry which leverages 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 and overcoming non-unique sequences masking fusions. In previous studies, Hi-C 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 set of 110 NSCLC samples, Hi-C 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). The remainder of samples were previously determined by standard 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 this cohort, we have detected biomarkers related to drug sensitivity in 15 cases. These include targetable fusions such as NTRK2 (1), NRG1 (1), PRKCA (1), loss of function variants indicating sensitivity to checkpoint inhibitors (2 cases), or PARP inhibitors (6), and others (4). In addition, noncanonical fusions were detected in NRG1 (1), and ALK (1), both retaining their functional domains and potentially indicating sensitivity to inhibitors. Finally, we detected additional rearrangements proximal to targetable genes which led to increased and exogenous expression of their gene products, revealing additional potential targetable biomarkers. Conclusions: Encouraging results from this study suggest that Hi-C sequencing may be a valuable tool in the molecular classification of solid tumors and could lead to improvement in patient care. Hi-C 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. Citation Format: Alex Hastie. Hi-C DNA Sequencing of Solid Tumors for Rearrangements and Fusions Detects Targetable Biomarkers Missed by RNA Sequencing [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Fusion-Positive Cancer: From Discovery to Therapy; 2026 Jan 13-15; Philadelphia PA. Philadelphia (PA): AACR; Cancer Res 2026;86(1_Suppl):Abstract nr A013.