Fusions and rearrangement detection in gastrointestinal and lung tumors leveraging low-pass whole-genome sequencing based Hi-C chemistry

Introduction: Molecular profiling in solid tumors has enabled the detection of actionable oncogenic drivers that guide targeted therapy. While point mutations in genes such as EGFR and KRAS are well established, gene fusions that activate key signaling pathways have become increasingly important therapeutic targets. Although RNA sequencing remains the gold standard for fusion detection, clinically relevant events are still missed. This study evaluates the ability of Hi-C whole-genome sequencing to improve detection of actionable fusions and structural rearrangements in solid tumors. Methods: All cases had molecular testing such as FISH, DNA panel sequencing, and/or RNA transcriptome sequencing as part of clinical care. Hi-C sequencing is a novel whole-genome DNA assay optimized for structural variant detection from FFPE tissues. Its chemistry captures linked read pairs that originate near each other in both three-dimensional and linear genomic space. This increases breakpoint coverage, amplifies rearrangement signals, and allows detection of fusions obscured by non-unique or complex genomic regions. Results: A total of 60 solid tumor cases were evaluated, the majority of which were gastrointestinal-including pancreatic adenocarcinoma, gastric cancer, and colorectal cancer. Hi-C sequencing was first applied to detect known fusions and rearrangements (12 cases) like ALK, FGFR2, ROS1, NTRK3, with 100% concordance with FISH (8 cases), whole transcriptome (1 cases), and DNA panel sequencing (3 cases), and able to detect fusion partner in all cases. Next it was used to successfully identify actionable or potentially actionable structural variants across the cohort (48 cases) which had no targetable driver genes detected by NGS. Hi-C detected targetable gene fusions involving NRG1 in three cases, and PRKCB in another case. Additional rearrangements were detected proximally to genes whose overexpression may be linked to tumor progression like NRG1, KRAS, NOTCH3 , and CHST9 . Conclusions: Hi-C sequencing shows strong potential as a complementary tool for molecular classification of gastrointestinal and other solid tumors. By detecting gene fusions and rearrangements-including those missed by conventional testing-Hi-C may expand the number of patients who can be matched to targeted therapies.