FGFR2 Fusions in Pancreatobiliary and Ampullary Cancers: High Detection Rate in FFPE Specimens of Intrahepatic Cholangiocarcinoma with Limited RNA Yields Using Amplicon-Based NGS Assay

Fibroblast growth factor receptor 2 (FGFR2) fusions are identified in approximately 10–16% of patients with intrahepatic cholangiocarcinoma (iCCA) and represent actionable targets, with several FGFR inhibitors approved for clinical use. To evaluate the clinical utility and assay performance of an amplicon-based next-generation sequencing (NGS) approach in this setting, we assessed FGFR2 fusion detection using the Oncomine Comprehensive Assay Plus (OCA-P). A total of 75 formalin-fixed paraffin-embedded (FFPE) specimens from biliary, pancreatic, and ampullary malignancies submitted for FGFR2 fusion testing between 1 March 2023 and 30 June 2024 were retrospectively analyzed, including 40 cases of iCCA. All iCCA specimens were successfully analyzed. FGFR2 fusions were detected exclusively in iCCA, yielding a detection rate of 20%. RNA concentrations in iCCA specimens ranged from 0.02 ng/µL to 104 ng/µL; six cases (15%) exhibited yields below 1 ng/µL and 10 cases (25%) ranged between 1 and 2 ng/µL. Despite limited RNA input, OCA-P demonstrated robust performance, successfully identifying FGFR2 fusions at concentrations below 2 ng/µL, levels typically considered suboptimal for partner-agnostic NGS approaches. These findings support the robustness and clinical utility of the OCA-P assay for reliable FGFR2 fusion detection in iCCA, particularly in specimens with limited RNA input.