Clinical utility of comprehensive molecular profiling in cholangiocarcinoma.

Abstract

e16206 Background: Cholangiocarcinoma (CCA) comprises a heterogeneous group of biliary tract malignancies with distinct molecular types and features and increasing therapeutic relevance. Comprehensive genomic profiling is essential for clinical actionability, diagnostic relevance, and potential impact on therapeutic decision-making. The purpose of this study is to define the molecular profile of cholangiocarcinoma through a comprehensive Next Generation Sequencing (NGS) panel and to assess its implications for diagnosis and targeted therapy selection. Methods: A total of 151 FFPE tumor tissue samples from patients with CCA underwent comprehensive molecular profiling using a CE IVD hybrid capture–based NGS assay targeting 1,021 cancer-related genes, 38 genes for clinically relevant fusions and a thorough analysis of SNVs, Indels, CNVs, MSI, and TMB. Sequencing was carried out using the Next Generation Sequencing DNBSEQ-T7 platform. Results: Analysis of the results revealed a diverse genomic landscape with clinically relevant alterations in a substantial proportion of patients. On-label actionable alterations were identified in 28% of cases, including IDH1 mutations (18%), FGFR2 fusions (7%), and BRAF V600E mutations (3%). IDH1 mutations were enriched in tumors consistent with intrahepatic cholangiocarcinoma, supporting their diagnostic utility. FGFR2 fusions involved a broad range of partners, highlighting biological heterogeneity and the value of NGS target enrichment detection. Off-label potentially actionable alterations were observed in 38% of patients, including RAS alterations (21%), homologous recombination repair gene alterations such as ARID1a, BAP1 , BRCA2 , ATM, CHEK2 , PALB2 (7%) and PIK3CA mutations (4%). Biomarkers associated with immunotherapy response included MSI-H/TMB-high tumors (3%). Overall, 17% of patients harbored alterations associated with clinical trial eligibility, while TP53 alterations were detected in 28%, reflecting underlying widespread genomic dysregulation. Conclusions: Comprehensive genomic profiling provides clinically meaningful insights into the molecular heterogeneity of cholangiocarcinoma. Broad NGS testing facilitates accurate molecular classification, supports differential diagnosis, and identifies actionable alterations relevant to targeted and biomarker-driven therapies. In summary, a percentage of 66% of patients harbored at least one clinically significant alteration. These findings support the routine implementation of comprehensive capture-based NGS panels in the clinical management of cholangiocarcinoma.