Genomics driven precision oncology in advanced biliary tract cancer improves survival

Background: Biliary tract cancers (BTCs) including intrahepatic, perihilar, and distal cholangiocarcinoma as well as gallbladder cancer, are rare but aggressive malignancies with few effective standard of care therapies. Methods: We implemented integrative clinical sequencing of advanced BTC tumors from 124 consecutive pa-tients who progressed on standard therapies (N = 92 with MI-ONCOSEQ and N = 32 with commercial gene panels) enrolled between 2011-2020. Results: Genomic profiling of paired tumor and normal DNA and tumor transcriptome (RNA) sequencing identified actionable somatic and germline genomic alterations in 54 patients (43.5%), and potentially actionable alterations in 79 (63.7%) of the cohort. Of these, patients who received matched targeted therapy (22; 40.7%) had a median overall survival of 28.1 months compared to 13.3 months in those who did not receive matched targeted therapy (32; P < 0.01), or 13.9 months in those without actionable mutations (70; P < 0.01). Additionally, we discovered recurrent activating mutations in FGFR2, and a novel association between KRAS and BRAF mutant tumors with high expression of immune modulatory protein NT5E (CD73) that may represent novel therapeutic avenues. Conclusions: Overall, the identification of actionable/ potentially actionable aberrations in a large proportion of cases, and improvement in survival with precision oncology supports molecular analysis and clinical sequencing for all patients with advanced BTC.

Automated summary

In this study, integrative clinical sequencing was performed on advanced biliary tract cancer (BTC) tumors. The results revealed actionable and potentially actionable genomic alterations in a significant portion of the patients, and those who received matched targeted therapy showed improved overall survival. The study also identified recurrent mutations in FGFR2 and a novel association between KRAS and BRAF mutations with high expression of immune modulatory protein NT5E (CD73).