Abstract
PURPOSE: An estimated 25% of patients with biliary tract cancer (BTC) do not undergo genotyping, representing a missed opportunity for therapeutic targeting. METHODS: Cell-free DNA (cfDNA) and matched tumor sample from patients with BTC were analyzed using targeted next-generation sequencing (NGS) assay and compared. We sought to define the molecular profile of cancer-derived cfDNA, frequency of OncoKB level 1/2 alterations, plasma:tumor genotype concordance, the prognostic impact of cfDNA, and clonal evolution after targeted therapy progression. RESULTS: cfDNA-based genotyping was performed on 297 blood samples from 170 patients with BTC. The most frequently altered genes were TP53 (29%), FGFR2 (16%), ARID1A (13%), CDKN2A (11%), and KRAS (11%); 25% of patients had OncoKB level 1/2 alterations and 36.2% of potentially actionable alterations were detected in plasma alone. The cfDNA:tissue concordance accuracy was high (96% IDH1, 98% BRAF, 92% KRAS mutations, 99% ERBB2 amplifications, and 96% FGFR2 fusions). Detectable tumor-derived cfDNA after resection did not predict recurrence. In treatment-naïve metastatic BTC, high variant allele fraction was associated with worse progression-free survival and overall survival. RAS alterations not detected in samples before treatment were identified at progression in 24% of patients who received BRAF-, FGFR-, or HER2-directed therapy, identifying RAS alterations as a convergent mechanism of targeted therapy resistance. CONCLUSION: Molecular profiling of cfDNA from patients with BTC identified OncoKB level 1/2 gene alterations and putative genomic resistance mechanisms to targeted therapy. Concordance analysis suggests that cfDNA-based NGS is complementary to that of tissue-based sequencing in the identification of potentially actionable alterations.