Feasibility of Comprehensive Genomic Profiling for Biliary Tract Cancer Using Transpapillary Biopsy Samples: A Prospective Study

Background: Patients with biliary tract cancer (BTC) often have actionable mutations, and comprehensive genomic profiling (CGP) plays an important role. However, the feasibility of CGP using transpapillary biopsy (TPB) samples remains unclear.
Methods: Thirty patients with suspected BTC based on radiographic imaging were enrolled. Pre-analytical criteria for CGP suitability were based on the OncoGuide NCC Oncopanel System (NCCOP) and FoundationOne CDx (F1CDx). Each patient underwent six biopsies using an endoscopic introducer: five biopsy samples were preserved as formalin-fixed paraffin-embedded (FFPE) samples and one as a fresh frozen (FF) sample. DNA quality indicators were compared between the two groups.
Results: Malignancy was confirmed in 29 patients, and one had a benign biliary stricture. Suitability rate was 31% (9/29) for NCCOP and 3.4% (1/29) for F1CDx. Compared to FFPE samples, FF samples demonstrated significantly higher DNA concentration [ng/μL, interquartile range (IQR)], [0.34 (0.16–0.95) vs. 37.8 (11.6–67.6), p < 0.001] and DNA integrity number (IQR) [7.1 (6.8–7.3) vs. 8.9 (8.3–9), p = 0.021].
Conclusions: Introducer-assisted multipass TPB may increase the rate of obtaining adequate CGP specimens, but its suitability remains limited and strongly panel dependent. Since FF samples have better DNA quality, establishing a system detailing their use is desirable.
Trial Registration: ClinicalTrials.gov identifier: UMIN 000049826