DNA/RNA-Based Next-Generation Sequencing Improves the Early Diagnosis and Management of Neoplastic Bile Duct Strictures: A 6-Year, Prospective, Multi-Institutional, Real-Time Study

BACKGROUND & AIMS: The distinction between benign and neoplastic bile duct strictures remains challenging. Pathologic assessment of endoscopic retrograde cholangiopancreatography (ERCP)-obtained specimens has limited sensitivity, particularly among patients with primary sclerosing cholangitis (PSC). Next-generation sequencing of bile duct specimens provides a promising diagnostic approach, but a prospective, multi-institutional, and comprehensive DNA/RNA analysis is lacking. METHODS: A 6-year, prospective, multi-institutional study was conducted using BiliSeq version 2 (28 cancer-associated genes and 167 fusion genes) and BiliSeq version 3 (161 cancer-associated genes and 763 fusion genes) for 2908 ERCP-obtained brushings, biopsies, and bile from 2116 patients at 28 medical institutions. Molecular results were compared with clinical, imaging, and pathologic parameters including diagnostic pathology and/or at least 1-year follow-up. RESULTS: BiliSeqV2/V3 testing was performed for 2865 (99%) specimens from 2080 (98%) patients. Based on follow-up from 1979 (95%) patients, BiliSeq version 2/version 3 demonstrated 82% sensitivity and 98% specificity for a neoplastic stricture. In comparison, pathologic assessment had a sensitivity of 44% and a specificity of 99%. Combining BiliSeq version 2/version 3 testing with pathologic assessment improved the sensitivity to 88% and maintained a high specificity of 97%. High-risk populations, such as Hispanic, germline carrier, and PSC patients, also showed improvement in sensitivity with BiliSeq version 2/version 3 (74% to 86%) compared with pathologic assessment (26% to 50%). Further, actionable molecular alterations were identified in 20% of BiliSeq version 3-positive neoplasms and modified patient management in 30% of these cases. CONCLUSIONS: Applying BiliSeq version 2/version V3 testing to ERCP-obtained specimens improved the diagnostic evaluation of bile duct strictures, achieving higher sensitivity, especially for PSC, and maintained high specificity compared with traditional methods. This study highlights the importance of next-generation sequencing for precise diagnosis and therapeutic intervention.