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

Abstract

The distinction between benign and neoplastic bile duct strictures remains challenging. Pathologic assessment of ERCP-obtained specimens has limited sensitivity, particularly among patients with primary sclerosing cholangitis (PSC). Next-generation sequencing (NGS) of bile duct specimens provides a promising diagnostic approach; but a prospective, multi-institutional, and comprehensive DNA/RNA analysis is lacking. A 6-year, prospective, multi-institutional study was conducted using BiliSeqV2 (28 cancer-associated genes and 167 fusion genes) and BiliSeqV3 (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 to clinical, imaging, and pathologic parameters including diagnostic pathology and/or at least 1-year follow-up. BiliSeqV2/V3 testing was performed for 2865 (99%) specimens from 2080 (98%) patients. Based on follow-up from 1979 (95%) patients, BiliSeqV2/V3 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 BiliSeqV2/V3 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 BiliSeqV2/V3 (74% to 86%) compared to pathologic assessment (26% to 50%). Further, actionable molecular alterations were identified in 20% of BiliSeqV3-positive neoplasms and modified patient management in 30% of these cases. Applying BiliSeqV2/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 to traditional methods. This study highlights the importance of NGS for precise diagnosis and therapeutic intervention.