BiliSeq DNA/RNA Next-Generation Sequencing Improves the Diagnosis of Neoplastic Bile Duct Strictures: Gastroenterology | August 2026

Introduction:

Distinguishing benign from malignant biliary strictures remains one of the greatest challenges in pancreatobiliary endoscopy. Although ERCP brush cytology and biopsy have excellent specificity, their sensitivity is disappointingly low, particularly in patients with primary sclerosing cholangitis (PSC). This landmark 6-year prospective, multicenter study evaluated BiliSeq, a comprehensive DNA/RNA-based next-generation sequencing (NGS) platform, to determine whether molecular analysis of ERCP-obtained specimens could improve diagnostic accuracy and facilitate precision oncology.

Why was this study needed?

Conventional ERCP brush cytology and biopsy frequently miss malignant biliary strictures because of low sensitivity.

Diagnostic uncertainty often delays treatment or necessitates repeated invasive procedures.

Patients with PSC represent a particularly difficult group because conventional diagnostic methods perform poorly.

Previous NGS studies were limited by retrospective design and single-center experience.

Molecular profiling has the potential to both improve diagnosis and identify actionable therapeutic targets.

Results:

This prospective study included 2,908 ERCP-obtained specimens from 2,116 patients across 28 institutions, making it the largest real-world evaluation of biliary NGS to date.

BiliSeq (Version 2/3) achieved substantially higher sensitivity for detecting malignant biliary strictures than conventional pathology while maintaining excellent specificity.

Combining BiliSeq with routine pathology further increased diagnostic sensitivity without compromising diagnostic accuracy.

The greatest improvement was observed in high-risk populations, including patients with primary sclerosing cholangitis (PSC), Hispanic patients, and individuals with hereditary cancer syndromes, where conventional pathology has historically performed poorly.

Importantly, approximately one in five BiliSeq-positive tumors harbored actionable molecular alterations, enabling precision medicine approaches.

Molecular findings directly changed clinical management in nearly one-third of patients with actionable genomic alterations, supporting the role of NGS beyond diagnosis alone.

Clinical Impact:

This study establishes DNA/RNA-based BiliSeq testing as a major advance in the evaluation of indeterminate biliary strictures. When performed on routine ERCP brushings, biopsies, or bile samples, BiliSeq significantly improves early cancer detection while simultaneously identifying targetable genomic alterations that can influence treatment decisions. The benefits are particularly striking in PSC, where conventional cytology often fails. These findings strongly support incorporating NGS alongside routine pathology into the diagnostic algorithm for indeterminate biliary strictures at centers with molecular testing capabilities.

Bottom Line:

BiliSeq DNA/RNA next-generation sequencing markedly improves the diagnosis of malignant biliary strictures compared with conventional pathology while maintaining excellent specificity. Beyond improving early cancer detection, BiliSeq identifies actionable genomic alterations that can guide precision therapy, making it a valuable adjunct to ERCP-based tissue acquisition, particularly in high-risk patients such as those with primary sclerosing cholangitis.