Extra-hepatic cholangiocarcinoma diagnosis: from classical pathological analysis to the emerging omics tests

Extrahepatic cholangiocarcinoma (eCCA), comprising perihilar and distal cholangiocarcinoma, remains a major diagnostic challenge in the setting of an indeterminate biliary stricture. Definitive diagnosis still relies on histopathological examination of endobiliary samples. However, the diagnostic sensitivity of biopsy and brush cytology remains limited, at approximately 50% despite high specificity. This limitation has driven the development of novel omics-based assays aimed at improving diagnostic accuracy using solid tissue sampling, as well as liquid biopsies derived from blood, bile, or urine. The primary diagnostic challenge in eCCA is to establish malignancy while avoiding misclassification of benign biliary strictures, thereby preventing unnecessary high-morbidity surgical procedures. In addition, accurate histopathological classification of periampullary tumours is critical for guiding optimal therapeutic decision-making, particularly regarding systemic chemotherapy. Although histology remains the diagnostic gold standard, next-generation sequencing (NGS) has improved the diagnostic yield of endobiliary sampling. Among all the omics techniques developed in research, genomics is currently the most advanced for clinical application whereas other omics approaches remain largely investigational and have not yet been sufficiently validated in large cohorts for routine use. Nevertheless, despite its robust performance in solid biopsy specimens, which makes its implementation in routine practice feasible, NGS still shows substantial false-negative rates ranging from 15% to 25%. Future advances will likely include the development of tissue-based omics profiling approaches focusing on molecular readouts closer to the functional consequences of the gene expression on solid biopsies, as well as the development of serum- and bile-based liquid biopsies that can be translated from bench to bedside.