Biliary tract cancer (BTC) accounts for <1% of all cancers, but remains a highly fatal malignancy. Surgical resection is the only hope for cure, but most patients present with advanced disease when curative-intent surgery is not possible. The therapeutic options for patients with advanced disease are limited, primarily to chemotherapeutic regimens, which are based on empiric evidence without the use of biomarkers. These current treatment strategies have been largely ineffective in controlling the disease, resulting in poor survival outcomes of less than 1 year. An understanding of the molecular characteristics of biliary tract cancer may enable stratification of patients into therapies that target specific molecular alterations with greater efficacies and improved clinical outcomes. This study aims to investigate the feasibility and clinical utility of prospective molecular profiling of advanced biliary tract cancer. The primary endpoint of this study is to demonstrate the feasibility of returning whole genome sequencing results within 8 weeks of tumour biopsy for second-line treatment consideration (n=30 patients). In parallel, tumour whole transcriptome sequencing will be performed to identify actionable molecular alterations (e.g., fusion transcripts). Once the primary endpoint is met, the study will be expanded. Current funding allows expansion to 40 patients in total.

Inclusion Criteria:

• Patients must have a histological or radiological diagnosis of inoperable or metastatic BTC.
• Patient must have a tumour that is amenable to a core needle biopsy.
• Patients must have a measurable lesion by RECIST 1.1 in addition to the lesion that is going to be biopsied.
• Patients must be fit to safely undergo a tumour biopsy as judged by the investigator.
• Eastern Cooperative Group (ECOG) performance status ≤ 1.
• Life expectancy of greater than 90 days.
• Within 14 days of the proposed biopsy date, patients must have normal organ and marrow function.
• Patients must undergo systemic treatment with gemcitabine-based regimens as first-line standard systemic palliative treatment with or without other investigational agents within a clinical trial.
• Ability to understand and willing to sign a written informed consent document.

Exclusion Criteria:

• Patients with one or more contraindications to tumour biopsy.
• Patients who have had any prior chemotherapy or other anti-cancer agent in the advanced stage setting.
• Patients who are currently on anti-cancer treatment.
• Patients with known brain metastases.
• Uncontrolled concurrent illness that would limit compliance with study requirements.
• Any other condition that would contraindicate the patient's participation due to safety concerns or compliance with clinical study procedures.