Molecular profiling for patients with Cholangiocarcinoma in Scotland
What is molecular profiling?
Cholangiocarcinoma tumours are not all the same. Even when they start in the same place, one person’s cancer cells can be different from another person’s. In part, this depends on which gene faults might be present. These faults can alter the way the cancer cells look, behave, and react to different treatments. Gene faults can sometimes be used to our advantage because they can be treated with targeted medication.
Molecular profiling of tumour cells is needed to identify which of these gene faults are present to allow the right treatment to be used. Approximately 40% of patients have treatable gene faults, although this proportion will increase, as other relevant mutations are identified and new treatments are developed.
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Background
The British Society of Gastroenterology (BSG) guidelines for the diagnosis and management of cholangiocarcinoma, published in 2024, recommend that cholangiocarcinoma patients should “be subjected to molecular profiling at the earliest opportunity, and results and treatment options should be reviewed by clinicians with appropriate expertise”.
Despite this, until February 2026 the NHS in Scotland was only funding molecular profiling for a single gene fault in cholangiocarcinoma patients. As a result, some patients would miss opportunities to access NHS-approved life-extending targeted treatments and clinical trials. This created inequity compared with England, resulting in some Scottish patients with the means paying privately to access testing and treatment across the border.
A campaign calling on the Scottish Government to fund a full panel of molecular profiling tests was launched in 2024, supported by Benjamin Carey (who was diagnosed with cholangiocarcinoma the previous year), AMMF, and clinicians including Professor Tim Kendall (Consultant Liver Pathologist at the Royal Infirmary of Edinburgh) and Professor Chiara Braconi (Consultant Medical Oncologist at Beatson West of Scotland Cancer Centre). Campaign activities included:
- Ben Macpherson MSP raising the issue during a parliamentary debate on liver disease
- AMMF hosting an evening reception at the Scottish Parliament
- Marie McNair MSP securing a parliamentary debate about cholangiocarcinoma
In December 2025, Jenni Minto MSP (Minister for Public Health and Women’s Health) announced that the Scottish Government would be supporting the implementation of the molecular testing programme for cholangiocarcinoma. Funding was released on 27 February 2026 to the NHS Scotland Genomic Laboratories to deliver this service. The testing programme for cholangiocarcinoma was prioritised ahead of wider reforms to the genomic medicine service, outlined in the Scottish Government’s Genomic Medicine Strategy.
What molecular tumour tests are available to NHS Scotland patients?
Testing of tumour samples is available to all patients with biliary tract cancer, including cholangiocarcinoma and gallbladder cancer, in NHS Scotland
If the sample contains enough tumour cells for testing, it will undergo the following:
- Staining to identify HER2 amplification
- Sequencing of tumour DNA to identify mutations in several genes including BRAF, ERBB2 (HER2), IDH1, IDH2, and KRAS genes
- Sequencing of tumour RNA to identify abnormalities in FGFR2, RET, NTRK1/2/3, and MET genes
- Tumour microsatellite instability testing
How is tumour testing requested?
Molecular testing of tumour samples from patients with cholangiocarcinoma and gallbladder cancer should be requested by the physician managing treatment. Test results should be available within 2-3 weeks of the lab receiving the tumour sample and will be fed back to the consultant.
The testing request goes directly to the Genomic Laboratory covering testing for patients in their hospital area.
What if a tissue sample cannot be safely obtained for molecular profiling?
For some cholangiocarcinoma patients, molecular profiling may not be possible due to insufficient tissue from a solid biopsy or their tumour(s) being located where a biopsy sample cannot be safely obtained.
For patients who cannot have molecular profiling of their tumour, liquid biopsy tests that detect ‘circulating tumour DNA’ (ctDNA) shed by tumours could potentially identify treatable gene faults. However, liquid biopsy testing for cholangiocarcinoma is still being investigated and is not currently offered by the NHS.
Liquid biopsy testing for cholangiocarcinoma is currently available privately. If you think it may be helpful, we recommend you discuss it with your consultant.
Does molecular profiling need to be repeated?
Molecular profiling of cholangiocarcinoma is considered highly reliable and is recommended as part of standard practice for advanced and metastatic disease.
However, it is possible for solid biopsies to produce inaccurate results because only a small sample is obtained which could miss the cancer cells or may not represent the entire tumour’s composition.
There is some anecdotal evidence from cholangiocarcinoma patients who report that a liquid biopsy has identified potentially treatable gene faults which were not found from their original solid tissue biopsy. If you are concerned this could apply to your case, we recommend you discuss it with your consultant.
