Biomarker testing can open the door to additional, personalized treatment options, including clinical trials.

Get the Right Tests & Find the Right Treatment for Cholangiocarcinoma

Biomarker testing can open the door to additional, personalized treatment options, including clinical trials.

If you’ve been diagnosed with cholangiocarcinoma, it is important that you and your doctor get as much information as possible about your tumour. Knowing your tumour’s biomarkers will help you both to make important decisions about your treatment.

“Thank goodness for research! Biomarker testing, also known as molecular profiling, has literally been a life-saver for me.  Identifying my mutations opened up clinical trial treatment options.  I am currently enrolled in a clinical trial and it has given me hope and life!”

Bekki Slater
Cholangiocarcinoma Patient

What are biomarkers?

Your body is made up of different types of cells. You can think of each cell as a little factory that produces all sorts of molecules that keep the factory running smoothly. Each type of cell produces a unique set of molecules, called a molecular “signature”. This signature helps to identify each cell and its activities.

A biomarker is any molecule that can be measured in tumor tissue, blood, or other bodily fluids.

The term “biomarker” is short for “biological marker”. These markers provide a way for your doctor to monitor whether your body is operating normally or if there are signs of a disease or other condition.

When you have a routine blood test, your laboratory report lists a variety of biomarkers, like your thyroid hormone levels, glucose level, and red and white blood cell counts. This lets your doctor see how your body is functioning. It can also tell your doctor how you are responding to a medication.

What are cancer biomarkers?

Cancer cells were once healthy cells. Damaged genes caused the cells to go rogue. These rogue cells quickly multiply, forming a tumor that crowds out healthy cells. Cancer cells can “go rogue” in many different ways. If we took a close look at the tumor cells from three people with cholangiocarcinoma, we would likely find that different molecules are driving each of their tumors.

The term “cancer biomarkers” refers to molecules that are produced either by tumor cells or by other cells in the body reacting to a tumor. You might also hear them called “tumor markers” or “driver mutations”.

Cancer biomarkers can take several forms

Gene mutations

Inside each of your cells is your DNA, which contains thousands of genes. Each gene provides the recipe for how to assemble a specific protein to help the cell function. If any of the instructions for building the protein are damaged, the protein that gets made will be faulty.

Damaged genes are said to be “mutated”.  Mutations can be inherited or acquired.

  • Inherited mutations are present in all of your cells. They are passed down through generations and can affect your risk for getting certain kinds of cancer. Testing for inherited mutations is called “genetic testing”. This is done mainly for risk assessment, often for those who do not have cancer.
  • Acquired mutations are only present in tumor cells and are identified through biomarker testing. Knowing these biomarkers is helpful in making treatment decisions. Learn more.


Proteins are made by both healthy and cancerous cells. But cancer cells often produce too much of a protein or an abnormal protein. This can be detected through biomarker testing.

How are cancer biomarkers used?

Cancer biomarkers may be diagnostic, prognostic, or predictive. They all offer important clues that can help direct your care.

  • Diagnostic biomarkers can tell you and your doctor whether you have cancer and help determine the type and form of your cancer.
  • Prognostic biomarkers help to tell you how likely a cancer is to come back or progress. They can also forecast how you are likely to do, with or without therapy.
  • Predictive biomarkers can help to identify which therapies might work for your particular tumor and which might be wrong for you. These treatments may be:
Biomarkers can also provide information that leads to
  • FDA-approved (Australian Approved) therapies for cholangiocarcinoma,
  • A therapy already approved to treat another cancer that is being studied in a clinical trial to see if it is effective in cholangiocarcinoma, or
  • A therapy still in development that is being studied in a clinical trial.

Why do biomarkers matter for people with cholangiocarcinoma?

To date, researchers have discovered that there are many biomarkers associated with cholangiocarcinoma. Each person with cholangiocarcinoma has some of these biomarkers.

Many of the biomarkers seen in cholangiocarcinoma are also seen in other types of cancer. That is especially important for cholangiocarcinoma patients because some of these other cancers have treatments that may also work in cholangiocarcinoma. In fact, there are many clinical trials going on that are studying the potential effects of these treatments on cholangiocarcinoma patients who have certain biomarkers.

That’s why your biomarkers matter!

More than 50% of patients with cholangiocarcinoma have at least one biomarker that can be treated with a known therapy. We call these biomarkers “actionable”.

Knowing which biomarkers are driving your individual tumor can help you and your doctor decide the best way to treat your cancer. It can also open the door to newer drugs and clinical trials that are only available to patients with specific biomarkers.

Which biomarkers matter in cholangiocarcinoma?

The biomarkers driving your cancer may determine the type of treatment you are offered.

Targeted Therapy

Targeted therapies focus on cells with a specific mutation, while minimizing harm to healthy cells.

Having at least one of the following biomarkers may make you eligible for treatment with an FDA-approved targeted therapy:

  • FGFR2 fusions*
  • NTRK fusions*

Other biomarkers may make you eligible for a clinical trial for a targeted therapy that is either still in development or already approved to treat another cancer.

* Gene fusions occur when a part of one gene attaches to part of another gene.

“While having a cancer diagnosis and trying to figure out treatment options can be very overwhelming, cholangiocarcinoma is one of the cancers that has the highest chance of having at least one molecular abnormality that we have a really effective drug to target. So, by getting your tumor tested, you have a real chance of getting treatment that is tailored specifically for you.”

Nilofer Azad
Sidney Kimmel Comprehensive Cancer Center
John Hopkins University


Immunotherapies use the power of your own immune system to treat your cancer.

Having any of the following biomarkers may make you eligible for treatment with an immunotherapy:

  • Microsatellite Instability/Mismatch Repair deficiency (MSI/dMMR)
  • PD-L1
  • High Tumor Mutational Burden (TMB-high)

How can I find out my tumour’s biomarkers?

Biomarker testing will tell you and your doctor about your tumor’s biomarkers. You might also hear it called “genomic testing”, “tumor testing” or “molecular profiling”.

There are different kinds of biomarker tests that will look only for specific biomarkers. To get a complete picture of the mutations or proteins that may be fueling (driving) your tumors growth, ask your doctor for Comprehensive Biomarker Testing.

There are 2 types of tests that are ordered

Immunohistochemistry: (IHC)

3-5 day cost-effective local laboratory test.
IHC is a common application of immunostaining. It involves the process of selectively identifying proteins in cells of a tissue section. IHC takes its name from the roots “immuno”, in reference to antibodies used in the procedure, and “histo”, meaning tissue.

Immunohistochemical staining is widely used in the diagnosis of abnormal cells such as those found in cancerous tumors. Specific molecular markers are characteristic of particular cellular events such as the proliferation of unrepaired DNA mistakes (mutations) or cell death (apoptosis).

The tissue sample is stained to highlight the presence of known biomarkers that relate to current clinical trials, immunotherapy, or targeted treatments. IHC tests can reveal whether checkpoint inhibitor treatments are a potential treatment option. PD-L1 expression and also identify proteins absent in the tumor sample, indicating that one of the Lynch syndrome genes might not be working properly. Lynch syndrome mutations affect whether the MLHL, MSH2, MSH6, and PMS2 proteins are made and located in the correct place, this also points to a MSi status.

Ref Immunohistochemistry screening + Applications of immunohistochemistry

Molecular (Genomic) Profiling:

Also known as…
NGS -Next Generation Sequencing.
4-6 week specialist NGS laboratory facility.
Most often it will be you the patient that will need to insist on having this test carried out.

Genomic Profiling looks at the whole composition of a tumour including your inherited (germline/genetics) and any acquired (somatic) influences. Somatic mutations are changes to your DNA that happen after conception to cells other than the egg and sperm, ie acquired or influenced after you were born. Click this link to learn more about the differences

Extra Note
  • IHC test results are also included within a full Molecular (Genomic) Profiling.
  • The reason you or your doctor would order an IHC test is for its speed in providing important information that could provide early options that match current clinical trials. (Targeted or Immunotherapy)
  • You can have both tests (Ideally) but ensure that enough tissue sample (Biopsy) has been obtained to do both. In fact enough for further retesting is very advisable.
  • You will need to ensure that you ask for the specific biomarkers mentioned on this page ie PD-L1, MSi etc


Don’t confuse genomic testing with genetic testing. 

Genomic Profiling/testing checks your tumor cell’s whole molecular composition and looks for known biomarkers that can reveal what mutations (DNA mistakes) are present in the tissue sample being examined. These mutations are also described as your cancer’s mutational drivers. 

Genetic testing is done using a sample of blood, urine, saliva, hair, amniotic, or other body fluid, to test for inherited mutations from your parents that could increase your risk for certain types of cancer.


As a Newly Diagnosed Patient, you do not know what you do not know.

The CCA Patient Toolkit is a dedicated resource developed for patients diagnosed with bile duct cancer. You can access the mobile web app Toolkit voa a QR code on the back of the CCA Patient Navigator Journal

Biomarker testing requires a sample of your tumor tissue, usually collected via a biopsy. So if you’re having a biopsy, ask your doctor to collect enough tissue for biomarker testing as well. The tissue is then sent to a laboratory to find out which biomarkers may be responsible for your cancer.

This testing identifies any markers that can be targeted with current therapies as well as markers for which there may not yet be approved treatments; that way, if a new treatment becomes available down the road, your biomarker report could make you eligible for that therapy.

It’s a good idea to ask for a copy of the report for your own medical records.

When should I get biomarker testing?

Ideally, you want biomarker testing performed when you’re first being diagnosed with cholangiocarcinoma so you and your doctor will know all of your treatment options.

If you are having a biopsy because cancer is suspected:

  • Tell your doctor you are interested in biomarker testing and ask that they collect enough tissue.

If you’ve already had a biopsy:

  1. Ask whether your tumor was tested for biomarkers.
  2. If it wasn’t: Ask whether biomarker testing can be conducted with the sample that was taken; that way you won’t need a second biopsy.
  3. If it was: Ask whether you qualify for any targeted therapies, immunotherapies, or clinical trials. Also be sure to ask for a copy of the report!

The Cholangiocarcinoma Foundation (UAS) has a list of clinical trials open to those with cholangiocarcinoma.

Over time, if a therapy stops working or your cancer comes back, that may mean that your tumor cells have evolved and developed new mutations. At that point, ask your doctor about having a second biomarker test. That may reveal new biomarkers that could be targeted.

Does insurance cover biomarker testing?

Recognising the value of biomarker testing for cholangiocarcinoma, many good insurance companies are beginning to cover this testing, so please check this directly with your insurance company.

What if my doctor doesn’t think I need biomarker testing?

Tell your doctor you want to know your biomarkers so you will both know all of your treatment options.

Your Doctor should be fully aware of participating laboratories in Australia, please ask them to arrange this process for you.

Reference Articles

Beneath the Surface: Advancing Treatment for Cholangiocarcinoma

Progress in cholangiocarcinoma treatment was long-stalled, but now scientists are identifying genetic drivers likely to respond to novel drugs.A new understanding of the genetic mutations that drive the rare and difficult-to-treat cancer cholangiocarcinoma, along with the testing of targeted drugs and immunotherapies in people with the disease, are laying the groundwork for long-awaited advances in therapy… continue reading

Taking the brake off T cells

The Nobel Prize recognizes Allison’s breakthrough work with T cells, the “soldiers” of the immune system that battle invaders and abnormal cells like cancer, bacteria and viruses. While T cells are fierce opponents of disease, they don’t attack every invader that comes along. If they did, the body would be in a constant state of fever, rash, inflammation or other immune system response. “Brakes” on the immune system prevent T cells from attacking everything, which is, in part, how cancer is able to develop…continue reading

Common biomarkers

The acronym ALK, which stands for Anaplastic lymphoma receptor tyrosine kinase, is a gene that produces a specific active protein to help cell growth.

Several types of alterations in the ALK gene have been found.

It has been found in many solid tumours, including 5-10% in lung and uterine cancers, as well as skin melanoma, and less than 5% in the colon, breast, prostate, and hepatobiliary cancers.

Two ALK inhibitors have received FDA approval for certain ALK-positive hematological and solid tumours but not including cholangiocarcinoma so far.

Currently, there are ongoing clinical trials for ALK-positive solid tumors, which include cholangiocarcinoma patients (NCT02568267).

ATM is a tumor suppressor gene that, when working properly, prevents abnormal cell growth and helps repair your cell DNA damage.

An alteration in this gene leads to abnormal cell growth and increases the risk of cancer development.

Several types of alterations in ATM have been found, with ATM D2320N being one of the common mutations.

ATM alteration has been found in many solid tumors, including 5-10% of cholangiocarcinoma patients.

Currently, there is no FDA-approved drug for cancer patients harboring ATM gene alteration. However, there are many preclinical, phase I, and II clinical trials, including one for cholangiocarcinoma patients, that are evaluating whether patients with ATM gene alteration are more sensitive to drugs targeting ATR and PARP as well as immune checkpoint inhibitors, and some chemotherapeutic agents.

BRAF, which encodes a protein called serine/threonine-protein kinase B-RAF kinase, is an essential gene that plays a crucial role in cell proliferation.

BRAF V600E is one of the common BRAF mutations that is found in more than 70% of hairy cell leukemia and more than 35% of thyroid cancer and melanoma patients.

It has also been found in many other solid tumors, including more than 10% of colorectal cancer patients and around 5% of cholangiocarcinoma, breast, and bladder cancer patients.

Currently, there are established targeted therapy for BRAF-V600E-mutant melanoma, colorectal cancer, anaplastic thyroid cancer, and non-small cell lung cancer.

A phase 2 multi-center clinical trial formulated as a basket trial, a system in which each patient receives the same treatment assessed the use of dabrafenib (BRAF inhibitor) in combination with trametinib (MEK inhibitor) for BRAF V600E mutated solid tumors, including advanced and metastatic cholangiocarcinoma patients. In this trial, 36% of cholangiocarcinoma patients achieved a partial response with 9.2 months median progression-free survival and 11.7 months median overall survival.

The acronym EGFR stands for Epidermal Growth Factor Receptor; it is also known as Erb or HER.

There are 4 different types of EGFR (Erb, HER) genes. Regardless of the EGFR type, all EGFRs regulate cell growth, proliferation, and survival.

The most common alterations in the EGFR pathway are EGFR1 and HER2.

The highest prevalence of EGFR genetic alterations has been found in lung cancer and brain tumors. It has also been found in many other solid tumors, including 5-10% of melanoma, stomach, head, and neck cancers, and less than 5% in the colon, breast, bladder, and hepatobiliary cancers.

Currently, there are several ongoing phases I and II clinical trials for EGFR-altered cholangiocarcinoma patients (NCT02836847, NCT03768375, NCT02465060).

The acronym ERFFI1 stands for ERBB receptor feedback inhibitor 1.

This gene cancels the function of EGFR family members. There is no available data about the approximate prevalence and types of genetic alteration of this gene in cholangiocarcinoma patients.

IDH2 is known as isocitrate dehydrogenase 2.

Several types of alterations in IDH2 have been found, with IDH2 R172K being one of the common mutations.

Genetic alterations in this gene were found in more than 10% of patients with acute myeloid leukemia and certain types of T-cell lymphoma and brain tumors and in less than <5% of patients with breast, lung, prostate, cholangiocarcinoma, and many other solid tumors.

Currently, there are 3 ongoing clinical trials recruiting patients with solid cancer harboring IDH2 (NCT03212274, NCT04521686, NCT03878095).

MDM2 (Mouse double minute 2 homolog) is an important inhibitor of the p53 tumor suppressor gene (TP53), which induces cancer cell death.

MDM2 binds to p53, leading to its degradation or breakage.

In tumors where there is a high level of MDM2 gene copy number, TP53 is decreased, so, TP53 can’t inhibit cancer cell growth leading to a poor prognosis.

Treatment with an MDM2 inhibitor has been shown to induce tumor regression, and a clinical trial for cholangiocarcinoma patients who have MDM2 gene copies equal to or more than 8 with no mutations in the TP53 gene will start soon.

MSi – Microsatellite Instability

The microsatellite is a short piece composite of 1 to 4 DNA base pairs repeated together in a row along the DNA molecule.

Each person has hundreds of places in human DNA that contain microsatellites.

Alteration in the number of DNA base pairs in the microsatellite may occur and is known as microsatellite instability (MSI).

According to the MSI score, we classified cancer into

  1. MSI-high (MSI-H), defined as instability in 2 or more microsatellite loci;
  2. MSI-low (MSI-L), is defined as instability in only one locus; and
  3. Microsatellite Stable (MSS), is defined as the absence of any evidence of microsatellite loci instability.

MSI-H (high) has been reported in many cancer, with the highest incidence in Uterine cancer, gastric cancer, and colorectal cancer.

Several studies showed that MSI-H is a predictor of a better response to immunotherapy.

The NOTCH1 gene produces a protein called Notch 1, which increases cell proliferation, differentiation, and survival.

When NOTCH1 gene mutations are found, this leads to uncontrolled cell growth and division, which can result in the development of cancer.

NOTCH1 genetic alterations have been reported in more than 10% of chronic lymphoblastic leukemia, head and neck cancers, and less than 5% of bladder, colorectal, breast, and hepatopancreatic biliary cancers.

Currently, there are several NOTCH1 targeted therapies being examined in cholangiocarcinoma cell lines and animal models. So far, none of them have moved forward into a clinical trial.

The acronym NRG1 stands for Neuregulin 1 gene.

NRG1 gene encodes a protein that binds to the HER/ERBB family receptors and activates this pathway leading to tumor cell proliferation leading to their activation.

NRG1 has been found, with the most common one being NRG1 fusions.

The NRG1 fusions have been found in multiple solid cancer but are extremely rare, with an incidence of around 0.5%. The use of Seribantumab (NCT04383210) and Zenocutuzumab (NCT02912949), which inhibit HER2 and HER3 led to favorable tumor response and was tolerable in NRG1 fusion tumors, including cholangiocarcinoma patients.

There is an acronym NTRK which stands for neurotrophic receptor tyrosine kinase.

NTRK gene fusions lead to abnormal proteins called TRK fusion proteins, which may cause cancer cells to grow.

NTRK 1, 2, and 3 genes fusion have been found in more than 25 different types of adult and pediatric solid tumors. This includes more than 80% of breast, salivary gland, and sarcoma patients, 5-25% of certain types of melanoma and thyroid cancer patients, and less than 5% of cholangiocarcinoma, lung, colorectal, melanoma, thyroid, and head and neck cancer patients.

Both larotrectinib and entrectinib are NTRK inhibitors that received accelerated approval from the US FDA in 2018 and 2019, respectively, to be used for the treatment of patients with solid tumors harboring an NTRK fusion gene, including cholangiocarcinoma.

PIK3CA is a gene that plays a critical role in cell growth, proliferation, and survival.

Mutations in the PIK3CA gene may cause the PI3K enzyme to become overactive, which may cause cancer cells to grow.

Several types of alterations in PIK3CA have been found, with PIK3CA E542K being one of the common mutations.

PIK3CA has been reported in around 7% of cholangiocarcinoma patients. Currently, there are no available data on the prevalence of different genetic alteration subtypes.

The ROS1 gene is a proto-oncogene (a group of genes that cause normal cells to become cancerous when they are mutated).

Alterations can result in uncontrolled growth/cancer.

The highest prevalence of ROS1 gene alteration has been found in melanoma patients, while the prevalence is <5% in hepatobiliary, lung, breast, bladder, and many other solid tumors.

Currently, there is one trial for solid cancers, including cholangiocarcinoma harboring ROS1 genetic alterations (NCT02568267).

Tumour mutational burden (TMB) is measured by counting the number of genetic alterations/mutations (density)in a tumour sample.

These alternations can occur in any of the cells of the body except the germ cells (sperm and egg) and therefore are not passed on to children; it also can but does not always cause cancer or other diseases.

TMB can be measured in molecular profiling tests using tumour tissue samples or via liquid biopsy.

Depending on the number of alterations (mutations), tumours are classified into low, intermediate, or high-TMB.

Several studies showed that TMB-high is a predictor of good treatment response, and patients with TMB-high have a better response to immunotherapy.