What is being tested?

BCR-ABL1 refers to a fusion gene sequence found in an abnormal chromosome 22 of some people with certain forms of leukaemia.

Humans have 23 pairs of chromosomes containing inherited genetic information in each cell. These chromosomes are made of DNA, and contain the blueprints in the form of genes for producing the proteins that our bodies rely on to function properly. When there are changes in the chromosomes or genes, abnormal proteins may be produced which have abnormal function. Some genetic changes are inherited from a parent (germline changes). Other genetic changes occur during a person’s lifetime (somatic or acquired changes). These acquired changes can happen due to exposure to various environmental factors (e.g., radiation, certain chemicals) but more often for unknown reasons.

The BCR-ABL1 fusion gene sequence is one such acquired change that is formed when pieces of chromosome 9 and chromosome 22 break off and switch places. This type of change is called a reciprocal translocation and is often abbreviated as t(9;22). When this occurs, the ABL1 region in chromosome 9 fuses with the BCR region in chromosome 22. The resulting derivative chromosome 22 which has the BCR-ABL1 fusion gene sequence is known as the Philadelphia (Ph) chromosome.

The BCR-ABL1 fusion gene encodes an abnormal protein. This abnormal protein is a type of signalling protein called tyrosine kinase, which has become abnormally and permanently switched “on”. This leads to uncontrolled cell growth and is responsible for the development of CML and a type of ALL. When large numbers of abnormal leukaemic cells start to crowd out the normal blood cell precursors in the bone marrow, signs and symptoms of leukaemia start to emerge. Treatment of these leukaemias typically involves a tyrosine kinase inhibitor (TKI) such as Imatinib (Glivec®), given as daily oral tablets.

Testing for BCR-ABL1 detects the Philadelphia chromosome, the BCR-ABL1 fusion gene, or BCR-ABL1 transcripts, which are the RNA copies made by the cell from the abnormal fusion gene. The presence of the BCR-ABL1 abnormality confirms the clinical diagnosis of CML or a type of ALL.

There are several different types of BCR-ABL1 tests available, including:

• Chromosome studies (cytogenetics or karyotyping)

This test looks at chromosomes under a microscope to detect structural and/or numerical abnormalities. Cells in a sample of blood or bone marrow are grown in the laboratory and then examined to determine if the Philadelphia chromosome is present. Other chromosomal abnormalities can also be detected.

• Fluorescence in situ hybridization (FISH)

This test method uses differently-coloured fluorescent dye-labelled probes to "light up" the BCR and the ABL1 gene sequences. Cells are examined under a microscope to determine the proportion if any where the coloured dots are fused together, indicating a BCR-ABL1 translocation. This is a more sensitive method of detection than cytogenetics.

• Molecular testing (qualitative or quantitative)

Polymerase chain reaction (PCR)-based qualitative and quantitative tests detect and measure the level of BCR-ABL1 gene transcripts, or gene product units, in a patient's blood and/or bone marrow samples. This is the most sensitive test for BCR-ABL1. It is used to monitor the response to treatment with tyrosine kinase inhibitors (TKIs). It is also used to diagnose the minority of cases negative for the Philadelphia chromosome.

• ABL1 mutation testing
  Secondary mutations may arise within BCR-ABL1 in the kinase domain. These can be detected by DNA sequencing methods. These mutations may be responsible for treatment resistance to TKIs. If the response to treatment is suboptimal, mutational analysis may tell your doctor which TKIs will be more effective. 

How is it used?

BCR-ABL1 testing is requested to detect the Philadelphia (Ph) chromosome or the BCR-ABL1 gene sequence. It is used to:

• Help diagnose chronic myelogenous leukaemia (CML), a type of acute lymphoblastic leukaemia (ALL) or very rarely another type of leukaemia called acute myeloid leukaemia
• Monitor treatment
• Monitor for recurrence
• Detect resistance to therapy

Chromosome studies (cytogenetics), qualitative BCR-ABL1 molecular genetic test, and/or fluorescent in-situ hybridisation (FISH) may be requested to help establish the initial diagnosis of CML or Ph-positive ALL. It is often performed along with other tests if a doctor suspects that a patient has leukaemia and is trying to diagnose or rule out CML and Ph-positive ALL. The chromosomal studies and FISH can also help to determine what percentage of a patient's blood or bone marrow cells are affected.

The qualitative BCR-ABL1 test can also help determine the breakpoint variant of BCR-ABL1 that is being produced. The size (molecular weight) of the BCR-ABL1 protein produced depends upon where the break in chromosome 22 occurred. In CML, the breakpoint in BCR is almost always in the major breakpoint cluster region (M-BCR), leading to the production of BCR-ABL1 protein of a larger size (p210). Breaks in the minor breakpoint cluster region (m-BCR) leads to a shorter fusion protein (p190), which is more frequently associated with Ph-positive ALL. Knowing whether a patient has a break in the major or minor BCR is important because the quantitative BCR-ABL1 molecular genetic test may be set up to measure a specific variant, p210 or p190, but not both.

The quantitative BCR-ABL1 molecular test is requested once the BCR-ABL1 gene sequence has been detected and the breakpoint variant established. It may be requested at the time of the initial diagnosis to establish a baseline value and then used periodically to monitor the person's response to treatment and, if the person achieves remission, to monitor for recurrence.

When is it requested?

BCR-ABL1 testing is requested when a health practitioner suspects that a person has CML or Philadelphia chromosome (Ph)-positive ALL. Initial testing may be indicated when a person has nonspecific signs or symptoms such as:

• Fatigue
• Weight loss
• Joint or bone pain
• Enlarged spleen
• As follow-up to abnormal findings on a full blood count (FBC)
• Early in the disease, a person may have few or no symptoms. As time passes and normal blood cells are crowded out of the bone marrow and the number of abnormal leukaemic cells increases, a person may experience anaemia, prolonged bleeding, and recurrent infections.

Once CML or Ph-positive ALL has been diagnosed, BCR-ABL1 quantitative genetic testing is requested periodically (typically every three months) to monitor the response to treatment and to monitor for recurrence.

When a person is not responding and treatment resistance is suspected or disease recurrence occurs after remission, the BCR-ABL1 kinase domain mutation analysis may be performed to guide further treatment.

What does the result mean?

If a person has abnormal white blood cells in the bone marrow and has the Philadelphia (Ph) chromosome and BCR-ABL1 gene sequence, then the individual is diagnosed with CML or Ph-positive ALL.

Of those who have CML, 90 - 95 per cent have the Ph chromosome if tested by cytogenetics and 100 per cent have the BCR-ABL1 gene sequence by FISH and/or qualitative BCR-ABL1 molecular testing. About 25 per cent of adults with ALL and 2 - 4 per cent of children with ALL are positive for the Ph chromosome and/or the BCR-ABL1 gene sequence.

A small percentage of people with CML will have the BCR-ABL1 gene sequence but not the Ph chromosome. These cases either have variant translocations that involve a third or even a fourth chromosome in addition to 9 and 22 or have a hidden translocation involving 9 and 22 that cannot be identified by routine chromosomal studies. Since the treatment for BCR-ABL1-related leukaemias specifically targets the tyrosine kinase protein produced, these people may still be able to be monitored with quantitative BCR-ABL1 molecular testing.

Very rarely some people thought to have CML do not have either the Ph chromosome or a BCR-ABL mutation. This means that other gene mutations may be causing the symptoms so a classification of true CML may not be made.

In general, if the amount of BCR-ABL1 in the blood or bone marrow decreases over time, then the person is responding to treatment. If the quantity of BCR-ABL1 drops below the test's detection limit and the person's blood cell counts are normal, then the person is considered to be in remission.

If the BCR-ABL1 level rises, then it indicates disease progression or recurrence. It may also indicate that the person has become resistant to the tyrosine kinase inhibitor (TKI) being used to treat them. Additional genetic testing is often performed to detect the development of BCR-ABL1 kinase domain mutations associated with resistance to different TKIs. Depending on the mutation identified, a different TKI may be given.

If a person with ALL is not positive for the Ph chromosome or the BCR-ABL1 gene sequence, then that person will not be given a tyrosine kinase inhibitor drug and BCR-ABL1 molecular testing cannot be used to monitor the person.

Is there anything else I should know?

Recognition of disease progression and transformation is important for prognosis and treatment. CML goes through three phases:

• Chronic phase—most people with CML are diagnosed in the chronic phase, which usually has an insidious onset, meaning that leukaemia symptoms may be absent or subtle. The chronic phase may last for a month to several years. This is the phase when there are few or no symptoms and also the time period when treatment is most successful.
• Accelerated phase—changes include but are not limited to increasing white blood cell (WBC) counts and additional changes to cells like an increase in blasts in blood and/or bone marrow (but less than 20 per cent) and lack of therapeutic response to standard treatment
• Blast phase—when blasts are 20 per cent or more of the cells in the blood or bone marrow or when there is blast proliferation outside the bone marrow

Both blood and bone marrow are often evaluated as part of the initial diagnosis, but the majority of follow-up monitoring is performed on blood samples. There is significant test variability among laboratories using different test platforms. Therefore, for a given patient, the quantitative BCR-ABL1 molecular testing should be performed by the same laboratory or referred to a laboratory that follows universal reporting criteria (e.g. reporting based on the international scale). Rising and falling levels of BCR-ABL1 are usually more important than a single test result.

Common questions

• Why would the chromosome studies be done more than once?

Your health care provider may request chromosome studies periodically to determine if you have developed any additional chromosome abnormalities. Additional changes are often seen with disease progression and acceleration.

• If I have the Philadelphia chromosome and BCR-ABL1 gene, should my close family members be tested?

No. This genetic change is one that is acquired during a person's lifetime and is not inherited.

• Should everyone with leukaemia be tested?

Testing is only indicated when your health practitioner suspects that you have chronic myelogenous leukaemia (CML), acute lymphoblastic leukaemia (ALL), or wants to rule them out. The majority of people with other types of leukaemia will not have the Philadelphia chromosome or BCR-ABL1 fusion gene.

• Can BCR-ABL1 testing be done in my doctor's office?

BCR-ABL1 testing requires specialised equipment and expertise. It must be performed by a specialised hospital laboratory or a reference laboratory.

What is the difference between chronic myelogenous leukaemia and chronic myeloid leukaemia?

They are two terms for the same condition and both are referred to as CML.

• Is there a Medicare rebate for BCR-ABL1 testing?

Yes, BCR-ABL1 testing attracts a Medicare rebate when used in the diagnosis and monitoring of patients with laboratory evidence of certain types of leukaemia.

More information

Cancer Australia: Leukaemia

Leukaemia Foundation: CML

Cancer Council NSW: CML