Genetic tests on your chronic myeloid leukaemia (CML) cells

You have tests on your blood and bone marrow to look for changes in certain genes Open a glossary item. This helps to diagnose your type of leukaemia and learn more about your chronic myeloid leukaemia (CML) cells. It can also help the doctors see how well your treatment is working.

The tests on the cells look for two changes in particular:

  • the Philadelphia chromosome 
  • the BCR-ABL gene 

They also look for other abnormal chromosomes Open a glossary item.

You might hear these tests called cytogenetic tests, chromosomal analysis or molecular analysis. The doctors are looking for changes in genes and chromosomes in the leukaemia cells.  

This is different to testing you to see if you have an inherited faulty gene that increases your risk of getting cancer in the first place. These genetic tests on your leukaemia cells should not be confused with tests that look for an inherited faulty gene. Having gene changes does not mean you can pass CML on to your children.

Why you might have these tests

The results of these tests:

  • help doctors diagnose your leukaemia
  • check how well your treatment is working
  • provide information about how your CML might behave – this helps your doctor talk to you about your outlook (prognosis)

You usually have these tests at diagnosis. And then at regular intervals during your treatment.

What are genes and chromosomes?

Most body cells contain chromosomes. Chromosomes are made up of thousands of genes. There are 23 pairs of chromosomes in human cells and each chromosome has a number from 1 to 23. These are a bit like an instruction manual for building the body and keeping it healthy. 

Sometimes a change happens in the genes when a cell divides. This happens by chance when a cell is dividing. It is not something you inherit. So you were not born with it and it can't be passed on to your children. 

CML develops when an abnormal change happens to chromosome 9 and chromosome 22.

Understanding your results

The BCR-ABL1 gene

This gene is made when a change happens to two chromosomes.

On chromosome 9 there is a gene called the ABL1 gene. And on chromosome 22 there is a gene called BCR. A completely new gene called BCR-ABL1 is made when the ABL1 gene breaks off and sticks to the BCR gene. This is known as a fusion gene.

The BCR-ABL1 gene causes the cell to make too much of a protein called tyrosine kinase. This protein encourages leukaemia cells to grow and multiply. The main treatment for CML are drugs called tyrosine kinase inhibitors (TKIs). These drugs work by switching off (inhibiting) the tyrosine kinase that the BCR-ABL1 gene makes. 

The Philadelphia chromosome

The BCR-ABL1 gene changes chromosome 22. It looks shorter than normal. It is called the Philadelphia chromosome. Most people with CML have the Philadelphia chromosome. 

Doctors can see the Philadelphia chromosome when they look at blood and bone marrow under the microscope. So they use it to help diagnose CML and to monitor response to treatment.

Watch this 2 minute video to explain what Philadelphia positive leukaemia is. 

Types of tests

There are different types of tests.

Cytogenetic tests

This is a standard (conventional) test that doctors use to look at chromosomes. It's also called karyotyping or G-banding. It is when scientists use a microscope to look at the chromosomes in your blood and bone marrow. They look at the size, shape and number of chromosomes.

The best time to see chromosomes is when the cell is dividing. So the scientists have to grow a sample of blood or bone marrow in the laboratory. Then they look at the sample when the cells start to divide. It can take some time to get the results of this type of test.

The scientists are looking for the Philadelphia chromosome Open a glossary item. They also look for other changes. This is known as additional chromosomal abnormalities (ACA).

You usually have cytogenetic analysis to help diagnose your CML. You might then have this test to see how well treatment is working.

FISH tests

Another type of testing is called a FISH test. FISH stands for fluorescence in situ hybridisation. The FISH technique uses a special fluorescent dye. This makes it easier to see particular gene and chromosome changes.

The doctors don’t need to grow the cells first, so it is a quicker test than cytogenetic analysis.

Doctors use the FISH test to look for the BCR-ABL1 gene on the chromosomes. This test can be useful if the doctors haven’t seen the Philadelphia chromosome in your cytogenetic test, but they still think you might have CML. Doctors can also use FISH tests alongside other tests to help assess your response to treatment.

Polymerase chain reaction (PCR) tests

This test looks for genetic changes in the blood or bone marrow cells. Doctors use it to look for the BCR-ABL1 gene. It is a very sensitive test, which can detect tiny amounts of the BCR-ALB1 gene. So it is a very useful test for monitoring CML.

Doctors like to use this test to monitor CML because:

  • they don’t need to grow the cells first, so it can be quicker test than cytogenetic analysis
  • it is much more sensitive than karyotyping and FISH tests
  • they can do the test on a blood sample which is easier to take than a bone marrow sample

PCR tests can measure how much BCR-ALB1 is there. It is the most useful test to check how well treatment is working. You have this test at diagnosis and then at regular intervals during your treatment.

Sometimes scientists can adapt the PCR test to look for changes within the BCR-ABL1 gene. Cancer drugs called tyrosine kinase inhibitors (TKI) are a common treatment for CML. Looking for particular changes can be useful if you are not responding to a certain tyrosine kinase inhibitor (TKI). It can also help doctors select the right type of TKI for your leukaemia.

What happens

The doctor can do these tests on:

  • a blood sample
  • a bone marrow sample

You have blood tests at diagnosis and regular blood tests during treatment.

You usually have a bone marrow test at diagnosis. You sometimes need bone marrow tests during treatment. Your doctor will discuss this with you

How do doctors use your test results?


Your doctor looks for the Philadelphia chromosome and BCR-ABL1 gene to confirm your diagnosis of CML.

They also look for other chromosomal abnormalities. Your doctor will talk with you about any other changes and what they mean. For example, they will tell you if they find any changes that might affect how well you respond to treatment.

Response to treatment

The aim of treatment is to put your CML into remission. Remission means there are no signs of CML in your blood.  The doctors refer to remission as ‘response to treatment’.

There are different tests that look for signs of CML. The test results provide information about how well the treatment is working to control your leukaemia.

Your doctor looks at:

  • your full blood count and size of your spleen (haematological response)
  • the amount of Philadelphia chromosome in your blood and bone marrow (cytogenetic response)
  • the amount of BRC-ABL1 gene in your blood (molecular response)
  • European LeukemiaNet 2020 recommendations for treating chronic myeloid leukemia
    A. Hochhaus and others
    Leukemia (2020) Volume 34, pages 966–984

  • Chronic myeloid leukaemia
    J Cortes and others
    Lancet 2021, Volume 398, issue 10314, pages 1914-1926

  • A British Society for Haematology Guideline on the diagnosis and management of chronic myeloid leukaemia
    G Smith and others
    British Journal  of  Haematology, 2020, volume 191 pages 171–193

  • Chronic myeloid leukaemia: ESMO Clinical Practice Guidelines for diagnosis, treatment and follow-up
    A Hochhaus and others
    Annals of Oncology (2017) Volume 28, Supplement 4, Pages 41– 51

Last reviewed: 
10 Sep 2021
Next review due: 
06 Sep 2024

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