To scuba and other veterans about mutations

Hello. I am stuck on a plateau at about 0.25% and have been moved from imatinib to dasatinib. The local laboratory mutation test registers "zero mutations". I have been registered on the CALLS trial to search for mutations using next generation sequencing.

It is possible therefore that the CALLS trial could find mutations whereas normal testing identifies zero mutations.

https://www.hra.nhs.uk/planning-and-improving-research/application-summa...

Research summary
Patients diagnosed with Chronic Myeloid Leukaemia (CML) and Philadelphia chromosome positive acute lymphoblastic leukaemia (Ph+ALL) can have genetic mutations in the DNA of their disease cells which affects the effectiveness of drugs called tyrosine kinase inhibitors which can successfully treat CML and Ph+ALL for long periods. There are over one hundred mutations that affect the effectiveness of TKIs and some patients may have more than one mutation present.

The current technique for identifying mutations can pick up those present in more than 20% of disease cells, but a new technique called Next Generation Sequencing (NGS) is more sensitive and can identify mutations present in more than 3% of disease cells.

This study is measuring the proportion of patients in the UK who have genetic mutations present in >3% of their disease cells using NGS. At present this information is unknown. The results may benefit this patient population in the future by affecting how patients are managed.

When mutations are identified during the study, the patient's treating physician will be informed and he/she will discuss the results with the patient and may make changes to the patient's treatment. This study is non-interventional and any changes to treatment are at the treating physician's discretion.

The study will be conducted in 40 sites (400 patients) around the UK in Haematology Departments who care for patients with CML and Ph+ALL. Each patient will provide written informed consent and will then provide a blood sample, and a form detailing demographics, diagnosis and treatment history will be completed to send with the blood sample. In some cases a repeat blood sample will be required.

Selected anonymous blood samples will be shared with one of the study investigators based at the University of Wales who will use them to validate another more sensitive technique for measuring a specific mutation.

Does the mutation test always find the correct mutation?.

• Mutation testing in CML looks to find if a mutation is present in the kinase domain where bcr-abl is active. There are many bcr-abl mutations possible for which many respond to TKI drugs, but with varying levels of response. One particular mutation, T315I, is very resistant to first line therapies (see chart in second link below ), but is showing response to newer drugs (Ponatinib). When TKI response is poor, and changing drugs is not effective, a mutation analysis may reveal a resistant clone of bcr-abl (e.g. T315I).
• http://www.haematologica.org/content/92/4/437
• https://www.dropbox.com/s/4mnvw6sg3of9yyz/Kinase_domain_mutations.png?dl=0

Is there any chance that mutation test doesn't find mutation even if there is mutation present?

• Unlikely, mutation testing is an assay that compares normal amino acid sequences in the kinase domain where bcr-abl functions in comparison to a test DNA sequence. The difference reveals where the mutation(s) is occurring. This is often reported as molecular weight of the amino acid pairs which are different from the test case.
• https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3883366/
• https://jmd.amjpathol.org/article/S1525-1578(10)60202-4/fulltext

If mutation test is taken after two years from becoming imatanib resistant, still can we find any mutation?.

• Yes, a mutation can occur at any time and progress. Mutation testing will usually reveal this event (after other TKI's have failed). It is also possible that a mutation had always been present, but masked by the dominant clone and unable to proliferate (quiescence or blocked). As the dominant clone is eradicated by imatinib, these minor clones may be able to expand and proliferate maintaining disease. This is a key reason why some researchers advocate rotating TKI treatment as a means to hit more clones simultaneously in order to prevent progression and provide an even deeper remission (see chart above for TKI clone sensitivities).

If mutation is present and treatable,does it affect prognosis.

• If mutation is present and treatable, prognosis is likely to improve dramatically.