BCR::ABL1 Kinase Domain mutation screen


In some patients with “Philadelphia positive disease”, molecular monitoring may demonstrate primary or secondary resistance to TKI therapy as evidenced by a failure to achieve established molecular milestones or the loss of a previously attained molecular milestone (see NCCN guidelines 2021, ELN guidelines 2020). Both primary and secondary resistance, in some patients, has been demonstrated to be due to the acquisition of mutations in the BCR::ABL1 kinase domain.  Results of this analysis may serve to inform the choice of alternative therapies.


To aid in the choice follow-up therapy of patients with demonstrated primary or secondary resistance to TKI therapy. This assay is felt to be most informative if the overall BCR::ABL1 molecular burden is in excess of -2.00 (log BCR::ABL1/reference transcript) and testing is initiated after a confirmed 1.0 log increase.


Any treating physician

At its discretion, this test may be initiated reflexively by the laboratory.


  1. Completed CGL Myeloid Testing requisition form
  2. One of the following specimens (please see our Specimen GuidelinesRNA Molecular test type)
    • Preferred:
      • 20mL Peripheral Blood in EDTA tubes (purple top)
    • Alternatives:
      • 5.0mL Bone marrow aspirate in EDTA tubes (purple top) 
      • Peripheral blood derived white blood cells fixed in methanol/acetic acid (residual cytogenetic specimen)
      • Bone marrow specimen fixed in methanol/acetic acid (residual cytogenetic specimen)


See our Guidelines for Specimens and Transport


Total RNA is extracted from the submitted specimen. The BCR::ABL1 kinase domain is specifically amplified via nested RT-PCR using first round amplification primers which bridge the BCR::ABL1 junction. The sequence of the BCR::ABL1 kinase domain is then determined by standard bi-directional Sanger sequencing.


Demonstration of a BCR::ABL1 kinase domain mutation known to be associated with TKI resistance is cause to consider a change in TKI therapy.  The choice of therapy will depend in part on the mutation identified. On occasion a variant of unknown clinical significance may be identified.


Results are reported within ten working days from activation of test.


NCCN guidelines – CML v1.2021 (https://www.nccn.org/guidelines/category_1)

Hochhaus et al European LeukemiaNet 2020 recommendations for treating chronic myeloid leukemia. (2020) Leukemia 34:966-984 (PMID: 32127639).