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ABL Kinase Domain Mutation in CML, Cell-based

Test code(s) 16029

ABL kinase domain mutations often emerge after treatment with tyrosine kinase inhibitors (TKIs) such as imatinib (Gleevec®), dasatinib (Sprycel®), and nilotinib (Tasigna®).

The National Comprehensive Cancer Network® (NCCN®)1 recommends ABL kinase domain mutation testing when 1 or more of the following occurs:

  1. Inadequate initial response to TKI therapy
  2. Loss of hematologic or cytogenetic remission
  3. Rise in BCR-ABL1 transcript by 1 log over at least 2 time points, resulting in loss of major molecular remission
  4. Progression to accelerated or blast phase

Mutation testing is not recommended for patients with newly diagnosed chronic phase CML, during routine monitoring, or when there is no evidence of TKI resistance.1,5

Yes. The ABL kinase domain mutation test uses reverse transcription–polymerase chain reaction (RT-PCR) to amplify the BCR1-ABL fusion transcript before sequence analysis of the ABL kinase domain. If the patient’s tumor burden is low, RT-PCR may not generate enough of the BCR-ABL1 transcript for sequence analysis of the ABL kinase domain. Therefore, BCR-ABL1 Gene Rearrangement, Quantitative, PCR (test code 91065) should be performed no more than 2 weeks before ABL kinase domain mutation testing, to ensure adequate BCR1-ABL transcript levels for sequence analysis. 

RNA is isolated from blood or bone marrow and reverse transcribed. A first round of polymerase chain reaction (PCR) selectively amplifies BCR-ABL1 fusion product in chronic myeloid leukemia (CML) cells. A second round of PCR then amplifies the ABL kinase domain, which is directly sequenced.  

The ABL kinase domain mutation test screens for mutations in ABL kinase exons 4 to 9 covering codons/amino acid positions 234 to 507 (NM_005157.4). This region covers most drug resistance mutations, including the most frequent T315I mutation.The resistance mutations screened, and the associated drugs are listed in the below table. The test also screens for mutations contraindicated for targeted therapy, such as A337T, E255K/V, F317L, F311L/V/I/C, F359V/C/1, F359V/I/C, G250E, P465S, T315I, T315I/A, V299L, and Y253H, which will aid in the selection of kinase inhibitor therapies. 

Clinical data have indicated that the resistance pattern varies among the different mutations.2 For example, patients with the T315I mutation can respond to ponatinib3, but not to other FDA-approved tyrosine kinase inhibitors. Patients with V299L, T315A, or F317L/V/I/C mutations may respond to nilotinib therapy, whereas those with Y253H, E255K/V, or F359 V/C/I may respond to dasatinib.

When a detected mutation is reported, information about commonly observed kinase inhibitor reactions (response vs resistance) associated with that mutation are provided.

Mutations in the ABL kinase domain play a role in about 50% of chronic myeloid leukemia (CML) cases with secondary tyrosine kinase inhibitor (TKI) resistance. Next-generation sequencing (NGS) with a myeloid mutation panel should be considered for patients with no identifiable BCR-ABL1 mutations.1 Other mechanisms include altered drug transport and metabolism, amplification of the Philadelphia chromosome, and acquisition of additional chromosomal abnormalities.

To evaluate a patient for BCR-ABL1-independent mutations, consider ordering the LeukoVantage Myeloid (test code 39194). To evaluate a patient for amplification of the Philadelphia chromosome, consider ordering the FISH, CML/ALL, BCR-ABL, Translocation 9;22 (test code 12070). To evaluate a patient for acquisition of additional chromosomal abnormalities, consider ordering the Chromosome Analysis, Hematologic Malignancy (test code 14600).  

Tyrosine kinase inhibitors (TKIs) are combined with chemotherapy to treat ALL and lymphoblastic leukemias and lymphomas (ALL/LBL) that have t(9;22)/BCR-ABL1 rearrangements. ABL kinase domain mutations, particularly T315I, F317L, and Y253H, are frequently present in ALL/LBL patients who lack initial response or who relapse. Identification of the particular resistance-causing mutation(s) can help guide therapy for such patients.4


  1. National Comprehensive Cancer Network. NCCN clinical practice guidelines in oncology: chronic myelogenous leukemia. Version 1.2024. Accessed October 24, 2023.
  2. Cortes J, Jabbour E, Kantarjian H, et al. Dynamics of BCR-ABL kinase domain mutations in chronic myeloid leukemia after sequential treatment with multiple tyrosine kinase inhibitors. Blood. 2007;110(12):4005-4011. doi: 10.1182/blood-2007-03-080838. Epub 2007 Sep 4.
  3. Cortes JE, Kantarjian H, Shah NP, et al. Ponatinib in refractory Philadelphia chromosome–positive leukemias. New Engl J Med. 2012;367(22):2075-2088. doi: 10.1056/NEJMoa1205127.
  4. Jones D, Kamel-Reid S, Bahler D, et al. Laboratory practice guidelines for detecting and reporting BCR-ABL drug resistance mutations in chronic myelogenous leukemia and acute lymphoblastic leukemia; a report of the Association for Molecular Pathology. J Molec Diag. 2009;11(1):4-11. doi: 10.2353/jmoldx.2009.080095. Epub 2008 Dec 18.
  5. Soverini S, Hochhaus A, Nicolini FE, et al. BCR-ABL kinase domain mutation analysis in chronic myeloid leukemia patients treated with tyrosine kinase inhibitors: recommendations from an expert panel on behalf of European LeukemiaNet. Blood. 2011;118(5):1208–1215. doi: 10.1182/blood-2010-12-326405. Epub 2011 May 11.


This FAQ is provided for informational purposes only and is not intended as medical advice. Test selection and interpretation, diagnosis, and patient management decisions should be based on the clinician’s education, clinical expertise, and assessment of the patient.


Document FAQS.113 Version: 2

Version 2: Effective 11/19/2023 to present

Version 1: Effective 05/30/2019 to 11/19/2023
Version 0: Effective 11/21/2013 to 05/30/2019