Chronic Myelogenous Leukemia - CML

Primary Author: Kelley, Todd, MD, MS.

  • Key Points
  • Diagnosis
  • Monitoring
  • Pharmacogenetics
  • Background
  • Lab Tests
  • References
  • Related Topics
  • Videos

Monitoring Chronic Myelogenous Leukemia

Chronic myelogenous leukemia is a chronic disease that is managed with tyrosine kinase inhibitor (TKI) therapy.  Most patients are able to achieve a sustained response from these agents. Use of TKIs requires serial testing to monitor response and to detect relapse of disease and/or the development of drug resistance.

Resistance develops in a subset of individuals receiving TKI therapy.  A 5- to 10-fold increase in the levels of BCR-ABL1 fusion transcripts by quantitative PCR suggests resistance. BCR-ABL1 kinase domain mutation testing is recommended to guide choice of second-line TKI therapy. The BCR-ABL1 T3151 mutation imparts resistance to all currently approved TKIs.

Content in tables below based on Cortes J, 2011; Hochhaus A, 2011; Hughes, 2009; Kantarjian H, 2007; Saglio G, 2012; Yeung, 2011.

Features of test types

Indications for Testing

  • Abnormal CBC, splenomegaly

Laboratory Testing

  • Presumptive diagnosis from blood cell counts and examination of blood film
    • White blood cell count shows leukocytosis
      • Median 100 K/μL (range 12-1,000 K/μL)
      • Blasts rare; basophilia and eosinophilia common
      • Platelet count ranges from normal to 1x1013
    • Cytochemical staining for leukocyte alkaline phosphatase useful in differentiating CML from leukemoid reaction – low score is consistent with CML
  • Karyotyping (using cytogenetics or FISH)
    • Requires cells from bone marrow aspirate
    • Use to determine complete cytogenetic response (CCR)
    • t(9;22) (q34; q11.2) Philadelphia (Ph) chromosome testing (BCR-ABL1)
      • t(9;22) translocation may occasionally be found in acute lymphoblastic leukemia (ALL)
      • Translocation found in acute myeloid leukemia (AML) may reflect a blast crisis in previously unrecognized CML
      • Patients without Ph chromosome still carry a BCR-ABL1 fusion due to a cytogenetically cryptic insertion identifiable by FISH or PCR
      • Provides information about additional genetic abnormalities in addition to t(9;22)
  • Quantitative PCR (performed simultaneously with karyotyping)
    • Identify BCR-ABL1 fusion transcripts – allow for monitoring of response to therapy
      • Considered standard of care for detection of minimal residual disease (MRD)
      • Quantitative testing – p210 fusion is most frequent (p190 fusion rare)
      • Used in determination of CCR
      • Helpful in determining relapse
    • Next generation sequencing increases sensitivity over Sanger sequencing
      • Covers SH2, SH3, and kinase domains
      • Can potentially determine in cis and in trans if 2 mutations present
  • Immunophenotyping
    • Not required for diagnosis in chronic or accelerated phase CML
    • Used in patients presenting with acute leukemia to identify disease lineage
      • Generally 2/3 myeloid, 1/3 B-lymphoid
      • T-cell lineage rare


  • Bone marrow biopsy
    • Increased cellularity with myeloid hyperplasia, small megakaryocytes
    • Usually <5% blasts
    • Reticulin fibrosis in 30%


  • Karyotype
    • Evolution of cytogenetic abnormalities associated with poor prognosis
    • Early cytogenetic response associated with good prognosis
  • Recent literature (Valent, 2008) suggests histamine and tryptase levels may be used in prognosis
  • Molecular response – quantitative PCR for BCR-ABL1 is essential for detecting major molecular response (MMR) and for assessing prognosis
  • CML calculator of relative risk – assess prognosis; based on Sokal and Hasford scoring systems

Differential Diagnosis

  • Serial hematologic, cytogenetic, and molecular testing should be performed throughout the course of therapy
    • Quantitative real-time PCR for BCR-ABL1 t(9;22) (molecular) – p210 fusion most common; p190 fusion is rare
      • Should be reported in standardized format (%) on the BCR-ABL1 international scale (IS)
        • 100% on the IS corresponds to standardized baseline value at diagnosis as determined by original trial of imatinib therapy in chronic phase CML patients (IRIS trial)
        • A 3-log reduction from baseline (0.1% IS) constitutes a major molecular response (MMR) to tyrosine kinase inhibitor (TKI) therapy
        • When IS>10%, recommend karyotyping for Ph evolution
  • Cytogenetics – karyotyping
    • Examination of at least 20 bone marrow metaphases
    • Cytogenetic evolution in Ph positive clone associated with poor prognosis
      • Complete response – no detectable abnormal metaphases
      • Major response – 1-35% abnormal metaphases
      • Minor response – >35% abnormal metaphases
    • Repeat every 3-6 months from initiation of therapy until cytogenetic complete remission (CCR) achieved; after CCR achieved, repeat every 12-24 months
      • Also repeat if patient appears to have rising BCR-ABL1 transcript levels (1 log increase)
  • Mutations in the BCR-ABL1 gene lead to tyrosine kinase inhibitor (TKI) resistance of varying degrees
    • Resistance develops secondary to
      • Kinase domain mutations
        • T3151 mutation resistant to most TKIs – indicates poor prognosis
          • Ponatinib – new pan BCR-ABL1 inhibitor which includes T3151 mutations
      • Amplification or overexpression
      • Quiescent CML stem cells
      • Low bioavailability
    • Resistance may be overcome with
      • Dose adjustments
      • Change in therapy
    • Indications for testing
      • Perform testing for BCR-ABL1 kinase domain mutations
        • If patient is unresponsive to treatment
        • If there is a 5- to 10-fold increase in BCR-ABL1 fusion transcripts detected by PCR
      • For management of CML, see recommendations from European LeukemiaNet
      • Initial treatment resistance testing – performed only in patients with accelerated phase disease and multiple mutations
        • Not routinely performed prior to first therapy in other patients
        • Low incidence of mutations found prior to TKI therapy in chronic phase CML
        • Next generation sequencing offers benefits over Sanger sequencing techniques

Chronic myelogenous leukemia (CML) is a hematopoietic stem cell disease accounting for 15% of all leukemias.


  • Incidence – 1-2/100,000 annually in U.S.
  • Age – median is 67 years, but may be seen in all age groups
  • Sex – M>F, 1.5:1
    • Females may have a survival advantage

Risk Factors

  • Exposure to significant quantities of ionizing radiation
  • Benzene or alkylating agents


  • Clonal expansion of stem cells characterized by reciprocal translocation between chromosomes 9 and 22 that form the Philadelphia chromosome (Ph)
    • t(9;22) translocation causes a fusion of the ABL1 gene and BCR gene
      • BCR-ABL1 fusion codes for an abnormal protein possessing constitutive tyrosine kinase activity
      • Patients with CML typically have the p210 form of the BCR-ABL1 fusion resulting from translocations between BCR exon 13 or 14 and ABL1 exon 2 (e13a2, e14a2)
      • Very rarely, patients with CML may have the p190 form of the BCR-ABL1 fusion resulting from a translocation between BCR exon 1 and ABL1 exon 2 (e1a2)
  • Mechanism of treatment resistance and relapse
    • Standard of care – treatment with tyrosine kinase inhibitors (TKI), including imatinib, nilotinib, or dasatinib
      • Resistance to initial therapy may require increased dosing or use of a different TKI
        • Second-generation TKIs include dasatinib, nilotinib, bosutinib, ponatinib
    • Relapse after effective chemotherapy mainly a result of outgrowth of leukemic subclones resistant to current TKIs
      • Mutations in BCR-ABL1 kinase are the most common cause of relapse due to imatinib resistance but not the only cause

Clinical Presentation

  • CML categorized into three phases
    • Chronic phase
      • 20-40% of patients are asymptomatic and identified through routine blood count
      • Untreated chronic phase CML will progress to accelerated phase within 3-5 years
    • Accelerated phase
      • Insidious onset with vague signs and symptoms – weight loss, fatigue, abdominal discomfort due to splenomegaly, fever
      • May demonstrate increased myeloblasts (10-19%) in bone marrow
      • Basophilia (>20% in blood of bone marrow) may also occur
      • Thromboses with vaso-occlusive crisis – cerebral vascular accident (stroke), myocardial infarction (heart attack), visual disturbances
    • Blast phase
      • 10% present with de novo blast crisis (aggressive advanced phase)
      • Splenomegaly, leukocytosis with 20% or more myeloid blasts in blood and/or bone marrow, but full range of myeloid maturation, normochromic normocytic anemia, thrombocytosis
      • Lymphadenopathy is unusual
Tests generally appear in the order most useful for common clinical situations. Click on number for test-specific information in the ARUP Laboratory Test Directory.

Leukocyte Alkaline Phosphatase 0049000
Method: Cytochemical Stain


Helpful first-line screening test; however, does not definitively diagnose CML

Chromosome Analysis, Bone Marrow 2002292
Method: Giemsa Band


Repeat every 3-6 months from initiation of therapy until CCR achieved; after CCR achieved, repeat every 12-24 months

Also repeat if patient appears to have rising level (1-log increase) of BCR-ABL1 transcripts

BCR-ABL1 Mutation Analysis for Tyrosine Kinase Inhibitor Resistance by Next Generation Sequencing 2008420
Method: Massively Parallel Sequencing


A negative result does not exclude mutations below the level of detection or mutations outside the sequenced region of this test

BCR-ABL1, Major (p210), Quantitative 2005017
Method: Quantitative Reverse Transcription Polymerase Chain Reaction


Does not detect p210 or p230

BCR-ABL1, Qualitative with Reflex to BCR-ABL1 Quantitative 2005010
Method: Reverse Transcription Polymerase Chain Reaction

Chromosome FISH, Interphase 2002298
Method: Fluorescence in situ Hybridization

BCR-ABL1, Minor (p190), Quantitative 2005016
Method: Quantitative Reverse Transcription Polymerase Chain Reaction


Does not detect the p210 or p230 form

Myeloproliferative Disorders Panel by FISH 2002360
Method: Fluorescence in situ Hybridization


Only detects rearrangements targeted by the probes

The translocation partners of the PDGFRB gene on 5q33 and FGFR1 gene on 8p11 have multiple translocation partners; these translocation partners are not identified by this test


Baccarani M, Pileri S, Steegmann J, Muller M, Soverini S, Dreyling M, ESMO Guidelines Working Group. Chronic myeloid leukemia: ESMO Clinical Practice Guidelines for diagnosis, treatment and follow-up. Ann Oncol. 2012; 23 Suppl 7: vii72-7. PubMed

European LeukemiaNet Recommendations for the Management of Chronic Myeloid Leukemia (CML). Update 2013. European LeukemiaNet. [Accessed: Nov 2015]

Goldman J. Recommendations for the Management of BCR-ABL-positive Chronic Myeloid Leukaemia. British Committee for Standards in Haematology. London, UK [Accessed: Sep 2015]

NCCN Clinical Practice Guidelines in Oncology, Chronic Myelogenous Leukemia. National Comprehensive Cancer Network. Fort Washington, PA [Accessed: Nov 2015]

Protocol for the Examination of Specimens From Patients With Hematopoietic Neoplasms Involving the Bone Marrow. Based on AJCC/UICC TNM, 7th ed. Protocol web posting date: Jun 2012. College of American Pathologists (CAP). Northfield, IL [Accessed: Jun 2015]

Soverini S, Hochhaus A, Nicolini FE, Gruber F, Lange T, Saglio G, Pane F, Müller MC, Ernst T, Rosti G, Porkka K, Baccarani M, Cross NC, Martinelli G. 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): 1208-15. PubMed

General References

Apperley J. CML in pregnancy and childhood. Best Pract Res Clin Haematol. 2009; 22(3): 455-74. PubMed

Cortes J, Quintás-Cardama A, Kantarjian HM. Monitoring molecular response in chronic myeloid leukemia. Cancer. 2011; 117(6): 1113-22. PubMed

Hochhaus A. Educational session: managing chronic myeloid leukemia as a chronic disease. Hematology Am Soc Hematol Educ Program. 2011; 2011: 128-35. PubMed

Hughes TP, Branford S. Monitoring disease response to tyrosine kinase inhibitor therapy in CML. Hematology Am Soc Hematol Educ Program. 2009; 477-87. PubMed

Kantarjian H, Schiffer C, Jones D, Cortes J. Monitoring the response and course of chronic myeloid leukemia in the modern era of BCR-ABL tyrosine kinase inhibitors: practical advice on the use and interpretation of monitoring methods. Blood. 2008; 111(4): 1774-80. PubMed

Malley D, Vardiman J. Chronic Myelogenous Leukemia and Related Disorders. In Kjeldsberg C. Practical Diagnosis of Hematologic Disorders, 4th ed. Chicago: ASCP Press, 2006.

Saglio G, Fava C. Practical monitoring of chronic myelogenous leukemia: when to change treatment. J Natl Compr Canc Netw. 2012; 10(1): 121-9. PubMed

Vigil CE, Griffiths EA, Wang ES, Wetzler M. Interpretation of cytogenetic and molecular results in patients treated for CML. Blood Rev. 2011; 25(3): 139-46. PubMed

Yeung DT, Parker WT, Branford S. Molecular methods in diagnosis and monitoring of haematological malignancies. Pathology. 2011; 43(6): 566-79. PubMed

References from the ARUP Institute for Clinical and Experimental Pathology®

Jones D, Kamel-Reid S, Bahler D, Dong H, Elenitoba-Johnson K, Press R, Quigley N, Rothberg P, Sabath D, Viswanatha D, Weck K, Zehnder J. 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 Mol Diagn. 2009; 11(1): 4-11. PubMed

Khorashad JS, Kelley TW, Szankasi P, Mason CC, Soverini S, Adrian LT, Eide CA, Zabriskie MS, Lange T, Estrada JC, Pomicter AD, Eiring AM, Kraft IL, Anderson DJ, Gu Z, Alikian M, Reid AG, Foroni L, Marin D, Druker BJ, O'Hare T, Deininger MW. BCR-ABL1 compound mutations in tyrosine kinase inhibitor-resistant CML: frequency and clonal relationships. Blood. 2013; 121(3): 489-98. PubMed

Ridges S, Heaton WL, Joshi D, Choi H, Eiring A, Batchelor L, Choudhry P, Manos EJ, Sofla H, Sanati A, Welborn S, Agarwal A, Spangrude GJ, Miles RR, Cox JE, Frazer K, Deininger M, Balan K, Sigman M, Müschen M, Perova T, Johnson R, Montpellier B, Guidos CJ, Jones DA, Trede NS. Zebrafish screen identifies novel compound with selective toxicity against leukemia. Blood. 2012; 119(24): 5621-31. PubMed

Rowe LR, Brothman AR, Nibley WE, Gaffney MR, Chen Z. An inv(16) in Ph-negative cells of a chronic myelogenous leukemia patient after imatinib treatment. Cancer Genet Cytogenet. 2007; 174(1): 54-6. PubMed

Talpaz M, Paquette R, Afrin L, Hamburg SI, Prchal JT, Jamieson K, Terebelo HR, Ortega GL, Lyons RM, Tiu RV, Winton EF, Natrajan K, Odenike O, Claxton D, Peng W, O'Neill P, Erickson-Viitanen S, Leopold L, Sandor V, Levy RS, Kantarjian HM, Verstovsek S. Interim analysis of safety and efficacy of ruxolitinib in patients with myelofibrosis and low platelet counts. J Hematol Oncol. 2013; 6(1): 81. PubMed

Tomasic NL, Piterkova L, Huff C, Bilic E, Yoon D, Miasnikova GY, Sergueeva AI, Niu X, Nekhai S, Gordeuk V, Prchal JT. The phenotype of polycythemia due to Croatian homozygous VHL (571C>G:H191D) mutation is different from that of Chuvash polycythemia (VHL 598C>T:R200W). Haematologica. 2013; 98(4): 560-7. PubMed

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Last Update: September 2016