Chronic Myelogenous Leukemia - CML

Key Points

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 10fold 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.  

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

  • Diagnosis

    ARUP Tests

    • Chromosome Analysis, Bone Marrow  2002292
    • Chromosome FISH, Interphase 2002298
    • BCR-ABL1, Qualitative with Reflex to BCR-ABL1 Quantitative 2005010
      • Recommended if diagnosis is uncertain
    • BCR-ABL1, Major (p210), Quantitative 2005017
      • Major transcript characterized by p210 fusion gene product is typical in CML

    Cytogenetic Analysis (Bone Marrow)

    • Recommended test; considered gold standard

    FISH

    • May be used as alternate test if cytogenetics or molecular testing not available, or if cytogenetics are negative for BCR-ABL transcript
    • Order as baseline test if monitoring cytogenetic complete remission (CCR) with FISH

    Quantitative PCR (measures BCR-ABL transcript levels)

    • Most CML patients have p210 fusion; p190 fusions are rare in CML
    • May be used as alternate to cytogenetic testing
    Prior to complete cytological response (CCR)

    ARUP Tests

    • Chromosome Analysis, Bone Marrow  2002292
    • BCR-ABL1, Qualitative with Reflex to BCR-ABL1 Quantitative  2005010
      • Recommended if diagnosis is uncertain
    • BCR-ABL1, Major (p210), Quantitative  2005017
      • Major transcript characterized by p210 fusion gene product is typical in CML

    Cytogenetic Analysis (Bone Marrow)

    • Recommended test for establishing CCR
      • Perform every 3-6 months until CCR achieved

    Quantitative PCR (measures BCR-ABL transcript levels)

    • Perform every 3-6 months until CCR achieved
    Confirming CCR

    ARUP Tests

    • Chromosome Analysis, Bone Marrow  2002292
    • Chromosome FISH, Interphase  2002298
    • BCR-ABL1, Qualitative with Reflex to BCR-ABL1 Quantitative  2005010
      • Recommended if diagnosis is uncertain
    • BCR-ABL1, Major (p210), Quantitative  2005017
      • Major transcript characterized by p210 fusion gene product is typical in CML

    Cytogenetic Analysis (Bone Marrow)

    • Recommended test

    FISH

    • Alternative test to document CCR achieved

    Quantitative PCR (measures BCR-ABL transcript levels)

    • Alternative test to document CCR achieved when cytogenetics are not available
    Monitoring CCR

    ARUP Tests

    • Chromosome Analysis, Bone Marrow  2002292
    • Chromosome FISH, Interphase  2002298
    • BCR-ABL1, Qualitative with Reflex to BCR-ABL1 Quantitative  2005010
      • Recommended if diagnosis is uncertain
    • BCR-ABL1, Major (p210), Quantitative  2005017
      • Major transcript characterized by p210 fusion gene product is typical in CML

    Cytogenetic Analysis (Bone Marrow)

    • Every 12-24 months after CCR achieved
    • PCR has equivalent sensitivity 
    • Can detect secondary changes suggestive of transition to blast crisis

    FISH

    • Alternative to cytogenetic analysis once CCR achieved
    • Every 6 months after CCR achieved

    Quantitative PCR (measures BCR-ABL transcript levels)

    • Most CML patients have p210 fusion; p190 fusions are rare in CML
    • Alternative to cytogenetic analysis
    • Every 3-6 months after CCR achieved
    Consideration of major change in therapy

    ARUP Tests

    • Chromosome Analysis, Bone Marrow  2002292
    • BCR-ABL1, Qualitative with Reflex to BCR-ABL1 Quantitative  2005010
      • Recommended if diagnosis is uncertain
    • BCR-ABL1, Major (p210), Quantitative  2005017
      • Major transcript characterized by p210 fusion gene product is typical in CML
    • BCR-ABL1 Mutation Analysis by Next Generation Sequencing   2008420

    Cytogenetic Analysis (Bone Marrow)

    • At time of suspected relapse or suspected resistance to TKI

    Quantitative PCR (measures BCR-ABL transcript levels)

    • Most CML patients have the p210 fusion; p190 fusions are rare in CML
    • Use in combination with kinase domain mutation testing

    Mutational Studies (detects BCR-ABL KD mutations)

    • Recommended only when patient has 5- to 10-fold increase in values for PCR test
    • Evidence lacking that use of baseline mutation analysis and subsequent monitoring improves outcome
    • Next generation sequencing
      • Offers higher sensitivity over Sanger sequencing techniques
      • May be able to determine if mutation is in cis or trans loci
      • Offers additional testing of SH2 and SH3 domains

Features of test types

  • Cytogenetic analysis (bone marrow)
    • Marrow analyzed for at least 20 evaluable metaphases
    • CCR: 0% Ph-positive metaphases
      • Equivalent to quantitative PCR value of 1%
    • Time consuming
    • Painful procedure to obtain marrow
    • Wide confidence interval
    • Will detect translocation, but not insertion in BCR-ABL fusion gene (occurs in ~5% cases)
    FISH
    • Blood specimens analyzed for 200 interphase cells
    • Values not always interchangeable with cytogenetic values
    • Not usually used to confirm CCR
    • Detects both insertions and translocations resulting in BCR-ABL fusion
    Quantitative PCR
    • Reports ratio of BCR-ABL1 to reference gene with conversion to international scale (% IS) in blood or bone marrow specimen
      • Good correlation between blood and bone marrow samples
    • Major molecular response: reduction in transcript levels by at least 3-logs (<0.1% IS)
    • Complete molecular response: transcripts not detectable (in assay with at least 4-5 log range of detection)
    Mutational studies
    • Good correlation between bone marrow and blood samples

Diagnosis

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

Histology

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

Prognosis

  • 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

Monitoring

  • 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)

Pharmacogenetics and Therapeutic Drug Monitoring

  • 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

Clinical Background

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

Epidemiology

  • 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

Pathophysiology

  • 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

Indications for Laboratory Testing

  • 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
Test Name and Number Recommended Use Limitations Follow Up
Leukocyte Alkaline Phosphatase 0049000
Method: Cytochemical Stain

Differentially diagnose cases of neutrophilia, including CML and leukemoid reaction

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

 
Chromosome Analysis, Bone Marrow 2002292
Method: Giemsa Band

Establish diagnosis by detection of t(9;22)

Identify secondary cytogenetic changes predicting transformation into accelerated or blast phase such as an additional Ph chromosome (der 22), +8, iso 17q, or +19

Identify complete cytogenetic response (CCR)

 

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 by Next Generation Sequencing 2008420
Method: Massively Parallel Sequencing

Detects mutations in the BCR-ABL1 gene in tyrosine kinase inhibitor-resistant/refractory CML

Higher sensitivity than traditional Sanger sequencing techniques

Offers coverage of SH2 and SH3 domain mutations

If 2 mutations are present, this test can potentially determine if they are in cis or in trans

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

Identify and monitor p210 BCR-ABL1 mRNA fusion in CML (more common fusion than p190) and a subset of ALL with confirmed p210 Ph+

Assess treatment milestones and detect early signs of resistance to TKI therapy

Results must always be interpreted in context of morphologic and other relevant data and should not be used alone for diagnosis of malignancy

Samples identified as negative may still harbor BCR-ABL1 positive cells at levels below limit of detection

BCR-ABL1 mRNA with the minor breakpoint (e1a2; p190) are not detected

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

Recommended when submitting initial diagnostic sample for CML or Ph+ ALL (no previous BCR-ABL1 testing) 

If the qualitative test is positive, the appropriate corresponding quantitative test is performed

   
Chromosome FISH, Interphase 2002298
Method: Fluorescence in situ Hybridization

Alternate test if cytogenetics or PCR not available

Order as baseline test if monitoring CCR with FISH

Turnaround time faster than PCR testing

May be ordered concurrently with PCR qualitative BCR-ABL1 testing

Genes involved include BCR-ABL1 fusion

Indicate names of probes

ARUP Oncology FISH Probes menu

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

Aids in diagnosis and monitoring of individuals with CML or Ph+ ALL who have e1a2 transcripts (p190)

Does not detect the p210 or p230 form  
Myeloproliferative Disorders Panel by FISH 2002360
Method: Fluorescence in situ Hybridization

Provides prognostic and predictive information in CML

Detects both cryptic and noncryptic BCR-ABL1 translocations in suspected CML

Probes target BCR-ABL1 fusion, FGFR1 translocations, FIP1L1-PDGFRA region rearrangements, and PDGFRB translocations

Distinguish CML from other MPDs with aberrant tyrosine kinases

Detect CML, myeloid and lymphoid neoplasms with eosinophilia and abnormalities of PDGFRA, PDGFRB, and FGFR1

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

 
Additional Tests Available
 
Click the plus sign to expand the table of additional tests.
Test Name and NumberComments
CBC with Platelet Count 0040002
Method: Automated Cell Count

Initial evaluation for presence of leukocytosis