BCR-ABL mutation analysis has been proposed as a diagnostic test to detect secondary mutations in the ABL portion of the BCR-ABL oncogene that causes chronic myelogenous leukemia (CML). Standard treatment of newly diagnosed Philadelphia chromosome positive (Ph+) CML is typically an agent from the class of drugs called protein tyrosine kinase inhibitors. Most individuals have a good response to this first-line of therapy. However, some individuals develop secondary (acquired) resistance to the first-line therapeutic agent, which may be due to secondary mutations of the BCR-ABL gene.

Medically Necessary:

T315-I mutation analysis is considered medically necessary in the management of individuals with CML who have failed tyrosine kinase inhibitor (TKI) therapy.

Investigational and Not Medically Necessary:

All other indications and types of BCR-ABL mutation analysis are considered investigational and not medically necessary in the management of CML.

A commercially available BCR-ABL Mutation test (Genzyme Genetics, Westborough, MA) is designed to detect the presence of BCR-ABL kinase domain mutations. The test is a molecular diagnostic procedure which uses polymerase chain reaction (PCR) amplification and gene sequencing of exons 18-21 of the tyrosine kinase domain of the BCR-ABL fusion gene. The test examines both peripheral blood and bone marrow specimens. Documentation from the manufacturer does not define which specific mutations are included in this test. Technical staff at Genzyme Genetics verbally report that the sequencing assay will detect any BCR-ABL kinase domain point mutation present within >20% of cells when an appropriate specimen is submitted for analysis.

Identification of BCR-ABL mutations as a source of protein tyrosine kinase inhibitor resistance may be a useful research tool in understanding the natural history of CML and its transition to more aggressive phenotypes e.g. accelerated phase and blast crisis. Although certain BCR-ABL mutations may be associated with protein tyrosine kinase inhibitor resistance, the significance of many other mutations is unknown. In addition, the presence of a mutation does not invariably lead to protein tyrosine kinase inhibitor resistance (Khorashad, 2006; Willis, 2005).

Primary resistance to protein tyrosine kinase inhibitors is defined as failure to obtain a complete hematologic response, and occurs in roughly 5% of newly diagnosed CML individuals. While the mechanisms for primary resistance are poorly understood, it is felt to be independent of the BCR-ABL gene and known to be more common in later stage CML (30-50% of blast-phase individuals). Despite high initial response rates to protein tyrosine kinase inhibitors in newly diagnosed CML, approximately 16% of individuals who initially achieve hematologic or cytogenetic response will develop secondary resistance by 42 months of follow-up (Shah, 2005). Secondary resistance is defined as loss of a previously established response. Acquired or secondary resistance to protein tyrosine kinase inhibitors may be the result of gene amplification (approximately 10% of cases) where increased tyrosine kinase production occurs or specific point mutations in the BCR-ABL gene (approximately 90% of cases). Increasing the dosage of protein tyrosine kinase inhibitors can often overcome the resistance due to gene amplification. Resistance due to BCR-ABL gene mutation is more difficult to treat.

BCR-ABL mutations may confer resistance by a variety of mechanisms, but commonly affect conformation of the protein tyrosine kinase inhibitor binding site on the tyrosine kinase phosphate binding loop ("P-loop") or adenosine triphosphate (ATP) binding site such that protein tyrosine kinase inhibitor inactivation of tyrosine kinase is blocked. More than 40 different mutations have been associated with resistance to protein tyrosine kinase inhibitors. Jabbour and colleagues (2006) screened for mutations in 171 patients failing protein tyrosine kinase inhibitor therapy with a median follow-up of 38 months from start of therapy. Sixty-six mutations impacting 23 amino acids in the BCR-ABL oncoprotein were identified in 62 (36%) patients no longer responding to protein tyrosine kinase inhibitors. Factors associated with the development of mutations were older age, prior interferon therapy and accelerated or blast phase at the start of protein tyrosine kinase inhibitor therapy. By multivariate analysis, the only factors associated with a worse survival from the time of protein tyrosine kinase inhibitor failure were development of clonal evolution and higher percentage of peripheral blood basophils. The presence of a BCR-ABL kinase domain mutation had no impact on survival. In addition, when survival was measured from the time therapy started, non-P-loop mutations were associated with a shorter survival than P-loop mutations. The authors concluded that BCR-ABL P-loop mutations were not associated with a worse outcome suggesting that the prognosis of individuals who fails protein tyrosine kinase inhibitor therapy is multi-factorial.

Nicolini and colleagues (2006) retrospectively analyzed the predictive impact of 94 BCR-ABL kinase domain mutations found in 89 protein tyrosine kinase inhibitor resistant CML individuals. With a median follow-up of 39 months, overall survival was worse for P-loop and another point mutation (T315-I), but not for other BCR-ABL mutations. For individuals in chronic phase only, analysis demonstrated a worse overall survival for P-loop and worse progression free survival for T315-I mutations. These authors concluded that both mutations impair the outcome of protein tyrosine kinase inhibitor resistant CML individuals.

Desatinib, a second-generation tyrosine kinase (ABCR-ABL) inhibitor, has a 325-fold higher potency than imatinib against unmutated BCR-ABL in vitro (O'Hare 2005). Since imatinib failure is commonly caused by BCR-ABL mutations, Muller and colleagues (2009) analyzed data from three phase II/III clinical trials which studied the response to desatinib of individuals with chronic phase CML with or without BCR-ABL mutations after prior therapy with imatinib. Of 1,043 patients who underwent mutational assessment, 39% had a BCR-ABL mutation prior to dasatinib and 48% of 805 patients with either imatinib resistance or a poor response to imatinib had a BCR-ABL gene mutation. Sixty-three different BCR-ABL mutations were detected, with G250, M351, M244, and F359 most frequently found. After two years of follow-up, desatinib treatment of imatinib-resistant patients resulted in a complete cytogenetic response in 43% of patients with a BCR-ABL mutation and 47% of those without mutation. Progression free survival was 70% in patients with BCR-ABL mutation and 80% in those without a mutation. The authors concluded that overall, dasatinib has a durable efficacy in individuals with or without BCR-ABL mutations.

Second-generation TKIs have been approved (desatinib/nilotinib) and shown to be effective against imatinib-resistant CML, with the exception of the BCR-ABL mutant T315-I. Soverini (2007) studied 45 patients who were resistant or intolerant to imatinib and were treated with the second-generation TKI, dasatinib. With a median follow-up of 12 months, 21 patients showed either primary or secondary resistance to dasatinib or loss of hematologic response during treatment. Eight patients had primary resistance to dasatinib. Thirteen (13) patients had secondary resistance to dasatinib. The T315-I mutation accounted for dasatinib treatment failure in 13 of the 21 cases confirming that the T315-I mutation is highly resistant to dasatinib. Additional studies have also confirmed that the mutant T315-I is resistant to TKIs currently available (Baccarani, 2009; Branford, 2009; Muller, 2009). Clinical trials are underway studying a compound to treat CML individuals resistant to imatinib with the T315-I mutation.

In 2009, an estimated 5,050 new cases of chronic myelogenous leukemia (CML) were diagnosed in the United States (U.S.) and about 470 people in the U.S. died from CML (American Cancer Society, 2009). CML is a relatively uncommon disease, primarily affecting older adults at an average age of 66 years. CML is a disease in which the bone marrow makes too many white blood cells. These blood cells are abnormal and can build up in the blood and bone marrow so there is less room for the healthy white blood cells. CML can be diagnosed by the identification (either cytogenetic or molecular) of a clonal expansion of a hematopoietic stem cell possessing the Philadelphia chromosome. Most people with CML will have this genetic change called the Philadelphia chromosome. The genetic change is the result of a translocation of chromosomes 9 and 22, producing a fusion of the head of the BCR gene with the body of the ABL gene (Sawyers, 1999). This chimeric gene is transcribed into a hybrid BCR-ABL mRNA producing the bcr-abl fusion oncoprotein, p210. The mechanisms by which the p210 protein promotes the transition from a benign to a malignant state are not completely understood. It has been shown that the BCR attachment to ABL results in the ABL protein becoming an active, unregulated tyrosine kinase resulting in cell proliferation, de-differentiation and block of apoptosis (Faderl, 1999).

CML typically progresses via 3 phases: chronic, accelerated, and blast. CML is usually diagnosed in the chronic phase. Left untreated, CML typically progresses from a chronic phase to a transition period or accelerated phase and then on to rapidly fatal blastic phase. Definitions of accelerated phase vary, but the term is typically used to describe individuals who show certain signs of disease progression and resistance to therapy but who do not yet meet the criteria for blast therapy. Features of accelerated phase include significant increases in peripheral blood and bone marrow blasts or basophils, development of extramedullary disease, splenomegaly and persistent fever or bone pain. The blast phase or crisis are blasts > 20-30% of peripheral white blood cells, extramedullary blast proliferation and large foci or clusters of blasts in the bone marrow biopsy (National Comprehensive Cancer Network [NCCN], 2010).

Protein tyrosine kinase inhibitors are typically utilized in the treatment of CML. The protein tyrosine kinase inhibitors act to bind the inactive forms of the ABL kinase and function as a competitive inhibitor at the ATP binding site (P-loop) of the BCR-ABL protein. The primary effect is to block the auto-phosphorylation of the kinase a requirement for kinase activation and signal transduction. The bound BCR-ABL tyrosine kinase is acted upon by phosphatases and remains in an enzymatically inert state. Prior to the availability of protein tyrosine kinase inhibitors, the only curative option for CML was high-dose chemotherapy with allogeneic stem cell support. Several drugs in the protein tyrosine kinase inhibitor class have now been approved by the U.S. Food and Drug Administration for the treatment of CML. Clinical trials are in progress to research the use of additional medications in conjunction with other treatments such as chemotherapy and stem-cell transplants.

There are 3 different clinical responses in CML which can be monitored during therapy: hematologic, cytogenetic and molecular. An accepted goal of CML therapy is to achieve a Complete Cytogenetic Response (CCyR) within 18 months of initiating therapy. A cytogenetic response is defined as a decrease in the number of Ph-positive metaphases (stage of cell division during which the chromosomes align in the middle of the cell prior to division) determined by bone marrow aspirate and cytogenetic evaluation. Cytogenetic monitoring is a widely used technique for monitoring response in individuals with CML. A CCyR is defined as an absence of Ph-positive metaphases. Although conventional cytogenetics for Ph-positive metaphases is a standard technique for monitoring cytogenetic responses in CML, the sensitivity is approximately 5% if only 20 metaphases are examined. If conventional cytogenetics shows no metaphases, the cytogenetic response can be further evaluated by more sensitive techniques such as Fluorescence in situ hybridization (FISH) using 5'-BCR and 3'ABL probes. Cytogenetic evaluation is recommended at 6 and 12 months after start of therapy. If an individual shows only a partial cytogenetic remission at 12 months, repeat cytogenetic testing is recommended at 18 months.

A Complete Hematologic Response (CHR) is defined as a normalization of the peripheral blood counts with no immature cells, leukocyte count <10 x 10⁹/L and platelet count <450 x 10⁹/L. In a CHR, an individual is free of signs and symptoms of the disease with the disappearance of splenomegaly. A partial hematologic response indicates the presence of immature blood cells and/or platelet count less than 50 % of the pretreatment count but more than 450 x 10⁹/L and/or persistent splenomegaly (but less than 50% of pretreatment) (NCCN, 2010).

A more recently developed method of monitoring response to CML therapy involves the use of quantitative genomic techniques to measure the level of the BCR-ABL oncogene mRNA transcript. A complete molecular response (CMR) occurs when there is no detectable BCR-ABL mRNA as measured in a quantitative reverse transcriptase-polymerase chain reaction (RT-QPCR) assay. A major molecular response (MMR) is defined as at least a 3-log reduction in the quantitative BCR-ABL mRNA RT-QPCR assay. RT-QPCR is the most sensitive assay currently available to measure BCR-ABL mRNA. This assay can be used to measure BCR-ABL transcripts in either the blood or bone marrow and can detect one CML cell in a background of 100,000 normal cells.

While an MMR may be associated with a more durable long-term remission rate (Druker, 2006), other studies suggest that it does not predict a longer survival. In individuals achieving CCyR at 12 or 18 months, achievement of a molecular response at those time points did not affect overall survival (de Lavallade, 2008; Kantarjian 2006). Although a rising BCR-ABL level may be associated with an increased risk of BCR-ABL mutation in the future, the significance of this is unclear. A study by Marin et al (2008) demonstrated that although individuals who did not have an MMR at 18 months had a higher chance of losing CCyR, this was not reflected in a difference in progression free survival. The 2010 NCCN Practice Guideline, however, does recommend the use of QPCR to measure BCR-ABL mRNA transcripts at the time of diagnosis of CML and every 3 months while an individual appears to be responding to treatment and every 3-6 months after an individual reaches CCyR. Measurement of BCR-ABL transcript levels are also recommended when an individual appears to have a rising level (1 log increase) of BCR-ABL transcripts.

Apoptosis: a series of molecular steps resulting in a type of cell death; the body's normal way of getting rid of unneeded or abnormal cells; programmed cell death

First-line of therapy: the first or primary treatment for the diagnosis; may include surgery, chemotherapy, radiation therapy or a combination of these therapies

Mutation: a permanent transmissible change in DNA sequence; it can be an insertion or deletion of genetic information, or an alteration in the original genetic information

Oncogene: a gene having the potential to cause a normal cell to become cancerous

Translocation: transfer of part of a chromosome (gene fragment) from one chromosomal location to another

The following codes for treatments and procedures applicable to this document are included below for informational purposes.  Inclusion or exclusion of a procedure, diagnosis or device code(s) does not constitute or imply member coverage or provider reimbursement policy.  Please refer to the member's contract benefits in effect at the time of service to determine coverage or non-coverage of these services as it applies to an individual member.

When services may be Medically Necessary when criteria are met:

When services are Investigational and Not Medically Necessary:
When the code(s) describes a procedure indicated in the Position Statement section as investigational and not medically necessary.

Peer Reviewed Publications:

1. Baccarani M, Cortes J, Pane F, et al. Chronic myeloid leukemia: an update of concepts and management recommendations of European LeukemiaNet. J Clin Oncol. 2009; 27(35):6041-6051.
2. Branford S, Melo JV, Hughes TP. Selecting optimal second-line tyrosine kinase inhibitor therapy for chronic myeloid leukemia patients after imatinib failure: does the BCR-ABL mutation status really matter? Blood. 2009; 114(27):5426-5435.
3. de Lavallade H, Apperley JF, Khorashad JS, et al. Imatinib for newly diagnosed patients with chronic myeloid leukemia: incidence of sustained responses in an intention-to-treat analysis. J Clin Oncol. 2008; 26(20):3358-3363.
4. Druker BJ, Guilhot F, O'Brien SG, et al. Five-year follow-up of patients receiving imatinib for chronic myeloid leukemia. N Engl J Med. 2006; 355(23):2408-2417.
5. Faderl S, Talpaz M, Estrov Z, et al. The biology of chronic myeloid leukemia. N Engl J Med. 1999; 41(3):164-172.
6. Jabbour E, Kantarjian H, Jones D, et al. Frequency and clinical significance of BCR-ABL mutations in patients with chronic myeloid leukemia treated with imatinib mesylate. Leukemia. 2006; 20(10):1767-1773.
7. Kantarjian HM, Talpaz M, O'Brien S, et al. Survival benefit with imatinib mesylate versus interferon-alpha-based regimens in newly diagnosed chronic-phase chronic myelogenous leukemia. Blood. 2006; 108(6):1835-1840.
8. Khorashad JS, Anand M, Marin D, et al. The presence of a BCR-ABL mutant allele in CML does not always explain clinical resistance to imatinib. Leukemia. 2006; 20(4):658-663.
9. Marin D, Milojkovic D, Olavarria E, et al. European LeukemiaNet criteria for failure or suboptimal response reliably identify patients with CML in early chronic phase treated with imatinib whose eventual outcome is poor. Blood. 2008; 112(12):4437-4444.
10. Müller MC, Cortes JE, Kim DW, et al. Dasatinib treatment of chronic-phase chronic myeloid leukemia: analysis of responses according to preexisting BCR-ABL mutations. Blood. 2009; 114(24):4944-4953.
11. Nicolini FE, Corm S, Le QH, et al. Mutation status and clinical outcome of 89 imatinib mesylate-resistant chronic myelogenous leukemia patients: a retrospective analysis from the French intergroup of CML (Fi(phi)-LMC GROUP).Leukemia. 2006; 20(6):1061-1066.
12. O'Hare T, Walters DK, Stoffregen EP, et al. In vitro activity of Bcr-Abl inhibitors AMN107 and BMS-354825 against clinically relevant imatinib-resistant Abl kinase domain mutants. Cancer Res.2005; 65(11)4500-4505.
13. Sawyers CL. Chronic myeloid leukemia. N Engl J Med. 1999; 340(17):1330-1340.
14. Soverini S, Colarossi S, Gnani A, et al. Resistance to dasatinib in Philadelphia-positive leukemia patients and the presence or the selection of mutations at residues 315 and 317 in the BCR-ABL kinase domain. Haematologica. 2007; 92(3):401-404.
15. Willis SG, Lange T, Demehri S, et al. High-sensitivity detection of BCR-ABL kinase domain mutations in imatinib-naïve patients: correlation with clonal cytogenetic evolution but not response to therapy. Blood. 2005; 106(6):2128-2137.

Government Agency, Medical Society, and Other Authoritative Publications:

1. American Cancer Society. Detailed Guide: Leukemia - Chronic Myelogenous (CML). Revised: 11/05/2009. Available at: http://www.cancer.org/docroot/CRI/CRI_2_3x.asp?dt=83. Accessed on February 18, 2010.
2. National Cancer Institute. Chronic Myelogenous Leukemia Treatment (PDQ^®). Last updated on October 30, 2009. Available at: http://www.cancer.gov/cancertopics/pdq/treatment/CML Accessed on February 18, 2010.
3. National Comprehensive Cancer Network. Clinical Practice Guidelines in Oncology – v.2.2010. Chronic Myelogenous Leukemia. August 7, 2009. Available at: http://www.nccn.org/professionals/physician_gls/PDF/cml.pdf. Accessed on February 18, 2010.
4. Shah NP. Loss of response to imatinib: mechanisms and management. Hematology Am Soc Hematol Educ Program. 2005; 183-187.

1. The Leukemia and Lymphoma Society. Chronic Myelogenous Leukemia. Available at: http://www.leukemia-lymphoma.org/all_page?item_id=8501. Accessed on February 18, 2010.

BCR-ABL Mutation Analysis
Chronic Myelogenous Leukemia