BCR-ABL Analysis


The chromosomal translocation t(9;22) corresponds to the transfer of the ABL1 gene on chromosome 9 to the BCR breakpoint cluster region of chromosome 22. Real-time quantitative polymerase chain reaction (RQ-PCR) is used in the detection of the Philadelphia chromosome in patients with either chronic myelogenous leukemia (CML) or acute lymphoblastic leukemia (ALL). BCR-ABL1 has been detected in approximately 95% of patients with chronic myelogenous leukemia (CML).

Regular monitoring of the efficacy of tyrosine kinase therapies is important to ensure optimal treatment for patients with chronic myeloid leukemia (CML).  International guidelines recommend routine evaluation of BCR-ABL1 levels using a molecular test because only these tests provide the sensitivity and level of quantification required for accurate monitoring. The BCR-ABL1 assay has many uses including monitoring the effectiveness of treatment, prediction of early relapse, and prediction of patient’s prognosis.  With this procedure, amplification of the BCR-ABL1 fusion gene is used to quantify the amount of BCR-ABL1 versus normal control transcript ABL1. This ratio is indicative of the disease burden the patient maintains at different stages in treatment post diagnosis.  The assay is performed using Cepheid’s GeneXpert Dx Instrument Systems. The process is fully automated for both running the tests and viewing the results. The amount of BCR-ABL1 produced is compared to the amount of ABL for treatment purposes and is reported as a percentage ratio.  The percent ratio is then multiplied by a test-specific conversion factor to express the results on the International Scale (IS). The IS was established in 2005 to standardize quantitative BCR-ABL1 measurements across varying testing strategies and laboratories (Hughes et al., Blood 2006).   Clinical studies have demonstrated that achieving a major molecular remission (MMR), or a 3-log reduction in BCR-ABL1 expression from the standardized baseline level, is a key clinical outcome.


The RQ-PCR assay uses peripheral blood specimens labeled with fluorescent reporter dye probes to detect the p210 (b2a2 and b3a2) major breakpoint translocation and the ABL1 endogenous control sequence. The oncoprotein, p210, is the translated fusion product of BCR/ABL1. The basis of its oncoprotein function is increased ABL1 tyrosine kinase activity causing neoplastic cell transformation.


Testing is routinely performed using peripheral blood; however, bone marrow aspirates are also accepted.

Peripheral blood (5 mL whole blood, Minimum 1 mL) collected and labeled by standard techniques in tubes containing EDTA (Purple top) or sodium citrate (Blue top) as an anticoagulant. Specimen should be stored at room temperature. If delay in transport, up to 24 hours, specimen may be stored at 2-8 degrees Celsius. Specimens older than 48 hours may be considered suboptimal due to lability of RNA. Do not use heparin as an anticoagulant because it may inhibit the PCR reaction.

Bone Marrow aspirates (3 mL, Minimum 1 mL) are accepted.
Frozen specimens are unacceptable.
PCR will be attempted on all received specimens.


CPT CODE(S): 83391, 83902, 83898X2, 83896X4, 83912