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EPIC CODE: LAB5524 BCR/ABL1, Qualitative, Diagnostic Assay, Varies

Additional Codes

Sunquest:  BADXM
Mayo:         BADX

Reporting Name

BCR/ABL1, RNA-Qual, Diagnostic

Useful For

Diagnostic workup of patients with a high probability of BCR-ABL1-positive hematopoietic neoplasms, predominantly chronic myeloid leukemia and acute lymphoblastic leukemia

Performing Laboratory

Mayo Clinic Laboratories in Rochester

Specimen Type


Ordering Guidance

This test is only qualitative and should not be used for routine monitoring (ie, quantitative messenger RNA [mRNA] level).


Monitoring of most patients with chronic myeloid leukemia (CML) should be performed using BCRAB / BCR/ABL, p210, mRNA Detection, Reverse Transcription-PCR (RT-PCR), Quantitative, Monitoring Chronic Myelogenous Leukemia (CML), Varies.


Monitoring of patients known to carry a p190 fusion should be performed using BA190 / BCR/ABL, p190, mRNA Detection, Reverse Transcription-PCR (RT-PCR), Quantitative, Monitoring Assay, Varies.


For information on which test to order for various scenarios, see BCR/ABL1 Ordering Guide for Blood and Bone Marrow

Shipping Instructions

Refrigerate specimens must arrive within 5 days of collection, and ambient specimens must arrive with 3 days (72 hours) of collection. Collect and package specimens as close to shipping time as possible.

Necessary Information

The following information is required:

1. Pertinent clinical history including if the patient has a diagnosis of chronic myelogenous leukemia or other BCR/ABL1-positive neoplasm

2. Date of collection

3. Specimen source (blood or bone marrow)

Specimen Required

Submit only 1 of the following specimens:


Specimen Type: Whole blood


Preferred: Lavender top (EDTA)

Acceptable: Yellow top (ACD)

Specimen Volume: 10 mL

Collection Instructions:

1. Invert several times to mix blood.

2. Send whole blood specimen in original tube. Do not aliquot.

3. Label specimen as blood.


Specimen Type: Bone marrow


Preferred: Lavender top (EDTA)

Acceptable: Yellow top (ACD)

Specimen Volume: 4 mL

Collection Instructions:

1. Invert several times to mix bone marrow.

2. Send bone marrow specimen in original tube. Do not aliquot.

3. Label specimen as bone marrow.

Specimen Minimum Volume

Peripheral blood: 8 mL
Bone marrow: 2 mL

Specimen Stability Information

Specimen Type Temperature Time Special Container
Varies Refrigerated (preferred) 5 days PURPLE OR PINK TOP/EDTA
  Ambient  72 hours PURPLE OR PINK TOP/EDTA

Reference Values

A qualitative result is provided that indicates the presence or absence of BCR/ABL1 messenger RNA. When positive, the fusion variant is also reported.

Day(s) Performed

Monday through Saturday

Test Classification

This test was developed, and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. This test has not been cleared or approved by the US Food and Drug Administration.

CPT Code Information




LOINC Code Information

Test ID Test Order Name Order LOINC Value
BADX BCR/ABL1, RNA-Qual, Diagnostic 55135-8


Result ID Test Result Name Result LOINC Value
39466 Diagnostic BCR/ABL1 Result No LOINC Needed
MP001 Specimen Type 31208-2
19783 Interpretation 69047-9

Clinical Information

The t(9;22)/BCR-ABL1 abnormality is associated with chronic myeloid leukemia (CML) and "Philadelphia-positive" acute lymphoblastic leukemia of B-cell lineage (Ph+ ALL). Very rarely, this abnormality has also been identified in cases of acute myeloid leukemia and T-lymphoblastic leukemia/lymphoma. The fusion gene on the derivative chromosome 22q11 produces a chimeric BCR-ABL1 mRNA transcript and corresponding translated oncoprotein. Despite substantial breakpoint heterogeneity at the DNA level, a consistent set of BCR-ABL1 messenger RNA (mRNA) transcripts are produced that can be readily and sensitively detected by reverse transcription-polymerase chain reaction  (RT-PCR) technique. In CML, breakpoints in BCR result in either exons 13 or 14 (e13, e14) joined to exon 2 of ABL1 (a2). The corresponding e13-a2 or e14-a2 BCR-ABL1 mRNAs produce a 210-kDa protein (p210). Rare cases of CML are characterized by an e19-a2 type mRNA with a corresponding p230 protein. In Ph+ ALL, the majority of cases harbor an e1-a2 BCR-ABL1 mRNA transcript, producing a p190 protein. However, chimeric mRNA type is not invariably associated with disease type, as noted by the presence of p210-positive Ph ALL and very rare cases of p190-positive CML. Therefore, positive results from a screening (diagnostic) assay for BCR-ABL1 mRNA need to be correlated with clinical and pathologic findings.


In addition to the main transcript variants described above, rare occurrences of both CML and Ph+ ALL can have alternative break-fusion events resulting in unusual BCR-ABL1 transcript types. Examples include e6-a2 and BCR exon fusions to ABL1 exon a3 (eg, e13-a3, e14-a3, or e1-a3). In addition to detecting common BCR-ABL1 mRNA transcripts, this assay also can identify these rarer BCR-ABL1 transcript variants and is, therefore, a comprehensive screen for both usual and uncommon BCR-ABL1 gene fusions in hematopoietic malignancies. Given the nature of genetic events in tumors, however, this assay will not identify extremely rare and unexpected BCR-ABL1 events involving other exons (eg, case report level) and is, therefore, not absolutely specific but is predicted to detect more than 99.5% of BCR-ABL1 events. Therefore, it is recommended that for diagnosis, RT-PCR plus a second method (eg, BCR-ABL1 fluorescence in situ hybridization or cytogenetics) should be used. However, this RT-PCR assay is invaluable at diagnosis for identifying the precise BCR-ABL1 mRNA type (eg, for future quantitative assay disease monitoring), which cannot be done by complementary methods.


This assay is intended as a qualitative method, providing information on the presence (and specific mRNA type) or absence of the BCR-ABL1 mRNA. Results from this test can be used to determine the correct subsequent assay for monitoring of transcript levels following therapy (eg, BCRAB / BCR/ABL1, p210, mRNA Detection, Reverse Transcription-PCR (RT-PCR), Quantitative, Monitoring Chronic Myeloid Leukemia (CML), Varies; BA190 / BCR/ABL, p190, mRNA Detection, Reverse Transcription-PCR (RT-PCR), Quantitative, Monitoring Assay, Varies). Because the assay is analytically sensitive, it compensates for situations such as partially degraded RNA quality, or low cell number, but it is not intended for quantitative or monitoring purposes.


An interpretive report will be provided.


When positive, the test identifies the specific messenger RNA fusion variant present to guide selection of an appropriate monitoring assay.

Monitoring is available for common p210 or p190 fusion variant detected.

-Common fusion variants detected: e13-a2 or e14-a2 (p210), e1-a2 (p190), and e6-a2 (p205*)

-Rare fusion variants detected: e13-a3 (p210), e14-a3 (p210), e1-a3 (p190), e19-a2 (p230)

-Potential rare fusions detected: e12-a3, e19-a3

*This is formerly observed as the e6-a2 (p185) fusion form.


No significant cautionary statements

Clinical Reference

1. Burmeister T, Reinhardt R: A multiplex PCR for improved detection of typical and atypical BCR-ABL fusion transcripts. Leuk Res 2008 Apr;32(4):579-585

2. Melo JV: The diversity of BCR-ABL fusion proteins and their relationship to leukemia phenotype. Blood. 1996 Oct 1;88(7):2375-2384

3. Melo JV: BCR-ABL gene variants. Baillieres Clin Haematol. 1997 Jun;10(2):203-222

4. Tefferi A: The classic myeloproliferative neoplasms: Chronic myelogenous leukemia, polycythemia vera, essential thrombocythemia, and primary myelofibrosis. In: Valle DL, Antonarakis S, Ballabio A, Beaudet AL, Mitchell GA, eds. The Online Metabolic and Molecular Bases of Inherited Disease. McGraw-Hill; 2019, Accessed March 16, 2022. Available at

Method Description

Total RNA is extracted from the patient's blood or bone marrow at the time of diagnosis and messenger RNA (mRNA) is reverse transcribed into complementary DNA (cDNA). The cDNA is then subjected to polymerase chain reaction (PCR) using 4 separate multiplex reactions. A qualitative result, which will include the relative ratio of target translocation mRNA to control GUSB gene mRNA, will be provided. Although this method employs a quantitative PCR platform, the results can be used to evaluate the relative expression levels of the translocation mRNA relative to control mRNA, thus, providing an improved measure of RNA quality in the assay. Reporting of results will be qualitative; either BCR-ABL1 mRNA positive/detected (with transcript type) or negative/not detected.(Unpublished Mayo method)

Report Available

5 to 10 days

Specimen Retention Time

Blood/Bone marrow: 2 weeks; Extracted RNA: 3 months

Reject Due To

Gross hemolysis Reject
Other Moderately to severely clotted

NY State Approved


Method Name

Reverse Transcription-Polymerase Chain Reaction (RT-PCR) Multiplex PCR

Secondary ID



1. Hematopathology Patient Information (T676)

2. If not ordering electronically, complete, print, and send a Hematopathology/Cytogenetics Test Request (T726) with the specimen.