Home Cancer Genetics and Molecular Tumor Testing BCR-ABL1 Test: CML, Leukemia, Philadelphia Chromosome, and Results

BCR-ABL1 Test: CML, Leukemia, Philadelphia Chromosome, and Results

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Understand BCR-ABL1 testing for CML and Philadelphia-positive leukemia, including diagnostic methods, International Scale results, molecular response milestones, and resistance testing.

A BCR-ABL1 test detects or measures the fusion gene that drives chronic myeloid leukemia and a major subtype of acute lymphoblastic leukemia. The fusion usually forms when chromosomes 9 and 22 exchange material, creating the shortened chromosome 22 known as the Philadelphia chromosome. BCR::ABL1 produces an always-active tyrosine kinase that signals blood cells to grow and survive.

The same biomarker is used in different ways. At diagnosis, qualitative PCR, fluorescence in situ hybridization, or chromosome analysis can establish that BCR::ABL1 is present. During chronic myeloid leukemia treatment, standardized quantitative PCR measures the transcript level on the International Scale and shows how well a tyrosine kinase inhibitor is suppressing the leukemia. A falling result is expected; a confirmed rise may signal missed doses, drug interactions, resistance, or disease progression. Results must be interpreted by disease type, transcript form, treatment duration, laboratory sensitivity, blood counts, and bone-marrow findings.

  • BCR::ABL1 detected at diagnosis strongly supports CML or Philadelphia-positive leukemia when the blood and marrow findings fit.
  • CML monitoring uses quantitative PCR reported as BCR::ABL1 International Scale percentage, not simply positive or negative.
  • Major molecular response is BCR::ABL1 at or below 0.1% IS.
  • An undetectable result means no transcript was found at the assay’s stated sensitivity; it does not prove every leukemia cell is gone.
  • A confirmed increase or failure to reach expected milestones may prompt adherence review, repeat testing, and ABL1 kinase-domain mutation analysis.

Table of Contents

What BCR-ABL1 and the Philadelphia Chromosome Are

BCR::ABL1 forms through a reciprocal translocation written as t(9;22)(q34;q11.2). Part of ABL1 on chromosome 9 joins part of BCR on chromosome 22. The altered chromosome 22 is the Philadelphia chromosome, named for the city where it was first described. The fusion protein has continuously active ABL1 tyrosine kinase activity and stimulates pathways that promote cell division, survival, altered adhesion, and genomic instability.

Nearly all cases of chronic myeloid leukemia, or CML, have BCR::ABL1. A small percentage have a cryptic or complex rearrangement that is not obvious on routine chromosome analysis but can be found by FISH or molecular testing. BCR::ABL1 also occurs in Philadelphia chromosome-positive B-cell acute lymphoblastic leukemia, called Ph-positive B-ALL, and rarely in other acute leukemias.

Different breakpoints produce different messenger RNA transcripts and protein sizes. The most common CML transcripts are e13a2 and e14a2, which encode p210 BCR::ABL1. Ph-positive ALL more often has e1a2, which encodes p190, although p210 also occurs. Rare transcripts can encode p230 or other forms. Identifying the transcript at diagnosis matters because follow-up PCR must be able to measure that same form.

BCR::ABL1 is a somatic alteration in the leukemia cells. It is not usually inherited, does not arise from something a patient did, and does not mean relatives need testing for the same fusion. It differs from inherited variants detected by germline genetic testing.

The fusion is both a defining biomarker and a treatment target. Tyrosine kinase inhibitors, or TKIs, bind ABL1 and suppress the abnormal signal. Examples include imatinib, dasatinib, nilotinib, bosutinib, ponatinib, and asciminib, although selection depends on disease setting, mutations, health conditions, prior therapy, pregnancy considerations, and regulatory approval.

A positive fusion result is not interpreted without the blood and marrow picture. CML typically shows persistent leukocytosis with a full range of maturing myeloid cells, basophilia, and often an enlarged spleen. Acute leukemia shows a high proportion of blasts and requires immunophenotyping to establish lineage. Rarely, BCR::ABL1 can be detected at very low levels in situations that do not meet criteria for CML, so the integrated diagnosis remains essential.

Why BCR-ABL1 Testing Is Ordered

At diagnosis, testing is ordered when blood counts, a smear, symptoms, or marrow findings raise concern for CML or Ph-positive ALL. In established CML, it is repeated regularly to measure response to treatment. The purpose of the test should be clear on the order because diagnostic assays and monitoring assays answer different questions.

Common diagnostic reasons include:

  • Persistent high white blood cell count with neutrophils and immature myeloid cells
  • Basophilia or eosinophilia without another explanation
  • Enlarged spleen, fatigue, night sweats, weight loss, or early fullness
  • Bone-marrow findings suspicious for a myeloproliferative neoplasm
  • B-cell acute lymphoblastic leukemia or mixed-phenotype acute leukemia
  • An abnormal chromosome 22 or suspected t(9;22)
  • Distinguishing CML blast phase from a newly diagnosed acute leukemia

A complete CML workup generally includes a complete blood count, blood smear, bone-marrow examination, chromosome analysis, and BCR::ABL1 testing. Bone marrow gives information about blast percentage, fibrosis, and additional chromosome abnormalities. PCR defines the transcript and provides a baseline for future comparison.

After treatment starts, quantitative reverse-transcription PCR is usually performed about every three months until a stable major molecular response is achieved. Monitoring may later become less frequent in a consistently responding patient, while treatment-free remission requires much more frequent testing after the TKI is stopped. Exact schedules follow the treating center’s current guideline and the patient’s response.

Testing is also appropriate when response slows, blood counts worsen, a prior low level rises, or clinical progression is suspected. A result that appears inconsistent should generally be repeated before a major treatment change, unless there are clear signs of accelerated or blast-phase disease requiring urgent action.

In Ph-positive ALL, BCR::ABL1 is measured during and after therapy as a marker of measurable residual disease. The timing, specimen preference, assay, and treatment thresholds differ from CML. Some ALL programs use an immunoglobulin/T-cell receptor next-generation sequencing assay in addition to fusion PCR because BCR::ABL1 can occasionally be present in a broader blood-cell clone rather than only the lymphoblast population.

The test is not a general leukemia screening test in a person with normal blood counts and no clinical indication. A diagnostic genetic test is most useful when ordered to answer a defined clinical question.

Test Methods and Specimens

Reverse-transcription polymerase chain reaction

RT-PCR converts BCR::ABL1 messenger RNA into DNA and amplifies the fusion sequence. A qualitative or multiplex assay can identify whether a common transcript is present at diagnosis. A quantitative real-time assay measures the amount relative to a control gene and reports BCR::ABL1 on the International Scale, abbreviated IS, for standard CML transcripts.

The International Scale allows results from calibrated laboratories to be compared more reliably. It sets the standardized baseline at 100% and defines major molecular response as 0.1% IS, a three-log reduction from that baseline. A laboratory uses a validated conversion factor or reference-standardized method to report on the scale.

Digital PCR can also quantify low transcript levels and is accepted in appropriate validated settings. Every report should state the transcript, control-gene adequacy, sensitivity, and whether the result is on the International Scale. Rare transcripts may require a customized assay and may not be reportable on the conventional IS.

Fluorescence in situ hybridization

FISH uses fluorescent probes for BCR and ABL1. Fusion signals indicate that the genomic regions have joined. It works on dividing or nondividing cells and can be performed on blood or marrow. A FISH test is useful for diagnosis, especially when chromosome analysis is negative or unavailable, but PCR is more sensitive for routine molecular monitoring.

Chromosome analysis

Karyotyping examines dividing marrow cells and directly shows the Philadelphia chromosome or a variant translocation. It also reveals additional chromosome abnormalities that can influence phase and prognosis. Its sensitivity is lower than PCR, and it requires viable cells. It remains valuable at diagnosis and when progression or treatment resistance raises concern for clonal evolution.

Next-generation sequencing and mutation assays

RNA sequencing can detect common and unusual BCR::ABL1 transcripts. DNA sequencing can identify genomic breakpoints, although large introns make coverage challenging. Separate ABL1 kinase-domain sequencing looks for resistance mutations after inadequate response or loss of response. Next-generation sequencing can detect low-level mutation mixtures more sensitively than traditional Sanger sequencing in many laboratories.

Peripheral blood is usually sufficient for routine CML quantitative PCR. Bone marrow is often used at diagnosis and when cytogenetics, phase assessment, or unexplained resistance is being evaluated. Blood and marrow PCR values can differ slightly, so trends are easiest to interpret when the same specimen type and standardized laboratory are used consistently.

No fasting is required. The patient should tell the clinical team about current TKI dose, missed doses, interacting medicines, supplements, recent interruptions, and pregnancy status because these details can explain a changing result and affect treatment decisions.

Understanding Diagnostic Results

A diagnostic report may say detected, not detected, atypical transcript, low-level positive, equivocal, or insufficient. The result must be linked to the method and clinical context.

ResultUsual interpretationNext consideration
BCR::ABL1 detectedThe fusion is present in the tested cells or RNA.Integrate with blood, marrow, lineage, and transcript type to classify CML or acute leukemia.
Not detectedNo targeted fusion was found at the assay’s sensitivity.Review specimen adequacy and whether rare transcripts or another myeloid neoplasm remain possible.
Atypical transcriptA rare BCR::ABL1 junction is present.Arrange a transcript-specific quantitative monitoring method.
Equivocal or failedThe assay cannot provide a reliable positive or negative call.Repeat with a better specimen or complementary method.

In a patient with classic CML morphology, detection establishes the defining molecular lesion. If chromosome analysis shows t(9;22) but PCR is negative, the laboratory should consider a rare transcript, sample problem, or unusual breakpoint. RNA sequencing or a broader qualitative assay may resolve the discrepancy.

A negative result does not rule out every myeloproliferative neoplasm. Polycythemia vera, essential thrombocythemia, primary myelofibrosis, chronic neutrophilic leukemia, and other disorders have different defining mutations. If CML remains strongly suspected, FISH, karyotyping, and rare-transcript testing may be needed.

A very low positive result near the detection limit should be confirmed and interpreted carefully. Technical contamination is uncommon in well-controlled laboratories but possible. More importantly, the diagnosis should not rest on a trace molecular signal without compatible clinical findings. Repeat testing on fresh blood or marrow and expert hematopathology review can clarify the situation.

In acute leukemia, a positive result requires lineage studies. Flow cytometry distinguishes B-lymphoblastic, myeloid, or mixed-phenotype disease. Blast percentage, cytogenetics, additional genomic changes, age, and clinical presentation guide classification and treatment. The p190 transcript is common in Ph-positive ALL but is not exclusive to it.

CML Molecular Monitoring and Milestones

Quantitative PCR turns CML response into a trend. The baseline diagnostic value is not necessarily 100% in an individual patient; the International Scale is a standardized reference. Each later result should be compared with prior values, treatment duration, and laboratory precision.

Important molecular response levels include:

  • BCR::ABL1 at or below 1% IS: approximately corresponds to complete cytogenetic response in many settings.
  • Major molecular response, MR3: at or below 0.1% IS.
  • MR4: at or below 0.01% IS with enough control-gene copies to support that sensitivity.
  • MR4.5: at or below 0.0032% IS with adequate assay sensitivity.
  • MR5: at or below 0.001% IS when technically supported.

An undetectable transcript is reported with the assay’s sensitivity, such as “not detected, MR4.5 sensitivity achieved.” The older phrase “complete molecular response” is discouraged because no blood assay can prove that all leukemia cells have disappeared.

Current European LeukemiaNet recommendations assess BCR::ABL1 IS at approximately 3, 6, and 12 months. A level at or below 10% at 3 months, at or below 1% at 6 months, and at or below 0.1% at 12 months represents favorable treatment progress in commonly used milestone frameworks. The 2025 recommendations emphasize interpreting milestones as gradients rather than automatic pass-or-fail rules. A single delayed value should be confirmed and considered with the starting risk, trend, treatment interruptions, toxicity, and the patient’s goals.

After major molecular response is stable, monitoring usually continues because loss of response can occur. A change from 0.02% to 0.04% is a doubling, but both values remain in MMR and may fall within biological or laboratory variation. A larger confirmed rise, loss of MMR, or abnormal blood counts deserves prompt review.

Deep molecular response is especially relevant for treatment-free remission. Selected adults who have received a TKI for several years and maintained MR4 or deeper for a sustained period may attempt discontinuation under a specialist protocol. They need access to highly sensitive standardized PCR and frequent monitoring, commonly monthly early after stopping. Roughly half of carefully selected patients remain in remission without treatment; most molecular recurrences happen in the first six months and usually respond when the TKI is restarted.

Treatment should never be stopped merely because one result is undetectable. Eligibility includes disease phase, transcript measurability, duration of therapy and deep response, adherence history, informed preference, and ability to complete rapid follow-up.

Rising Levels, Resistance, and Mutation Testing

A rising BCR::ABL1 level is a signal to investigate, not proof that the current TKI has failed. The first step is often to repeat the PCR and review the entire treatment history. Temporary interruptions, missed tablets, vomiting, dose reductions, and drug interactions can increase the level.

Acid-suppressing medicines, enzyme-inducing drugs, supplements, and food requirements affect some TKIs. Side effects may lead a patient to skip doses without telling the team. A nonjudgmental adherence conversation can identify a correctable cause and prevent an unnecessary drug change.

Resistance can also result from an ABL1 kinase-domain mutation. These mutations change the drug-binding region and reduce sensitivity to one or more TKIs. T315I is a well-known example that resists several ATP-binding TKIs but can be treated with agents active against that mutation, depending on indication and patient factors. Other mutations have different sensitivity patterns.

Kinase-domain mutation testing is considered when there is treatment failure, loss of a prior response, progression to advanced phase, or an unexplained significant increase. It is not routinely needed at initial chronic-phase diagnosis. The test must have enough BCR::ABL1 transcript to analyze; extremely low levels may be technically unsuitable.

A negative mutation test does not exclude resistance. Leukemia may use BCR::ABL1 amplification, altered drug transport, additional chromosome changes, or BCR::ABL1-independent pathways. Bone marrow, cytogenetics, broader sequencing, and a medication review may be necessary.

Urgent evaluation is warranted if rising molecular levels accompany increasing blasts, worsening anemia or thrombocytopenia, new basophilia, spleen enlargement, fever, bone pain, or rapidly changing symptoms. These can indicate accelerated biology or blast phase. Molecular change without clinical progression still deserves timely specialist review but is not usually an emergency by itself.

Treatment choices balance mutation sensitivity with cardiovascular, lung, liver, pancreatic, kidney, and metabolic risks. The most potent drug is not always the safest individual choice. Shared planning also considers fertility, pregnancy, dosing schedule, cost, prior toxicities, and the depth of response needed for a future treatment-free remission attempt.

BCR-ABL1 in Acute Leukemia

Ph-positive B-ALL is an acute leukemia in which lymphoblasts carry BCR::ABL1. It occurs in children and adults and becomes more common with age. Modern treatment combines a TKI with chemotherapy, corticosteroids, immunotherapy, or other leukemia-directed treatment. Regimens vary by age, fitness, protocol, and access.

Diagnostic testing should establish B-lineage, identify the transcript, and characterize additional abnormalities. Some cases have deletions or mutations involving IKZF1 and other genes that refine risk. Central nervous system prophylaxis remains part of treatment because systemic TKIs and immunotherapies do not eliminate all sanctuary-site risk.

Measurable residual disease is checked at defined points during therapy. A rapid and deep molecular response generally supports a better outlook, but PCR interpretation can be complex. In some patients, BCR::ABL1 is found in non-lymphoid cells as part of a multilineage clone. The fusion level may then remain detectable even when the lymphoblastic clone is cleared. Comparing fusion PCR with flow cytometry or an immunoglobulin/T-cell receptor clone assay can help.

BCR::ABL1-like, or Ph-like, ALL is different. It has a gene-expression pattern similar to Ph-positive ALL but lacks the BCR::ABL1 fusion. Some Ph-like cases have other ABL-class fusions that may respond to TKIs, while others activate JAK-STAT or different pathways. A negative BCR::ABL1 test therefore does not exclude Ph-like ALL and may lead to broader fusion testing.

Rare acute myeloid leukemias contain BCR::ABL1. Distinguishing de novo AML with the fusion from CML in blast phase requires prior blood counts, spleen findings, basophils, marrow morphology, transcript type, and additional genetics. This distinction should be made by an expert hematopathology team because classification and treatment differ.

Molecular follow-up after transplantation or other acute-leukemia therapy uses disease-specific schedules. Any reappearance or confirmed rise needs prompt review, but the threshold for action depends on assay, treatment phase, and whether other residual-disease markers agree.

Limitations and Questions to Ask

PCR is extremely sensitive but not infallible. Poor RNA quality, delayed specimen transport, insufficient white cells, an unrecognized rare transcript, or inadequate control-gene amplification can cause a false-negative or failed result. Results from different laboratories may vary even when both report on the International Scale, especially at very low levels.

A one-time percentage is less informative than a series from the same laboratory. The report should include the date, specimen, transcript, IS percentage, molecular response depth, and sensitivity. Keep copies or a simple graph so trends are visible during appointments.

Useful questions include:

  • Which transcript was identified at diagnosis?
  • Is this result reported on the International Scale?
  • What molecular response level has been reached?
  • Is the change large enough to exceed expected assay variation?
  • Should the PCR be repeated before treatment changes?
  • Were missed doses, interruptions, or interactions reviewed?
  • Is ABL1 kinase-domain mutation testing indicated?
  • Are bone marrow and chromosome studies needed now?
  • Does the result affect eligibility for treatment-free remission?
  • In acute leukemia, do PCR and other residual-disease tests agree?

The laboratory number should be discussed with the treating hematologist rather than interpreted as a general cancer percentage. A result of 1% IS does not mean 1% of the body contains leukemia, and a tenfold change at a very low level may have a different meaning from the same change above a treatment milestone.

Prompt contact with the care team is appropriate after a report of loss of MMR, a major confirmed rise, a new resistance mutation, or a failed test that delays an important decision. Seek urgent care for fever during treatment, unusual bleeding, severe weakness, breathing difficulty, confusion, rapidly worsening abdominal fullness, or neurologic symptoms.

The most useful BCR::ABL1 report connects a technically valid measurement to a timeline. Transcript type, treatment start date, TKI dose, previous values, blood counts, and clinical status turn the percentage into an actionable result.

References

Disclaimer

This article is educational and does not replace diagnosis, molecular interpretation, or treatment planning by a hematologist and qualified laboratory. BCR::ABL1 trends must be reviewed with transcript type, assay sensitivity, treatment duration, adherence, blood counts, marrow findings, and current guidelines. Do not stop or change a tyrosine kinase inhibitor based on a laboratory result without the treating team’s direction.

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