What does the BCR/ABL (Breakpoint Cluster Region/Abelson) Qualitative by RT-PCR (Reverse Transcription Polymerase Chain Reaction) test detect?

BCR/ABL Qualitative by RT-PCR Test Detection

BCR/ABL Qualitative by RT-PCR is the mandatory test for detecting the BCR::ABL1 fusion gene transcripts resulting from the Philadelphia chromosome translocation t(9;22), which is essential for diagnosing chronic myeloid leukemia (CML) and Philadelphia chromosome-positive acute lymphoblastic leukemia (Ph+ ALL). 1

What the Test Detects

The BCR/ABL Qualitative RT-PCR test specifically detects:

• The presence of BCR::ABL1 fusion transcripts resulting from the reciprocal translocation between chromosomes 9 and 22 [t(9;22)(q34;q11)]
• The exact transcript type (isoform) of the BCR::ABL1 fusion gene, including:
  • Common transcripts: e13a2 (b2a2) and e14a2 (b3a2), which encode the p210 fusion protein typical in CML
  • Less common transcripts: e1a2 (encoding p190, more common in Ph+ ALL), e19a2, e6a2, e8a2, e13a3, e14a3, and other rare variants 1

Clinical Significance

This test is crucial for:

1. Confirming diagnosis: It's the only routine technique that can determine the exact BCR::ABL1 transcript type 1
2. Treatment planning: Different transcript types may respond differently to tyrosine kinase inhibitors (TKIs) 1
3. Establishing baseline: Provides a reference point for subsequent monitoring of treatment response 1
4. Enabling monitoring: Identification of the specific transcript type allows for appropriate quantitative monitoring during treatment 1

Technical Aspects

• The test uses reverse transcription polymerase chain reaction (RT-PCR) to detect BCR::ABL1 mRNA transcripts in peripheral blood or bone marrow
• It can detect one CML cell in a background of 100,000 or greater normal cells 1
• Results are reported qualitatively (positive or negative) and specify the transcript type detected 1
• The test is more sensitive than cytogenetics or FISH for detecting the BCR::ABL1 fusion 1

Important Considerations

• For centers using RT-PCR as the primary screening method, it's essential that the methodology detects both typical and atypical BCR::ABL1 variants 1
• Screening only for transcripts that encode p210 or p210 plus p190 BCR::ABL1 is considered poor practice and may result in up to 2% of CML cases being misdiagnosed 1
• Identification of atypical BCR::ABL1 variants may be challenging, as there are no standardized commercial tests available to detect most rare isoforms 1
• The test should be performed prior to starting treatment to facilitate accurate assessment of measurable residual disease during therapy 1

Pitfalls to Avoid

• False negatives: May occur with atypical transcripts if limited primer sets are used 1, 2
• Inadequate sampling: Insufficient cell numbers can lead to false negatives 3
• Delayed processing: Samples should be processed within 24-36 hours to prevent RNA degradation 3
• Nested RT-PCR: Should generally be avoided due to risk of artifacts and contamination 1

For comprehensive diagnostic workup of suspected CML, qualitative RT-PCR should be combined with cytogenetics to detect additional chromosomal abnormalities and/or FISH to confirm the presence of the BCR::ABL1 fusion 1.