Lab Med Online.  2023 Oct;13(4):370-374. 10.47429/lmo.2023.13.4.370.

A Case of Chronic Myeloid Leukemia with Micro BCR::ABL1 Rearrangement: Precaution in Reverse Transcription PCR to Prevent False Negativity

  • 1Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul
  • 2Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, Korea


We report a patient negative for BCR::ABL1 in qualitative reverse transcription (RT)-PCR but subsequently reported to be positive for t(9;22) (q34;q11.2) in conventional karyotyping. The patient was finally diagnosed with micro-type chronic myeloid leukemia after re-examining RT-PCR and performing targeted RNA sequencing. Through this case, we highlight the risk of false negativity when interpreting RT-PCR to detect microtype fusion. Upon re-examining RT-PCR results, the patient’s internal control band was thicker than others. After extending the electrophoresis run time, a 911-bp internal control band and a target band around the level of 1.0 kb were separated. We confirmed a fusion breakpoint (BCR exon 19 and ABL1 exon 2) by targeted RNA sequencing, and it corresponds to 1,012 bp-sized e19a2 (c3a2) type among four micro-type fusion transcripts that RT-PCR HemaVision ® kit M6B can detect.


Chronic myeloid leukemia; BCR::ABL1; p230; Thrombocytosis; False negative


  • Fig. 1 Presentation of (A) peripheral blood smear (×200 magnification) and (B) a bone marrow aspiration at initial diagnosis (×200 magnification).

  • Fig. 2 Qualitative BCR::ABL1 RT-PCR results using a HemaVision® kit (DNA Technology, Aarhus, Denmark). (A) Gel electrophoresis of the M6B lane at initial diagnosis. The index patient’s IC band (yellow arrow) appeared thicker than that of other patients (triangles) without the BCR::ABL1 transcript. (B) Repeated gel electrophoresis with a prolonged run time of up to 50 min revealed a separate band with a larger molecular size (1,012 bp, yellow arrow) than the IC band (911 bp). Abbreviations: L, molecular size ladder (3.0 kb, 2.0 kb, 1.5 kb, 1.0 kb, 800 bp, 600 bp, 500 bp, 400 bp, 300 bp, 200 bp, and 100 bp size from the top); Pt, index patient; NTC, no template control; PC, e13a2 type positive control with 472 bp size.

  • Fig. 3 Targeted RNA sequencing analysis (FusionPlex Pan-Heme Panel; ArcherDX, Boulder, CO, USA) confirmed breakpoints in BCR exon 19 and ABL1 exon 2. The fusion reads of BCR::ABL1 numbered 634 (64.63 % of total reads). Breakpoint visualization was performed with the Integrative Genomics Viewer (Broad Institute, Cambridge, MA, USA).


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