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Rare BCR::ABL1 Fusion Gene in Chronic Myeloid Leukaemia: A Case Report

  • Ruddy Dalfeor1,
  • Danilo de Oliveira Tavares1,
  • Israel Bendit2,
  • Luciana Nardinelli2,
  • Daniel Goldberg Tabak1 and
  • Robert Peter Gale3,* 
 Author information
Oncology Advances   2024;2(1):52-54

doi: 10.14218/OnA.2023.00040


Chronic myeloid leukemia with a BCR::ABL1 b2a3 transcript is difficult to detect by conventional polymerase chain reaction (PCR). This can result in an incorrect diagnosis. We report a man with typical features of chronic myeloid leukemia but with a negative conventional PCR test for BCR::ABL1 in whom we identified a BCR::ABL1 fusion gene by fluorescence in situ hybridization and PCR with custom BCR and ABL1 primers.


Chronic lymphocytic leukemia, BCR::ABL1, Polymerase chain reaction, Ph-chromosome


Three intronic chromosome breakpoint regions in BCR, when joined with ABL1, are associated with the development of chronic myeloid leukemia (CML) including: (1) major (M-BCR); minor (m-BCR); and (3) micro (u-BCR). The M-BCR region consists of BCR introns downstream of exon 13 (e13, previously b2) or 14 (e14, previously b3) linked to exon 2 (a2) of ABL1. BCR::ABL1 fusions e13a2 (b2a2) and e14a2 (b3a2) result in a P210BCR::ABL1 chimeric protein. m-BCR and u-BCR have uncommon breakpoints in the intronic region between BCR exon 2 and exons 19 and 20 which encode 190-kDaBCR::ABL1 (e1a2) and 230-kDaBRC::ABL1 (e19a2), resulting in P190BCR::ABL1 and P230BCR::ABL1. Several atypical BCR::ABL1 transcripts (e1a3, e13a3, e14a3, e19a3, e6a2 and e8a2) are reported resulting from breakpoints outside ABL1 intron 1 or BCR introns 1, 13 or 14 and may be missed using standard BCR and ABL1 primers in polymerase chain reaction (PCR).

We report the case of a young man with clinical and laboratory features of CML and a BCR::ABL1 b2a3 transcript. Despite a negative PCR test for BCR::ABL1 transcripts using conventional BCR and ABL1 primers a translocation was detected by fluorescence in situ hybridization (FISH) and confirmed using novel PCR primers. He responded rapidly to nilotinib.

Case report

In 2015 a routine blood test of an asymptomatic 19-year-old man showed leukocytosis and thrombocytosis; exact values are unknown. He was referred to a hematologist but demurred. In 2017, a blood study performed in an emergency department because of ethanol intoxication showed a hemoglobin concentration of 155 g/L, white blood cell (WBC) and platelet concentrations of 17 × 10E+9/L and 475 × 10E9/L with 72% granulocytes. Again, there was no follow-up. Six months later he saw a physician complaining of nausea, weight loss and palpitations. There was no lymph node, spleen or liver enlargement on physical exam. The hemoglobin concentration was 145 g/L, WBC concentration, 15.9 × 10E+9/L with 67% granulocytes and platelets, 599 × 10E+9/L. A computed tomography scan showed no abnormalities. He refused a bone marrow examination and no cytogenetic studies were done. A multiplex qualitative and quantitative PCR test using e14a2 and e13a2 primers for BCR::ABL1 transcripts was negative. FISH analyses with BCR and ABL1 probes were consistent with t(9; 22), leading to a presumptive diagnosis of CML. He received nilotinib, 800 mg/d. An RNA sample using an e13a3 qualitative primer confirmed CML. After 1 month, his hemoglobin concentration and WBC and platelet concentrations were normal. A bone marrow exam in late 2018 revealed a 46,XY karyotype in 20 metaphases studied. FISH was not repeated. Two years after starting nilotinib, he had a hemoglobin concentration of 151 g/L and WBC and platelet concentrations of 5.9 × 10E+9/L and 276 × 10E+9/L with 52% granulocytes. In early 2019, PCR was done using primers designed to detect the b2a3 transcript. A BCR exon 13 region-targeting forward primer (5′-CATCCGGGAGCAGCAGAAGAA-3′) and ABL1 exon a3 region-targeting reverse primer (5′-GTGTTTCTCCAGACTGTTGGCT) were used. A reverse transcription PCR test was negative indicating a > 4.5-log reduction in BCR::ABL1 transcripts on the International Scale (<MR4.5). The subject is well without symptoms or adverse events from nilotinib.


BCR::ABL1 transcripts with intronic breakpoints downstream of ABL a2 are rare. ABL a2 encodes part of Src homology 3 (SH3) domain which inhibits the SH1 kinase domain required for the activation of signal transducer and activator of transcription-5 by P210BCRABL1. This might result in a milder leukemia phenotype. Although the ABL a3 breakpoint does not affect the ATP/imatinib binding site sequence it potentially alters the tertiary structure of P210BCR::ABL1 and could increase (tyrosine kinase-inhibitor) TKI binding. We are testing this hypothesis by computer modeling and in vitro experiments.

There is considerable controversy regarding whether the specific BCR::ABL1 transcript correlates with the prognosis of people with CML, especially those receiving TKIs. Several studies have reported correlations between BCR::ABL1 transcript type and response to TKIs.1–15 We recently reported that the e14a2 BCR::ABL1 transcript was associated with a higher rate of therapy-free remission.13 Another study reported that the e14a2 transcript correlated with an increased response to imatinib, and conversely, the e13a2 transcript was associated with a worse response.14 A 3rd study reported higher rates of a 4.5-log reduction in BCR::ABL1 transcripts, better event-free survival and less risk of transformation to the acute phase in subjects with an e14a2 than in those with an e13a2 transcript, regardless of initial TKI therapy.15 Lower response rates to TKIs were reported in subjects with an e13a2 transcript. A registry of 45,503 newly diagnosed patients from 45 countries suggested that the transcript type may correlate with therapy-response and the likelihood of therapy-free remission.16 Another study of subjects receiving imatinib found that those with atypical BCR::ABL1 transcripts are younger, respond better to TKI therapy and have a better prognosis than those with CML with typical BCR breakpoints. Structural and laboratory analyses of the mechanism of action of TKIs in this setting are underway.

In conclusion, individuals with clinical and laboratory features of CML and a BCR::ABL1 b2a3 transcript may not be detected by routine PCR testing with conventional BCR and ABL1 primers. Cytogenetic FISH or PCR testing with specialized primers should be performed for individuals with suspected CML and a negative conventional PCR-test for BCR::ABL1.



chronic myeloid leukemia


fluorescence in situ hybridization


polymerase chain reaction


tyrosine kinase-inhibitors


white blood cell



RPG acknowledges support from the National Institute of Health Research (NIHR) Biomedical Research Centre funding scheme.

Ethical statement

The study was approved by the Ethics Committees of the respective institutions consistent with precepts of the Declaration of Helsinki (2013). The subjects gave written informed consent to publish the article.

Data sharing statement

All data are in the typescript.



Conflict of interest

RPG is a consultant to Antengene Biotech LLC, Ascentage Pharma Group and NexImmune, Inc.; Medical Director, FFF Enterprises, Inc.; A speaker for Janssen Pharma and Hengrui Pharma; Board of Directors: Russian Foundation for Cancer Research Support; and Scientific Advisory Boards, Nanexa AB and StemRad Ltd. The other authors have no conflict of interest to declare.

Authors’ contributions

RD and DGT conceived the typescript. DdOT, IB and LN did the laboratory studies. RPG revised the typescript. The authors approved the content, accepted responsibility for the content and agreed to submit the typescript for publication.


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  • Oncology Advances
  • eISSN 2996-3427
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Rare BCR::ABL1 Fusion Gene in Chronic Myeloid Leukaemia: A Case Report

Ruddy Dalfeor, Danilo de Oliveira Tavares, Israel Bendit, Luciana Nardinelli, Daniel Goldberg Tabak, Robert Peter Gale
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