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Chronic myelogenous leukemia

Analysis of chronic myeloid leukaemia during deep molecular response by genomic PCR: a traffic light stratification model with impact on treatment-free remission


This work investigated patient-specific genomic BCR-ABL1 fusions as markers of measurable residual disease (MRD) in chronic myeloid leukaemia, with a focus on relevance to treatment-free remission (TFR) after achievement of deep molecular response (DMR) on tyrosine kinase inhibitor (TKI) therapy. DNA and mRNA BCR-ABL1 measurements by qPCR were compared in 2189 samples (129 patients) and by digital PCR in 1279 sample (62 patients). A high correlation was found at levels of disease above MR4, but there was a poor correlation for samples during DMR. A combination of DNA and RNA MRD measurements resulted in a better prediction of molecular relapse-free survival (MRFS) after TKI stop (n = 17) or scheduled interruption (n = 25). At 18 months after treatment cessation, patients with stopped or interrupted TKI therapy who were DNA negative/RNA negative during DMR maintenance (green group) had an MRFS of 80% and 100%, respectively, compared with those who were DNA positive/RNA negative (MRFS = 57% and 67%, respectively; yellow group) or DNA positive/RNA positive (MRFS = 20% for both cohorts; red group). Thus, we propose a “traffic light” stratification as a TFR predictor based on DNA and mRNA BCR-ABL1 measurements during DMR maintenance before TKI cessation.

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Fig. 1: Comparison of BCR-ABL1RelDg data at mRNA and DNA levels.
Fig. 2: Correlation of the individual parameter estimates of mRNA and DNA BCR-ABL1 samples using the bi-exponential mixed effects models.
Fig. 3: Effects of covariates on the individual parameter estimates of mRNA and DNA BCR-ABL1 samples using the bi-exponential mixed effects models.
Fig. 4: Rates of DMR maintenance and molecular relapse after TKI cessation/interruption in three groups of patients that were divided according to DNA and mRNA BCR-ABL1RelDg MRD pattern evaluated by the deterministic model in samples measured by ddPCR before TKI stop/interruption in EURO-SKI and INTReg patients.
Fig. 5: Probability of molecular relapse-free survival after TKI cessation/interruption according to traffic light stratification model.


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This work was funded by the Project Grants #15–31540A and #16–30186A from the Czech Health Research Council and by the European Treatment and Outcome study (EUTOS) for CML. The authors thank for the institutional support #00023736 (Institute of Hematology and Blood Transfusion) and #00064203 (University Hospital Motol) from Ministry of Health of the Czech Republic and the Czech Leukaemia Study Group for Life. This work was further supported by ERA-Net ERACoSysMed JTC-2 project “prediCt” (project number 031L0136A) to IR. We would like to thank to Dr. Milada Småstuen (Oslo Metropolitan University) for the consolations on statistical analysis. The authors are grateful to the patients for providing their samples for this study.

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Authors and Affiliations



KMP designed the study, interpreted results and wrote the paper; HZ and EM performed ddPCR and qPCR analyses, analyzed data and provided data management; JZ supervised DNA PCR analysis, contributed to the writing of the paper; LH performed LD-PCR and characterized DNA BCR-ABL1 fusions; AG and IG performed statistical analysis using bi-exponential mixed effect models, interpreted results and reviewed the paper; JK performed bioinformatics of NGS data, designed primers and probes; PP performed statistical analysis; HK, MSM and DS supervised patient’s visits, evaluated and provided clinical data; AB and VP performed NGS analysis; TJ performed qPCR analysis; DZ and JM supervised patient’s visits, evaluated and provided clinical data; TE designed probes for NGS analysis; FXM and SS supervised the EURO-SKI study; IR supervised statistical analysis, advised the concept of the paper and critically reviewed the paper; NCPC contributed to the concept of the paper and the paper writing; AH supervised the work; all authors critically reviewed and approved the paper.

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Correspondence to Katerina Machova Polakova.

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Conflict of interest

KMP, TE, NCPC and AH received support by Novartis through the European Treatment and Outcome Study (EUTOS) for CML. The authors declare that they have no conflict of interest.

Ethical approval

This work was conducted in accordance with the principles of the Declaration of Helsinki and was approved by the Ethics Committees of the Institute of Hematology and Blood Transfusion, Prague and Faculty Hospital Brno.

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All patients provided written informed consent for the use of their samples for this research.

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Machova Polakova, K., Zizkova, H., Zuna, J. et al. Analysis of chronic myeloid leukaemia during deep molecular response by genomic PCR: a traffic light stratification model with impact on treatment-free remission. Leukemia 34, 2113–2124 (2020).

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