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

Abstract

This work investigated patient-specific genomic BCR-ABL1 fusions as markers of measurable residual disease (MRD) in chronic myeloid leukemia, 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 a molecular relapse-free survival (MRFS) of 80% and 100%, respectively, compared to 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.

Minimal residual disease monitoring via AML1-ETO breakpoint tracing in childhood acute myeloid leukemia

“…To overcome these drawbacks of these methods, we employed ddPCR to achieve accurate and sensitive detection of the AE fusion gene in childhood AML. This technology allows for the absolute quantification from only a small amount of DNA and exhibits excellent performance on detecting MRD in other diseases [ 15 , 16 , 17 , 18 ]. The DNA-based ddPCR monitoring method evaluated in this study was designed to target the AE fusion gene, which is not affected by the clonal evolution of gene mutations and AML progression.…”

Impact of BCR::ABL1 transcript type on RT-qPCR amplification performance and molecular response to therapy

“…ddPCR was performed using EAC-based BCR::ABL1 and ABL1 assays according to locally established procedures [ 19 ], or with the commercially available QXDx BCR::ABL1 %IS kit (BioRad, Hercules, California, USA), according to the manufacturer’s instructions. Both cell line and plasmid material were tested, however as ddPCR experiments can become saturated at very high levels of template copy number, only 4/6 plasmid dilutions were used for ddPCR experiments, spanning a concentration range of approximately 1 × 10 1 to 1 × 10 4 copies/µL.…”

“…Patient samples were analysed using RT-qPCR assays for BCR::ABL1 and GUSB [ 6 ]. The same samples were also analysed using an in-house RT-ddPCR for BCR::ABL1 [ 19 ]. The BCR::ABL1 assays used for RT-qPCR and ddPCR both co-amplified e13a2 and e14a2.…”

Definition, Epidemiology, Pathophysiology, and Essential Criteria for Diagnosis of Pediatric Chronic Myeloid Leukemia

“…gender, age, height, bodyweight in correlation to the TKI dose administered [108], -identification of mutations in the BCR-ABL1 kinase domain in patients with CML-AP and CML-BP, -identification of the BCR-ABL1 breakpoint on a genomic (DNA) level [63,66,[109][110][111][112],…”