The strategies here reported demonstrate clearly that the study of MRD in CML by the BCR-ABL1 DNA-based patient-specific probe is feasible: FISH and MinION steps, respectively, together with ddPCR analysis, greatly reduce the complexity that has impeded the use of “personalized monitoring” of CML in clinical practice. Here, BCR is linked to chronic myelogenous leukemia, BCR-ABL1 positive.