As participants in the exploratory investigations of the PhilosoPhi34 study that investigates the efficacy of nilotinib 300 mg BID in depleting bone marrow (BM) leukemic stem cells (CD34+/linPh+) in newly diagnosed chronic-phase (CP) CML patients at specific time points of treatment [13], we have analyzed a cohort of 82 CML patients with the goal to identify the patient-specific rearrangement of the BCR/ABL1 in order to evaluate the minimal residual disease (MRD) in the Ph+ CML patients after 6 or 12 months of nilotinib treatment. The gene discussed is BCR; the disease is chronic myelogenous leukemia, BCR-ABL1 positive.