New Pattern of Emerging Somatic Mutations in Optimal Responders Following Tyrosine Kinase Inhibitor Therapy in Chronic Myeloid Leukemia Patients

Tyrosine kinase inhibitors (TKIs) significantly improved outcomes for patients with chronic myeloid leukemia (CML), enabling optimal treatment responses and near-normal life expectancy. Despite optimal responses, clonal evolution (CE) in Philadelphia chromosome-negative (Ph-negative) cells occurs in 10–15% of optimal responders, typically detected via cytogenetics. The mutational dynamics underlying this phenomenon remain poorly understood. This study investigated mutational kinetics using targeted next-generation sequencing (NGS) of 40 leukemia-associated genes. A total of 119 serial peripheral blood samples from 51 newly diagnosed chronic-phase CML patients, with over 12 months of follow-up, were analyzed using single-molecule molecular inversion probe (smMIP)-based NGS. Remarkably, 24% of patients developed new somatic mutations during follow up, primarily in DNMT3a , TET2 and ASXL1. These mutations were absent at diagnosis and exhibited a median doubling time of 68 days. Notably, these mutations emerged despite patients maintaining deep molecular responses and without evidence for cytogenetic evolution. Our results highlight an ongoing clonal evolution in the Ph-negative clone suggesting the potential utility of longitudinal NGS every 6–7 months as an alternative to cytogenetic monitoring in CML.