Dissection of subclonal evolution by temporal mutation profiling in chronic lymphocytic leukemia patients treated with ibrutinib

The Bruton's tyrosine kinase (BTK) inhibitor ibrutinib is inducing durable responses in chronic lymphocytic leukemia (CLL) patients with refractory/relapsed disease or with TP53 defect, with BTK and phospholipase C gamma 2 (PLCG2) mutations representing the predominant mechanisms conferring secondary ibrutinib resistance. To understand the landscape of genomic changes and the dynamics of subclonal architecture associated with ibrutinib treatment, an ultra‐deep next‐generation sequencing analysis of 30 recurrently mutated genes was performed on sequential samples of 20 patients, collected before and during single‐agent ibrutinib treatment. Mutations in the SF3B1, MGAand BIRC3 genes were enriched during ibrutinib treatment, while aberrations in the BTK, PLCG2, RIPK1, NFKBIE and XPO1 genes were exclusively detected in posttreatment samples. Besides the canonical mutations, four novel BTK mutations and three previously unreported PLCG2 variants were identified. BTK and PLCG2 mutations were backtracked in five patients using digital droplet PCR and were detectable on average 10.5 months before clinical relapse. With a median follow‐up time of 36.5 months, 7/9 patients harboring BTK mutations showed disease progression based on clinical and/or laboratory features. In conclusion, subclonal heterogeneity, dynamic clonal selection and various patterns of clonal variegation were identified with novel resistance‐associated BTK mutations in individual patients treated with ibrutinib. What's new? Although the Bruton's tyrosine kinase (BTK) inhibitor, ibrutinib has revolutionized the treatment of chronic lymphocytic leukemia, 20% of patients still show disease progression. Comprehensive characterisation of mechanisms underlying ibrutinib resistance and the related changes in the subclonal architecture induced by the selective pressure of the treatment may usher in new clinical advances. This time‐resolved ultra‐deep genomic scrutiny of mutation target genes reveals unique patterns of highly dynamic clonal variegation associated with BTK inhibition and identifies novel resistance‐associated BTK mutations in individual patients. Furthermore, evidence suggests that sensitive molecular monitoring of treatment response can facilitate the early detection of impending relapse.