Ultra-Deep Sequencing Leads to Earlier and More Sensitive Detection of Known or Novel Mutations of BCR-ABL1 in Chronic Myeloid Leukemia

Detection of BCR-ABL1 mutations that inhibit tyrosine kinase inhibitors is important for the treatment of CML patients. Sanger sequencing (SS) technique is considered the gold standard for mutation detection in a clinical laboratory. We analyzed 40 clinical samples from 22 CML patients with TKI resistance by ultra-deep sequencing (UDS) and compared the results with classical SS-based tests. UDS facilitates the detection of low levels of mutations (<20% allele frequencies) that SS does not detect. In subgroups of cases with multiple mutations, UDS was also able to determine whether two mutations were on same BCR-ABL1 allele (compound) or not (polyclonal). We found a pair of compound mutations unreported: F359C/E450 which confer high-level resistance to first-generation TKI imatinib, second-generation TKIs dasatinib and nilotinib, third-generation TKI ponatinib and a new TKI GZD824. UDS provides a reliable method for identifying low levels of BCR-ABL1 mutations.