Sanger sequencing is the gold-standard method for detection of mutations in BCR–ABL1 in patients with chronic myeloid leukaemia (CML) undergoing treatment with BCR–ABL1 tyrosine-kinase inhibitors (TKIs), an approach recommended in most clinical practice guidelines. Now, the results of the NEXT-in-CML study provide a rationale for incorporating next-generation sequencing (NGS) into the guidelines.

In this multicentre study, the performance of NGS-based screening of loss-of-function BCR–ABL1 mutations was assessed prospectively in consecutive patients with CML and a ‘failure’ (n = 124) or ‘warning’ (n = 112) response to TKI treatment, defined according to the 2013 European LeukemiaNet criteria. BCR–ABL1 mutations were detected using Sanger sequencing and NGS in 60 and 111 patients (25% and 47%), respectively. Among 231 patients followed up, the detection of mutations informed decisions such as a change to another TKI (n = 85), allogeneic stem cell transplantation (n = 7) and an increased frequency of monitoring (n = 21).

Mutations detected using NGS only were referred to as low-level mutations. These mutations were related to resistance to imatinib or second-generation BCR–ABL1 TKIs in 69 of 80 patients. On-treatment monitoring demonstrated that the burden of low-level resistance mutations accumulates in patients who continue to receive or are switched to a TKI that is inactive against their specific mutation. Indeed, all of the 21 patients with a warning response whose treatment was not changed despite harbouring low-level resistance mutations subsequently had a failure response.

In summary, these results indicate that the clones that will ultimately result in drug resistance and drive disease progression are not always detectable using Sanger sequencing. The use of NGS as a new gold standard for monitoring patients with CML receiving BCR–ABL1 TKIs is worth considering.