Next-generation sequencing for sensitive detection of BCR-ABL1 mutations relevant to tyrosine kinase inhibitor choice in imatinib-resistant patients

Abstract

In chronic myeloid leukemia (CML) and Philadelphia-positive (Ph+) acute lymphoblastic leukemia (ALL) patients who fail imatinib treatment, BCR-ABL1 mutation profiling by Sanger sequencing (SS) is recommended before changing therapy since detection of specific mutations influences second-generation tyrosine kinase inhibitor (2GTKI) choice. We aimed to assess i) in how many patients who relapse on second-line 2GTKI therapy next generation sequencing (NGS) may track resistant mutations back to the sample collected at the time of imatinib resistance, before 2GTKI start (switchover sample) and ii) whether low level mutations identified by NGS always undergo clonal expansion. To this purpose, we used NGS to retrospectively analyze 60 imatinib-resistant patients (CML, n = 45; Ph+ ALL, n = 15) who had failed second-line 2GTKI therapy and had acquired BCR-ABL1 mutations (Group 1) and 25 imatinib-resistant patients (CML, n = 21; Ph+ ALL, n = 4) who had responded to second-line 2GTKI therapy, for comparison (Group 2). NGS uncovered that in 26 (43%) patients in Group 1, the 2GTKI-resistant mutations that triggered relapse were already detectable at low levels in the switchover sample (median mutation burden, 5%; range 1.1%–18.4%). Importantly, none of the low level mutations detected by NGS in switchover samples failed to expand whenever the patient received the 2GTKI to whom they were insensitive. In contrast, no low level mutation that was resistant to the 2GTKI the patients subsequently received was detected in the switchover samples from Group 2. NGS at the time of imatinib failure reliably identifies clinically relevant mutations, thus enabling a more effective therapeutic tailoring.

Utilization of Next-Generation Deep Sequencing to Analyze BCR-ABL1 Kinase Domain Mutation for Imatinib-Resistant Chronic Myeloid Leukemia Patients in Vietnam

“…Therefore, NGS is suitable for sensitive detection of BCR-ABL1 relevant to TKI choice in imatinib-resistant patients and this is strongly supported by Soverini et al [29]. This study proved that NGS at the time of imatinib failure reliably identifies clinically relevant mutations, thus enabling a more effective therapeutic tailoring ( Figure 5) [29].…”

Managing chronic myeloid leukemia for treatment-free remission: a proposal from the GIMEMA CML WP

“…Therefore, the data are not sufficient to make suggestions regarding the choice of the TKI in the second-or subsequent-line setting, apart from the differential sensitivity in patients with the presence of BCR-ABL1 point mutations (Table 6). Because the detection of a mutation is the only factor that can specifically guide the choice of another TKI, 85 when a switch is planned for resistance/failure, a mutational analysis should always be performed using at least Sanger sequencing (SS), and whenever possible using next-generation sequencing (NGS), which is not yet widely available, but being more sensitive than SS [86][87][88][89][90] can avoid a wrong choice in up to 25% of cases. Whether mutational analysis should be performed in the case of nonoptimal response has been debated, but a consensus was not reached.…”

Novel Illumina‐based next generation sequencing approach with one‐round amplification provides early and reliable detection of BCR‐ABL1 kinase domain mutations in chronic myeloid leukemia

“…Next‐generation sequencing (NGS) as an alternative method can provide enhanced sensitivity and earlier mutation detection. The NGS platform used most frequently for BCR‐ABL1 KD sequencing is 454 from Roche (Basel, Switzerland) (Machova Polakova et al ., ; Baer et al ., ; Soverini et al ., ; Erbilgin et al ., ). The use of Ion Torrent (Thermo Fisher Scientific, Waltham, MA, USA) technology and the widely implemented Illumina (San Diego, CA, USA) platform has been reported by fewer authors to date (Eyal et al ., ; Deininger et al ., ; Kizilors et al ., ).…”