Next‐generation sequencing improves BCR‐ABL1 mutation detection in Philadelphia chromosome‐positive acute lymphoblastic leukaemia

Abstract

BCR-ABL1 kinase domain mutation testing in tyrosine kinase inhibitor (TKI)-resistant Philadelphia chromosome-positive (Ph+) acute lymphoblastic leukaemia (ALL) patients is routinely performed by Sanger sequencing (SS). Recently, next-generation sequencing (NGS)-based approaches have been developed that afford greater sensitivity and straightforward discrimination between compound and polyclonal mutations. We performed a study to compare the results of SS and NGS in a consecutive cohort of 171 Ph+ ALL patients. At diagnosis, 0/44 and 3/44 patients were positive for mutations by SS and NGS respectively. Out of 47 patients with haematologic resistance, 45 had mutations according to both methods, but in 25 patients NGS revealed additional mutations undetectable by SS. Out of 80 patients in complete haematologic response but with BCR-ABL1 ≥0Á1%, 28 (35%) and 52 (65%) were positive by SS and NGS respectively. Moreover, in 12 patients positive by SS, NGS detected additional mutations. NGS resolved clonal complexity in 34 patients with multiple mutations at the same or different codons and identified 35 compound mutations. Our study demonstrates that, in Ph+ ALL on TKI therapy, NGS enables more accurate assessment of mutation status both in patients who fail therapy and in patients with minimal residual disease above 0Á1%.

Detection of kinase domain mutations in BCR::ABL1 leukemia by ultra-deep sequencing of genomic DNA

“…We also studied the impact of KD BCR::ABL1 mutations before starting the treatment. In our cohort, 2 out of 50 newly-diagnosed B-ALL patients showed mutations, in agreement with a recent study by Soverini et al 11 , who found 3 mutated patients out of 44 patients. This frequency increased when other more sensitive methods have been used 21 , 22 .…”

“…2 D). Most of the mutations observed were in failure and relapse stages for CML and B-ALL patients, respectively, as previously reported 11 , 19 .…”

“…Ultra-deep sequencing (UDS) by NGS can be used to track the mutation status along TKI treatment due to its high sensitivity. It can be used to discern between compound mutations or the presence of different subclones in case of multiple mutation findings 11 , 12 . Other techniques with similar sensitivity have served to confirm mutations in BCR::ABL1 such as digital PCR (dPCR) and allele-specific oligonucleotides-PCR (ASO-PCR) 13 , 14 .…”

Detection of Kinase Domain Mutations in BCR-ABL1 Leukemia by Ultra-deep Sequencing of Genomic DNA

“…2D). Most of the mutations observed were in failure and relapse stages for CML and B-ALL patients, respectively, as previously reported 11,19 .…”

“…Ultra-deep sequencing (UDS) by NGS can be used to track the mutation status along TKI treatment due to its high sensitivity. It can be used to discern between compound mutations or the presence of different subclones in case of multiple mutation ndings 11,12 . Other techniques with similar sensitivity have served to con rm mutations in BCR-ABL1 such as digital PCR (dPCR) and allelespeci c oligonucleotides-PCR (ASO-PCR) 13,14 .…”