Next-generation sequencing for BCR-ABL1 kinase domain mutation testing in patients with chronic myeloid leukemia: a position paper

Abstract

BCR-ABL1 kinase domain (KD) mutation status is considered to be an important element of clinical decision algorithms for chronic myeloid leukemia (CML) patients who do not achieve an optimal response to tyrosine kinase inhibitors (TKIs). Conventional Sanger sequencing is the method currently recommended to test BCR-ABL1 KD mutations. However, Sanger sequencing has limited sensitivity and cannot always discriminate between polyclonal and compound mutations. The use of next-generation sequencing (NGS) is increasingly widespread in diagnostic laboratories and represents an attractive alternative. Currently available data on the clinical impact of NGS-based mutational testing in CML patients do not allow recommendations with a high grade of evidence to be prepared. This article reports the results of a group discussion among an ad hoc expert panel with the objective of producing recommendations on the appropriateness of clinical decisions about the indication for NGS, the performance characteristics of NGS platforms, and the therapeutic changes that could be applied based on the use of NGS in CML. Overall, these recommendations might be employed to inform clinicians about the practical use of NGS in CML.

Chronic Myeloid Leukemia, Version 2.2021, NCCN Clinical Practice Guidelines in Oncology

“…Next generation sequencing (NGS) allows for the detection of low-level BCR-ABL1 kinase domain mutations as well as resistance mutations in genes other than BCR-ABL1 that may confer resistance to TKIs or portend disease progression. [62][63][64][65] In a recent prospective, multicenter study (NEXT-in-CML) that assessed the feasibility of NGS in detection of low-level mutations in 236 consecutive patients with CML and inadequate response to TKI therapy, NGS was more effective than conventional Sanger sequencing in the detection of low-level mutations. 65 Prospective monitoring of mutation kinetics demonstrated that TKI-resistant low-level mutations are invariably selected if the patients are not switched to another TKI or if they are switched to an inappropriate TKI or TKI dose.…”

Molecular Testing in CML between Old and New Methods: Are We at a Turning Point?

“…Such patients may have acquired point mutations in the kinase domain (KD) of BCR-ABL1 that impair TKI binding. Detailed lists of mutations conferring resistance to each TKI are currently available [5]. Although other mechanisms of resistance have been reported, BCR-ABL1 KD mutations are, at present, the only "actionable" one, since the detection of a TKI-resistant mutation mandates a change of therapy and the type of mutation may guide the selection of the second-or subsequent-line TKI [6].…”

RNA sequencing: new technologies and applications in cancer research

“…Computational analysis tools for RNA sequencing have dramatically increased during the past decade. The choice of a particular tool should be based on the purpose and accuracy of application [29][30][31]. A general RNA sequencing data analysis process involves the quality control of raw data, read alignment and transcript assembly, expression quantification and differential expression analysis (Fig.…”