Validation of a novel NGS based BCR::ABL1 kinase domain mutation detection assay in Indian cohort.

Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN: 2045-2322 (Electronic) Linking ISSN: 20452322 NLM ISO Abbreviation: Sci Rep Subsets: MEDLINE

Original Publication: London : Nature Publishing Group, copyright 2011-

Fusion Proteins, bcr-abl*/genetics ; High-Throughput Nucleotide Sequencing*/methods ; Leukemia, Myelogenous, Chronic, BCR-ABL Positive*/genetics ; Mutation*; Adolescent ; Adult ; Aged ; Female ; Humans ; Male ; Middle Aged ; Young Adult ; Cohort Studies ; DNA Mutational Analysis/methods ; India ; Protein Kinase Inhibitors/therapeutic use

The efficacy and treatment outcome of a CML patient are heavily dependent on BCR::ABL1 kinase domain (KD) mutation status. Next-generation sequencing technology is a bright alternative to the previously used sanger sequencing method due to its global presence in diagnostic setups, massive parallel sequencing ability, and far better sensitivity. In the present study, we have demonstrated a new protocol for kinase domain mutation analysis using the next-generation sequencing (NGS) method using the ion torrent sequencing platform. This protocol uses RNA as the starting material, followed by nested PCR to amplify the fusion transcript, which is subsequently used as a template for NGS. Initial validation and comparison of this assay with the sanger sequencing (SS) method yielded 95.23% agreement. CML samples (n = 121) with a failure to TKI response were subjected to this newly developed NGS-based assay to detect KD mutations, from which samples were found to have mutations with a sensitivity ranging from 2.32 to 93.41%. A total of 34.71% of samples (n = 42) were found to be positive for one or more KD mutations, whereas 65.29% of samples (n = 81) were found to be negative. Nine samples out of 42 positive samples, i.e., 21.42%, were found to have compound mutations. This is one of the first studies from India, which includes more than 160 samples and is analyzed by the NGS approach for KD mutation analysis.
(© 2024. The Author(s).)

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EC 2.7.10.2 (Fusion Proteins, bcr-abl)
0 (Protein Kinase Inhibitors)
EC 2.7.11.1 (BCR protein, human)
EC 2.7.10.2 (ABL1 protein, human)

Date Created: 20240708 Date Completed: 20240708 Latest Revision: 20240802

20240802

PMC11231265

10.1038/s41598-024-66310-8

38977756