Rapid Capture Next-Generation Sequencing in Clinical Diagnostics of Kinase Pathway Aberrations in B-Cell Precursor...

Area of Science:

• Hematology
• Oncology
• Genomics

Background:

• Ph-like B-cell precursor acute lymphoblastic leukemia (BCP-ALL) often harbors kinase and cytokine receptor rearrangements.
• These genetic alterations are potential targets for tyrosine kinase inhibitor (TKI) therapy.
• Accurate and rapid diagnostics are crucial for timely treatment initiation in high-risk BCP-ALL.

Purpose of the Study:

• To develop a rapid, PCR-independent next-generation sequencing (NGS) diagnostic panel for kinase pathway aberrations in BCP-ALL.
• To identify unknown 5' fusion partner genes and map genomic breakpoints.
• To assess the utility of the panel in detecting rearrangements in minimal residual disease (MRD)-high risk BCP-ALL.

Main Methods:

• Development of a custom NGS enrichment capture panel targeting recurrent genomic alterations in BCP-ALL.
• Application of a standardized bioinformatics algorithm for data analysis.
• Testing the panel on BCP-ALL patient samples with high postinduction MRD and IKZF1 alterations.

Main Results:

• The NGS panel successfully identified kinase and cytokine receptor rearrangements in the majority of tested BCP-ALL patients.
• The assay allowed for the identification of novel 5' fusion partners and precise breakpoint mapping.
• Rearrangements were frequently detected in patients with high MRD burden and IKZF1 mutations/deletions.

Conclusions:

• The developed NGS panel provides a rapid and comprehensive diagnostic method for kinase pathway aberrations in BCP-ALL.
• This approach is effective in identifying actionable targets for TKI therapy, particularly in high-risk and MRD-positive cases.
• The panel aids in the precise characterization of genomic alterations, including unknown fusion partners and variable breakpoints.