High-throughput diagnostic profiling of clinically actionable gene fusions in lung cancer

Area of Science:

• Oncology
• Genetics
• Molecular Biology

Background:

• Molecular profiling of non-small cell lung cancer (NSCLC) is crucial for guiding clinical decisions and targeted therapies.
• While massive parallel sequencing (MPS) is used for mutation detection, it's not yet standard for identifying gene rearrangements.
• ALK and ROS1 gene rearrangements are key targets for NSCLC therapies.

Purpose of the Study:

• To develop and evaluate an MPS-based panel sequencing assay for simultaneous detection of ALK, ROS1, and RET fusions, alongside somatic mutations.
• To assess the sensitivity and specificity of this multiplex assay using formalin-fixed paraffin-embedded (FFPE) tissues.
• To implement and validate the assay in a routine diagnostic workflow for NSCLC.

Main Methods:

• Development of a single multiplex assay using MPS to detect ALK, ROS1, and RET fusions and somatic mutations.
• Retrospective evaluation on 50 NSCLC samples (35 with fusions, 15 without) to determine assay sensitivity and specificity.
• Prospective screening of 109 NSCLC samples in a diagnostic setting, with FISH confirmation for detected fusions.

Main Results:

• The MPS assay demonstrated 100% sensitivity and specificity for detecting known gene fusions in the retrospective analysis.
• Prospective screening of 109 NSCLC samples identified four gene fusions, all confirmed by Fluorescence In Situ Hybridization (FISH).
• The assay successfully integrated into routine diagnostics, showing effective parallel detection of mutations and gene fusions.

Conclusions:

• The developed MPS assay enables simultaneous, high-throughput detection of gene fusions and somatic mutations in NSCLC.
• This approach can effectively replace conventional methods for molecular profiling in NSCLC diagnostics.
• The assay provides a comprehensive tool for personalized medicine in non-small cell lung cancer treatment.