Multigene NGS assay for biomarker identification in 621 colorectal cancer cases.

Abstract

e15168 Background: Colorectal cancer (CRC), a major cause of cancer-related mortality, is driven by diverse genetic and molecular alterations. Advances in next-generation sequencing (NGS) enabled comprehensive genomic profiling, transforming CRC diagnosis and treatment. In this study molecular profiling was performed on 621 CRC cases, including 4 actionable biomarkers: microsatellite instability (MSI), KRAS , NRAS , BRAF and PIK3CA. Methods: DNA was extracted from embedded paraffin tissue samples using the Qiasymphony DSP DNA Mini Kit (Qiagen). RNA was extracted using the RNeasy FFPE Kit (Qiagen). Μutation hotspot regions of 27 genes were amplified using an Ion AmpliSeq Panel (Thermo Fisher Scientific). Copy number variations, SNPs, and indels were analysed. Additionally, ALK, ROS1, RET, NTRK1, NTRK2 & NTRK3 fusions were tested using an Ion AmpliSeq RNA Fusion Panel (Thermo Fisher Scientific). Sequencing was carried out using the Next Generation Sequencing platform Ion GeneStudio S5 Prime System (Thermo Fisher Scientific). Results: Based on our findings 62% of patients were eligible for on-label therapy. Mutations in KRAS and NRAS, were found in 36% of CRC cases and among these, the KRAS G12C mutation, was detected in 3% of them. Furthermore, the BRAF V600E mutation, was detected in approximately 11% of cases. Additionally, PIK3CA mutations are present in 15% of CRC cases. In 8% of tumors, High microsatellite instability (MSI-H) was observed. Notably, 4% of metastatic CRC cases exhibited co-occurrence of MSI-H and BRAF V600E mutation while for the remaining MSI-H/BRAF wt cases should be referred for Lynch syndrome testing. Conclusions: The results emphasize the pivotal role of NGS in guiding treatment decisions, including stratification for therapies and identifying hereditary CRC syndromes. This study underscores the transformative potential of precision oncology in optimizing therapeutic outcomes, decision impact and advancing personalized care for CRC patients.