Comprehensive whole-genome analysis of colorectal cancer (CONDUCTOR study): Integrating RAS/BRAF, MSI status, and intron–exon alterations.

Abstract

181 Background: Molecular profiling of colorectal cancer (CRC) has traditionally centered on RAS, BRAF, and microsatellite instability (MSI) status, which inform therapeutic decision-making. However, the broader genomic landscape extending beyond these canonical biomarkers remains insufficiently characterized. Whole-genome sequencing (WGS) enables simultaneous interrogation of both coding (exonic) and non-coding (intronic and intergenic) regions, thereby providing deeper insights into tumor biology. Methods: We performed WGS in CRC patients who underwent curative-intent surgery. Genomic alterations were systematically compared with conventional biomarker data ( RAS , BRAF , and MSI/MMR) obtained using validated clinical methodologies. Variants were annotated by functional category (exonic, intronic, and intergenic), and mutational signatures were analyzed. Sequencing depth averaged ×30 for matched normal tissue and ×120 for tumor samples. Correlations with clinicopathological characteristics were assessed. Results: A total of 211 cases with successful WGS and review at a molecular tumor board were analyzed. Canonical mutations in RAS and BRAF demonstrated strong concordance with standard clinical assays ( RAS : sensitivity 95.1%, specificity 89.3%; BRAF : sensitivity 100%, specificity 100%), validating the analytic platform. MSI status determined by WGS showed high agreement with PCR-based/panel testing (sensitivity 85.7%, specificity 99.5%). Importantly, recurrent non-coding variants were identified in intronic regions affecting regulatory elements and splice sites, suggesting potential biological relevance. Distinct mutational signatures and structural variations were observed across exonic and intronic compartments. Pathogenic germline variants for hereditary tumor syndrome with autosomal dominant inheritance were detected in nine patients, involving APC, ATM, BARD1, BRCA1, MLH1 , PALB2 and PMS2 . Integrative analysis revealed novel associations between non-coding alterations and clinical subgroups that were not captured by standard biomarker testing. Conclusions: This study demonstrates the feasibility and clinical value of WGS in a large CRC cohort, confirming its robustness relative to established biomarkers while uncovering novel genomic alterations in both coding and non-coding regions. WGS may complement conventional assays by broadening the spectrum of clinically relevant information, thereby advancing precision oncology for CRC.