The landscape of the comprehensive genomic profile for patients with bowel cancer.

Abstract

189 Background: The aim of study was to clarify the landscape of comprehensive genomic profile in bowel cancer. Methods: This study included 57,103 patients between June 1, 2019 and August 18, 2023 (version 20230821) with a nationwide retrospective design. Patients underwent one of three CGP tests, including OncoGuide, FoundationOne CDx (F1CDx), and FoundationOne Liquid (F1LCDx) CDx, at the physician's choice. We evaluated the pathogenicity of the detected variants based on the public database and gene function. Results: Of the 57,103 patients, 9,595 (16.8%) were bowel cancer, including 911 for OncoGuide, 7,711 for F1CDx and 810 for F1LCDx. In the tumor site, COADREAD was the most common bowel tumor, followed by SBC and APAD. TP53 was the most common gene with SNV/Indels, followed by APC, TP53, KRAS and PIK3CA. FLT3 was the most frequently amplified gene, followed by CDK8 and FLT1. For gene deletions, SMAD4 was the most frequently deleted gene, followed by PTEN and CDKN2A. For genomic rearrangements, EML4-ALK was the most common. A total of 46 (5.0%) germline pathogenic variants were identified in OncoGuide in mismatch repair genes in 12 patients, in BRCA1/2 genes in 11 patients, and in the APC gene in 7 patients. Conclusions: The detected variants should be re-annotated due to the inclusion of several benign variants in the CGP testing, and the landscape of the variants derived from these results in the CGP testing, including FoundationOne CDx, FoundationOne Liquid CDx, and OncoGuide, will help researchers and physicians interpret these results.