Nationwide Genomic Data Analysis of Central Nervous System Tumors in Japan based on C-CAT Database

Background Comprehensive genomic profiling test (CGPT) using next-generation sequencing (NGS) plays a vital role in cancer diagnosis, treatment option, and prognostic evaluation. In Japan, three tissue-based CGPTs, FoundationOne® CDx, GenMineTOP, and NCC OncoGuide™, are reimbursed under public health insurance. However, their comparative performance in central nervous system (CNS) tumors remains unclear. Methods We conducted a nationwide, retrospective analysis using data from the Center for Cancer Genomics and Advanced Therapeutics database. A total of 1,151 patients with CNS tumors who underwent CGPT between August 2023 and April 2025 were included. Patient characteristics, genetic mutations, tumor mutation burden, and numbers of drug and clinical trial suggestions were compared across the three CGPTs. Results FoundationOne® CDx detected significantly more mutations and copy number alterations than GenMineTOP and NCC OncoGuide. It also proposed more off-label drugs and domestic clinical trials. Conversely, GenMineTOP demonstrated the highest detection rate of gene fusions (9.6%), including KIAA1549-BRAF, FGFR3-TACC3, and EGFR-SEPT14, and PTPRZ1-MET. Furthermore, GenMineTOP identified germline mutations in 4.6% of patients, commonly involving TP53, BRCA2, and MSH6. Conclusion FoundationOne® CDx exhibits greater number of mutations, copy number alterations, and generating therapeutic suggestions, while GenMineTOP excels in identifying fusion genes and germline variants. These findings underscore that each CGPT possesses distinct analytical strengths, and the choice of platform may influence the genomic landscape and therapeutic opportunities identified in CNS tumor patients.