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Background <p>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.</p> Methods <p>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.</p> Results <p>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.</p> Conclusion <p>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.</p>

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Nationwide genomic data analysis of central nervous system tumors in Japan based on C-CAT database

  • 期刊论文

  • 发表日期：

    2026年5月6日

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  • Daisuke Kawauchi,
  • Makoto Ohno,
  • Masamichi Takahashi,
  • Takafumi Koyama,
  • Kuniko Sunami,
  • Makoto Hirata,
  • Shunsuke Yanagisawa,
  • Takaki Omura,
  • Takuma Aoki,
  • Genta Fujii,
  • Koji Saito,
  • Tetsuya Yamamoto,
  • Hiromichi Suzuki,
  • Yoshitaka Narita

摘要

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.