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Multi-Cancer Genome Profiling for Neurotrophic Tropomyosin Receptor Kinase (NTRK) Fusion Genes: Analysis of Profiling
Hinano Nishikubo1, Kyoka Kawabata1, Saki Kanei1
1Molecular Oncology and Therapeutics, 1-4-3 Asahimachi, Abeno-ku, Osaka 545-8585, Japan.
Abstract:
Background/Objectives: The neurotrophic tropomyosin receptor kinase (NTRK) genes NTRK1, NTRK2, and NTRK3 encode tyrosine kinase receptors, and their fusion genes are known as the oncogenic driver genes for cancer. This study aimed to compare the diagnostic ability of NTRK fusion among five types of multi-cancer genome profiling tests (multi-CGP tests) and determine a useful multi-CGP test for NTRK fusion, recorded in the Center for Cancer Genomics and Advanced Therapeutics (C-CAT) database in Japan. This study aimed to compare the diagnostic results for NTRK fusions among the five different CGP tests. Methods: A total of 88,688 tumor cases were enrolled in the C-CAT profiling database from 2019 to 2024. The detection frequency of NTRK fusion genes was compared to the results for five multi-CGP tests: NCC Oncopanel, FoundationOne CDx (F1), FoundationOne Liquid (F1L), GenMineTOP (GMT), and Guardant360. Results: NTRK fusion genes were detected in 175 (0.20%) of the 88,688 total cases. GMT, which is equipped with RNA sequencing function, frequently detected NTRK fusion genes (20 of 2926 cases; 0.68%) in comparison with the other four multi-CGP tests that do not have RNA sequencing analysis. GMT showed significantly (p < 0.05) higher diagnostic ability for NTRK fusions compared with the other four multi-CGP tests. Especially, NTRK2 fusion was significantly (p < 0.001) more highly determined by GMT than it was by the other four multi-CGP tests. The detection rates for FGFR1 and FGFR3 were significantly higher in GMT than in other multi-CGP tests. In contrast, the detection rates of the ALK and RET fusion genes were significantly higher in F1L. Conclusions: GMT, which is equipped with RNA sequencing analysis, might show a useful diagnostic ability for NTRK fusions, especially for NTRK2 fusion genes.
Insights
GenMineTOP (GMT) with RNA sequencing showed superior diagnostic ability for neurotrophic tropomyosin receptor kinase (NTRK) fusions compared to other multi-cancer genome profiling tests. This RNA-seq equipped test is particularly effective for detecting NTRK2 fusions.
Area of Science:
- Oncology
- Genomics
- Molecular Diagnostics
Background:
- Neurotrophic tropomyosin receptor kinase (NTRK) genes (NTRK1, NTRK2, NTRK3) encode tyrosine kinase receptors, and their fusions are oncogenic drivers in cancer.
- Accurate detection of NTRK fusions is crucial for targeted cancer therapy.
- Multi-cancer genome profiling tests (multi-CGP) are increasingly used for comprehensive genomic analysis.
Purpose of the Study:
- To compare the diagnostic performance of five different multi-CGP tests for detecting NTRK fusions.
- To identify the most effective multi-CGP test for NTRK fusion detection in a Japanese cohort.
- To evaluate the utility of RNA sequencing in multi-CGP tests for identifying NTRK fusions.
Main Methods:
- Retrospective analysis of 88,688 tumor cases from the C-CAT profiling database (2019-2024).
- Comparison of NTRK fusion detection rates across five multi-CGP tests: NCC Oncopanel, FoundationOne CDx (F1), FoundationOne Liquid (F1L), GenMineTOP (GMT), and Guardant360.
- Statistical analysis to compare the diagnostic abilities of the tests, with a focus on GMT's RNA sequencing capability.
Main Results:
- NTRK fusions were detected in 175 (0.20%) of 88,688 cases.
- GenMineTOP (GMT), equipped with RNA sequencing, showed significantly higher detection rates for NTRK fusions (0.68%) compared to the other four tests (p < 0.05).
- GMT demonstrated superior detection of NTRK2 fusions (p < 0.001) and higher rates for FGFR1/FGFR3 fusions, while F1L showed higher rates for ALK and RET fusions.
Conclusions:
- GenMineTOP (GMT), utilizing RNA sequencing, demonstrates significant diagnostic utility for NTRK fusions, particularly NTRK2.
- The inclusion of RNA sequencing in multi-CGP tests enhances the detection of specific driver gene fusions like NTRK.
- GMT represents a valuable tool for comprehensive cancer profiling and identifying actionable NTRK fusions.
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