Detectability of druggable gene fusions by amplicon-based next generation sequencing in nationwide lung cancer genomic screening project (LC-SCRUM-Japan)

Background

Kinase gene fusions, such as ALK, ROS1 and RET fusions, are critical druggable targets for lung cancer, and the development of multiplexed testing for these fusions as well as gene mutations and amplifications is required in clinical settings. We evaluated the detectability of gene fusions by a next generation sequencing (NGS) system, which has been applied in our nationwide genomic screening project (LC-SCRUM-Japan) with academic-industrial collaboration since March 2015.

Methods

DNA and RNA extracted from lung cancer samples were subjected to a NGS system, Oncomine Comprehensive Assay, which is an amplicon-based sequencing and enables the simultaneous analysis of >4000 different genomic variants including 183 types of gene fusions. ROS1 and RET fusions were also analyzed using RT-PCR and detected fusions were confirmed by FISH.

Results

As of April 2016, 1,118 patients from 209 institutions across Japan had been enrolled in this project. Among 989 available samples, including 900 non-small cell carcinomas and 89 small cell carcinomas, gene fusions were detected in 83 samples (8%). The detected fusion genes were 34 ROS1 (3%), 25 RET (3%), 19 ALK (2%), 2 FGFR2 (0.2%) and 1 FGFR3 (0.1%). The concordance rates between NGS and RT-PCR for the detection of ROS1 and RET fusions were both 0.99, and the detection sensitivities/specificities of these two fusions in NGS assay were 0.94/1.00 and 0.95/1.00, respectively.

Conclusions

Our nation-wide large scale screening revealed that this amplicon-based NGS assay allows for the detection of various druggable gene fusions, especially of ROS1 and RET fusions with high sensitivities and specificities, indicating that this NGS assay is clinically applicable to a molecular diagnostics for targeted therapies in lung cancer.

Clinical trial identification

Legal entity responsible for the study

National Cancer Center

Funding

Japan Agency for Medical Research and Development (AMED)

Disclosure

S. Matsumoto, K. Yoh, K. Goto: Grants from Chugai Pharm., MSD, Astra Zeneka, Taiho Pharm., Ono Pharm., Eisai, Pfizer, Kyowa Hakko Kirin, Eli Lilly, Takeda Pharm., Novartis Pharma, Daiichi Sankyo, Astellas Pharma and Amgen Astellas BioPharma, during the conduct of the study. Y. Ohe: Grants and personal fees from AstraZeneca, Chugai, Lilly, Ono, Taiho, Novartis, Pfizer, Bristol Myers, Dainippon Sumitomo, Merck, Daiichi Sankyo, Nippon Kayaku, Boehringer Ingelheim, Bayer, MSD, Clovis Oncology and Sanofi, outside the submitted work. T. Seto: Grants and personal fees from AstraZeneca, Chugai, Lilly, Ono, Sumitomo, Taiho, Novartis, Merck, Daiichi Sankyo, Boehringer, MSD, Sanofi, Pfizer, Eisai, Fuji, Hisamitsu, Kyowa Hakko, Roche, Takeda, Astellas, Bayer and Yakult, outside the submitted work. T. Kohno: Grants from Daiichi Sankyo, outside the submitted work. K. Tsuchihara: Personal fees from Takeda, personal fees from Chugai Pharma, personal fees from AstraZeneca, personal fees from Eisai, personal fees from Merck Serono, outside the submitted work. All other authors have declared no conflicts of interest.