Genomics Inform.
2021 Dec;19(4):e41. 10.5808/gi.21061.
Development of an RNA sequencing panel to detect gene fusions in thyroid cancer
- Affiliations
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- 1Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Korea
- 2Department of Biochemistry, The Catholic University of Korea, Seoul 06591, Korea
- 3Precision Medicine Research Center, Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- 4Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- KMID: 2524332
- DOI: http://doi.org/10.5808/gi.21061
Abstract
- In addition to mutations and copy number alterations, gene fusions are commonly identified in cancers. In thyroid cancer, fusions of important cancer-related genes have been commonly reported; however, extant panels do not cover all clinically important gene fusions. In this study, we aimed to develop a custom RNA-based sequencing panel to identify the key fusions in thyroid cancer. Our ThyChase panel was designed to detect 87 types of gene fusion. As quality control of RNA sequencing, five housekeeping genes were included in this panel. When we applied this panel for the analysis of fusions containing reference RNA (HD796), three expected fusions (EML4-ALK, CCDC6-RET, and TPM3-NTRK1) were successfully identified. We confirmed the fusion breakpoint sequences of the three fusions from HD796 by Sanger sequencing. Regarding the limit of detection, this panel could detect the target fusions from a tumor sample containing a 1% fusion-positive tumor cellular fraction. Taken together, our ThyChase panel would be useful to identify gene fusions in the clinical field.
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