Genomics & Informatics

Korea Genome Organization (한국유전체학회)
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Development of an RNA sequencing panel to detect gene fusions in thyroid cancer

  • Kim, Dongmoung (Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea) ;
  • Jung, Seung-Hyun (Department of Biochemistry, The Catholic University of Korea) ;
  • Chung, Yeun-Jun (Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea)
  • Received : 2021.10.25
  • Accepted : 2021.11.12
  • Published : 2021.12.31
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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.

Keywords

Acknowledgement

This work was supported by a grant from the National Research Foundation of Korea (2017M3C9A6047615, 2019R1A5A202 7588, 2019R1C1C1004909). We thank KREONET (Korea Research Environment Open NETwork) and KISTI (Korea Institute of Science and Technology Information) for allowing us to use their network infrastructure.

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