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 fu-sions. 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.
| Original language | English |
|---|---|
| Article number | e41 |
| Journal | Genomics and Informatics |
| Volume | 19 |
| Issue number | 4 |
| DOIs | |
| State | Published - Dec 2021 |
Bibliographical note
Funding Information: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.
Publisher Copyright:
© 2021 Korea Genome Organization.
Keywords
- Fusion
- Next-generation sequencing
- RNA sequencing panel
- Thyroid cancer
