Related Experiment Video
Updated: Oct 3, 2025
Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
Published on: August 4, 2016
Development of an RNA sequencing panel to detect gene fusions in thyroid cancer
Dongmoung Kim1, Seung-Hyun Jung2,3, Yeun-Jun Chung1,3,4
1Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Korea.
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.
Insights
A new RNA-based sequencing panel, ThyChase, effectively identifies key gene fusions in thyroid cancer. This diagnostic tool can detect fusions down to a 1% tumor cellular fraction, aiding clinical applications.
Area of Science:
- Oncology
- Molecular Biology
- Genetics
Background:
- Gene fusions are significant drivers in cancer development and progression.
- Existing diagnostic panels for thyroid cancer have limitations in detecting all clinically relevant gene fusions.
- Accurate identification of gene fusions is crucial for targeted therapy selection in oncology.
Purpose of the Study:
- To develop and validate a custom RNA-based sequencing panel, named ThyChase, for comprehensive detection of gene fusions in thyroid cancer.
- To assess the analytical performance, including the limit of detection, of the developed ThyChase panel.
- To provide a valuable tool for clinical molecular diagnostics in thyroid cancer.
Main Methods:
- Design of a custom RNA-sequencing panel (ThyChase) targeting 87 gene fusions relevant to thyroid cancer.
- Inclusion of five housekeeping genes for RNA sequencing quality control.
- Validation using reference RNA (HD796) and confirmation of identified fusions (EML4-ALK, CCDC6-RET, TPM3-NTRK1) by Sanger sequencing.
Main Results:
- The ThyChase panel successfully identified three known clinically significant gene fusions in thyroid cancer.
- Sanger sequencing confirmed the breakpoint sequences of the detected fusions.
- The panel demonstrated a limit of detection as low as 1% fusion-positive tumor cellularity.
Conclusions:
- The custom ThyChase panel is a sensitive and specific tool for identifying key gene fusions in thyroid cancer.
- This panel has the potential to improve diagnostic accuracy and guide treatment decisions in clinical settings.
- The ThyChase panel represents a significant advancement in molecular profiling for thyroid cancer patients.
More Related Videos
09:49Oncogenic Gene Fusion Detection Using Anchored Multiplex Polymerase Chain Reaction Followed by Next Generation Sequencing
Published on: July 5, 2019
10:35A Blood-based Test for the Detection of ROS1 and RET Fusion Transcripts from Circulating Ribonucleic Acid Using Digital Polymerase Chain Reaction
Published on: April 5, 2018
