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RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

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Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

Accurate RET Fusion Detection in Solid Tumors Using RNA Sequencing Coverage Imbalance Analysis.

Ivan Gaziev¹, Anna Khristichenko², Daniil Luppov¹

¹Institute for Personalized Oncology, Biomedical Science & Technology Park, FSAEI HE I.M. Sechenov First Moscow State Medical University of MOH of Russia (Sechenovskiy University), 119991 Moscow, Russia.

International Journal of Molecular Sciences

|December 11, 2025

Summary

This study introduces a novel method for detecting REarranged during Transfection (RET) gene fusions using RNA-sequencing (RNA-seq) exon coverage imbalance. This approach achieves 100% accuracy, improving targeted cancer therapy identification.

Keywords:

RET rearrangement RNA sequencing Ret Proto-Oncogene (RET)clinical oncology fusion oncogene receptor tyrosine kinase tumor molecular diagnostics

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Published on: November 7, 2025

Area of Science:

Oncology
Genomics
Bioinformatics

Background:

Accurate detection of oncogenic gene fusions is crucial for targeted cancer therapies.
Current methods like IHC, FISH, and standard RNA-seq have limitations in sensitivity, specificity, and multiplexing capacity for fusion detection.
RET fusions are clinically actionable targets in various cancers, but their identification is challenging.

Purpose of the Study:

To develop and validate a novel, highly sensitive, and specific method for detecting clinically actionable REarranged during Transfection (RET) gene fusions.
To assess the utility of RNA-sequencing (RNA-seq) exon coverage imbalance analysis for identifying RET fusions in solid tumors.
To discover novel RET fusion partners and rare RET fusion events.

Main Methods:

A novel approach measuring the imbalance in RNA-sequencing (RNA-seq) read coverage of 3' and 5' exons of potential fusion oncogenes was developed.
1327 solid tumor RNA-seq profiles were screened, including non-small cell lung cancer and thyroid cancer samples.
RET fusion status was validated using targeted next-generation sequencing (NGS) and Sanger sequencing in selected cases.

Main Results:

The exon coverage imbalance analysis accurately discriminated between true and false positive RET fusions, achieving 100% sensitivity and specificity with optimized thresholds.
Validation in an independent cohort confirmed the reliability of the method.
Among 18 RET fusion-positive samples, one rare fusion (RUFY3::RET) and two novel fusions (FN1::RET, PPP1R21::RET) were identified.

Conclusions:

Exon coverage imbalance analysis is a robust and highly accurate method for detecting clinically relevant RET fusions.
This approach complements existing computational RNA-seq analysis pipelines, enhancing the identification of actionable gene fusions.
The findings support the clinical utility of this method for guiding targeted therapy decisions in oncology.