Gene Fusion Detection by Sequencing

Gene Fusion Detection by Sequencing

What is Gene Fusion Detection?

A fusion gene is indeed a hybrid gene formed by the merging of two separate genes, often as a result of structural chromosomal changes like translocations, inversions, or deletions. These genetic rearrangements can lead to the fusion of two previously independent genes, resulting in a single, chimeric gene with altered functions.

Gene fusion detection is a revolutionary technique that allows us to identify specific genetic alterations known as fusion genes. These fusion genes arise from structural changes in the DNA, where two separate genes merge to form a new hybrid gene. In many cases, these fusion genes play a critical role in cancer development and progression, making them crucial biomarkers for diagnosis and treatment decisions.

For instance, in lung cancer, common fusion genes like ALK, ROS1, RET, MET skipping, NTRK, and FGFR are prevalent, with the incidence reaching up to 15%. Take the classical ALK gene fusion as an example, where the fusion chaperone gene fuses to the functional kinase region of ALK, leading to its overexpression. A multitude of clinical ALK fusion isoforms can be detected through various methods such as FISH, IHC, and next-generation sequencing.

Our Gene Fusion Detection Solution is designed to provide you with invaluable insights into the genetic landscape of various diseases, particularly cancers, and pave the way for personalized treatment strategies.

How We Support Sequencing-based Detection of Gene Fusions?

Technology Level of Detection Strengths Custom Products
CDCAP NGS Hybridization capture DNA or RNA -Enables detection of known and unknown fusion genes
-Not requiring RNA purification, simplifying sample preparation and enhancing efficiency
Tailored Capture Panels (CDCAP) to suit your research needs and gene targets. Learn more.
CDAMP NGS Amplicon DNA or RNA - Lower RNA input required
- Effective with small and mid-sized panels
- Only anchored mPCR enables detection of known and unknown fusion gene events
- 5' and 3' imbalance evaluation can increase test analytical accuracy
Custom Amplicon Panels (CDAMP) for specific fusion gene targets or regions of interest. Learn more.
RNA Sequencing NGS RNA Compatible with diverse RNA samples, including fresh, frozen, FFPE tissues, and liquid biopsies, accommodating various research scenarios - Tailored RNA Sequencing for broader transcriptomic analysis
- See our CD RNA Fusion Gene Panel
PacBio Iso-Seq Long-Read Sequencing RNA - Sequencing of full-length RNA transcripts, including fusion variants
- Detailed characterization of alternative splicing events and complex fusion isoforms
- Gene expression changes and post-transcriptional modifications
Customize your Iso-Seq experiments for specific fusion genes or alternative splicing studies

In-house Data Analysis

- Comprehensive Annotation: leverages a robust and expansive database infrastructure, affording an exhaustive variant annotation approach. This augmentation greatly heightens the precision of gene fusion detection endeavors.

- Machine-Driven Variant Prioritization: Leveraging machine learning algorithms, our platform facilitates the prioritization of variants. Researchers are thereby empowered to concentrate their focus on the most clinically pertinent and actionable gene fusion events.

- Refined Filtering Mechanisms: Multiple filtering functionalities are integrated into the platform, enabling precise identification of the most significant gene fusion events amidst complex genomic data.

- Enhanced Integration Paradigm: Our synergistic integration offers an enriched landscape of therapeutic, diagnostic, and prognostic insights, profoundly augmenting the analytical capabilities for each discerned gene fusion variant.

- Customizable Reporting: We offer customizable variant reporting, ensuring that the findings are presented in a clear and tailored manner, facilitating communication of results and further analysis.

How to Get Started

Initiating your RNA fusion studies with our sequencing services or panels is as simple as  Contacting us for a consultation. Our team is ready to collaborate with you to ensure your research objectives are met efficiently and effectively.

Uncover the mysteries of gene fusion events with unprecedented accuracy and ease. Let us help you in advancing scientific knowledge and improving patient care through the power of RNA fusion studies.

Custom Cancer Panels CORE

1. Initial Consultation

Custom Cancer Panels CORE

2. Project Design

Custom Cancer Panels CORE

3. Validation

Custom Cancer Panels CORE

4. Sequencing & Delivery

Custom Cancer Panels CORE

5. Ongoing Support

Applications of Gene Fusion Detection

Case Studies

    • Fusion Gene Detection using RNA Sequencing

      • Background

        Identification of fusion genes is crucial for accurate diagnosis and treatment planning in various malignancies, including acute myeloid leukemia (AML). Traditionally, cytogenetics and targeted molecular genetics have been employed for fusion gene detection. However, the emergence of sequencing technologies offers the potential to enhance diagnostic accuracy and efficiency. This case study focuses on evaluating the performance of RNA-seq for fusion gene detection in AML patients, comparing it with standard diagnostic techniques.


        The conventional approaches for fusion gene detection have limitations, including time-consuming processes, restricted target coverage, and subjective interpretation. The challenge lies in assessing whether RNA-seq can provide a comprehensive and reliable alternative for fusion gene identification.


        In this study, a total of 806 RNA-seq samples from patients with AML were analyzed using two advanced software tools: Arriba and FusionCatcher. The aim was to determine the efficacy of RNA sequencing in detecting fusion events compared to routine diagnostic methods. Samples that exhibited discrepancies in fusion gene detection were subjected to a systematic analysis of sequence coverage to identify potential underlying causes.

        Detection workflow.Detection workflow. (Kerbs et al., 2022)


        The most significant outcomes of the study included the discovery of 157 novel fusion gene candidates that demonstrated robust evidence. Comparisons with established fusion gene databases (ChimerDB and Mitelman Database) revealed the recurrence of novel fusion genes in 14 cases, showcasing the power of RNA-seq in uncovering new fusion events.

        A particularly notable finding was the identification of the recurrent fusion gene NRIP1-MIR99AHG resulting from inv(21) (q11.2;q21.1) in nine patients and LTN1-MX1 resulting from inv(21)(q21.3;q22.3) in two patients. The study provided insights into the functional implications of the NRIP1-MIR99AHG fusion, including its role in overexpression of the 3' region of MIR99AHG and disruption of the tricistronic miRNA cluster miR-99a/let-7c/miR-125b-2. This mechanism is recognized in leukemogenesis, particularly in acute megakaryoblastic leukemia.

        Detection and validation of the novel NRIP1-MIR99AHG fusion gene.Detection and validation of the novel NRIP1-MIR99AHG fusion gene. (Kerbs et al., 2022)


        The case study demonstrated that RNA-seq holds significant potential to revolutionize the systematic detection of fusion genes in clinical applications. By outperforming conventional techniques, RNA-seq provides a valuable tool for fusion gene discovery, contributing to more accurate diagnoses and improved patient care in conditions such as acute myeloid leukemia. The study's findings underscore the importance of integrating cutting-edge sequencing technologies into routine clinical practices to enhance diagnostic precision and advance our understanding of disease mechanisms.


  1. Kerbs, Paul, et al. "Fusion gene detection by RNA-sequencing complements diagnostics of acute myeloid leukemia and identifies recurring NRIP1-MIR99AHG rearrangements." Haematologica 107.1 (2022): 100.
* For Research Use Only. Not for use in diagnostic procedures.

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