Gene Fusion Detection by 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.

Challenges

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.

Methods

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. (Kerbs et al., 2022)

Results

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. (Kerbs et al., 2022)

Conclusion

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.