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Updated: Jan 8, 2026
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Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
Published on: August 4, 2016
10.9K
Advancing diagnostic targeted RNA sequencing for haematological malignancies within an Australian sample exchange
Eric Wenlong Li1, Ing-Soo Tiong2, Clare Gould2
1Molecular Haematology Laboratory, Royal Prince Alfred Hospital, Sydney, NSW, Australia; The University of Sydney, Sydney, NSW, Australia; Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
Pathology
|December 16, 2025
Summary
Targeted RNA-based next-generation sequencing (RNA-Seq) shows high concordance for oncogenic gene fusion detection across laboratories. However, limitations exist in identifying novel fusions and standardizing diagnostic reports.
Area of Science:
- Molecular Diagnostics
- Oncology
- Genomics
Background:
- Targeted RNA-based next-generation sequencing (RNA-Seq) is a novel method for oncogenic gene fusion diagnostics.
- Lack of external quality assurance programs challenges quality management for targeted RNA-Seq.
Purpose of the Study:
- To assess the concordance of targeted RNA-Seq for oncogenic gene fusion identification across multiple laboratories.
- To identify limitations and variations in targeted RNA-Seq methodologies and reporting.
Main Methods:
- Four Australian molecular diagnostics laboratories participated.
- Laboratories utilized Archer FusionPlex or Qiagen Fusion XP platforms.
- Results were compared against a reference method using six diagnostic samples.
Main Results:
- High concordance was observed in identifying known gene fusions (BCR::ABL1, ETV6::RUNX1, NUP98::HOXD13, KMT2A::USP2).
- One laboratory missed the novel ETV6::SRR fusion; all missed the IGH::EPOR fusion.
- Variations in variant description nomenclature and reporting content were noted.
Conclusions:
- Targeted RNA-Seq demonstrates high concordance for established gene fusions.
- Current platforms have limitations in detecting non-chimeric rearrangements involving regulatory elements.
- Standardized practice guidelines and integration of gene expression analysis are recommended to improve diagnostic yield and reporting consistency.
