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Updated: Jan 11, 2026
Oncogenic Gene Fusion Detection Using Anchored Multiplex Polymerase Chain Reaction Followed by Next Generation Sequencing
Published on: July 5, 2019
Long read nanopore DNA sequencing with adaptive sampling to identify tyrosine kinase fusion genes
Matthew Salmon1,2, Nicole Naumann3, Jenny Rinke4
1Faculty of Medicine, University of Southampton, Southampton, UK.
Abstract:
Diverse haematological neoplasms are driven by tyrosine kinase (TK) fusion genes formed by recurrent or non-recurrent genomic rearrangements. The resulting chimeric proteins often present excellent targets for treatment with kinase inhibitors, and the fusion transcripts or genomic junctions can be used as specific targets for molecular monitoring. Whilst the TK genes involved are generally well characterised (e.g. ABL1, PDGFRA, FGFR1), the fusion partners are very diverse, presenting a challenge for detection and characterisation of these structural variants (SV) using current diagnostic methods. We assessed the ability of targeted nanopore sequencing using adaptive sampling to detect fusion genes in myeloid neoplasms. We sequenced genomic DNA from patients (n = 20) with a known or suspected TK gene fusion and identified rearrangements in 18 cases, including all cases with a known TK fusion, typical and atypical BCR::ABL1 rearrangements, an 843Kb deletion causing a FIP1L1::PDGFRA fusion, novel AGAP2::PDGFRB and NFIA::PDGFRB fusions, and a complex CCDC88C::PDGFRB rearrangement with multiple translocation events. The approach was fast (<72 h/sample from DNA to result), flexible with minimal hands-on laboratory time, and provided accurate, patient-specific characterisation of genomic breakpoints.
Insights
Targeted nanopore sequencing effectively detects diverse tyrosine kinase (TK) fusion genes in myeloid neoplasms. This rapid, flexible method accurately identifies genomic rearrangements for precise molecular monitoring and patient-specific characterization.
Area of Science:
- Genomics
- Molecular Diagnostics
- Hematology
Background:
- Tyrosine kinase (TK) fusion genes drive diverse hematological neoplasms.
- Genomic rearrangements create these fusion genes, which are key therapeutic targets.
- Diverse fusion partners pose challenges for current diagnostic methods.
Purpose of the Study:
- To assess targeted nanopore sequencing with adaptive sampling for detecting TK fusion genes in myeloid neoplasms.
- To evaluate the speed, flexibility, and accuracy of this diagnostic approach.
Main Methods:
- Targeted nanopore sequencing utilizing adaptive sampling.
- Analysis of genomic DNA from 20 patients with known or suspected TK gene fusions.
- Identification and characterization of structural variants (SVs) and genomic breakpoints.
Main Results:
- Successfully identified TK gene fusions in 18 out of 20 patients.
- Detected typical and atypical BCR::ABL1 rearrangements, novel AGAP2::PDGFRB and NFIA::PDGFRB fusions, and complex rearrangements.
- Characterized an 843Kb deletion causing a FIP1L1::PDGFRA fusion.
- The method provided results in under 72 hours per sample.
Conclusions:
- Targeted nanopore sequencing is a fast, flexible, and accurate method for detecting and characterizing TK fusion genes in myeloid neoplasms.
- This approach enables precise patient-specific molecular monitoring.
- It addresses the challenge of diverse fusion partners in TK-driven cancers.
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