Validation of the Archer® FusionPlex® Sarcoma panel

At a glance:

  • 81 sarcoma cases profiled
  • 90% concordance between FusionPlex®and conventional methods (FISH and RT-PCR)
  • In four cases, fusions were detected by AMP™ but went undetected by FISH or RT-PCR
  • Two novel USP6 fusion partners were detected using FusionPlex®

paper published in the September, 2018 issue of The Journal for Molecular Diagnostics shows a direct comparison between the Archer® FusionPlex® Sarcoma panel and conventional methods for gene fusion detection, including fluorescence in situhybridization (FISH) and reverse transcriptase-PCR (RT-PCR). As with all Archer® tests, the FusionPlex®Sarcoma panel utilizes Anchored MultiPlex PCR (AMP™) chemistry to create target-enriched libraries for next-generation sequencing (NGS).

The study was conducted at the Leiden University Medical Center in the Netherlands. The authors profiled 81 sarcoma cases and found a 90% concordance rate between Archer® FusionPlex®and the conventional methods. In 4 of the cases, fusions that were detected by AMP™ went undetected by FISH or RT-PCR. These cases were shown to be false-negatives in the initial FISH/RT-PCR screens. The fusions were later confirmed using additional FISH/RT-PCR analysis.

“In contrast to FISH, which can be hampered by a low percentage of cells carrying the translocation, the sensitivity of AMP-based targeted NGS is much higher.”

Furthermore, two novel USP6 fusion partners were detected using the FusionPlex®panel. AMP™ chemistry makes novel fusion detection possible because it utilizes open-ended, unidirectional gene-specific primers (GSPs) and molecular barcodes (MBC) adaptors.

“FISH with EWSR1 split-apart probes seems sufficient to establish the correct diagnosis. However, the fusion partner remains unrevealed, which can be of significant importance in the diagnostics of small blue round cell tumors as illustrated by our study case in which EWSR1 was fused with PBX1, indicating a myoepithelial carcinoma”

The authors note one case in which a fusion was detected by FISH, but not by AMP. They speculate that this fusion may involve an EWSR1 exon or nearby gene that is not targeted in FusionPlex®Sarcoma. Even so, the authors consider AMP™ chemistry to be a maximum method for fusion detection over the conventional methods.

Read the Paper.

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