RNA-Based Gene Fusion Detection: Next Generation Sequencing Applications and Sample Workflow Improvements

  • A discussion on the utility of gene fusion detection in research and the functions of these fusions in tumorigenesis by induced oncogene expression
  • Investigation methods for isolation of nucleic acids from formalin-fixed paraffin-embedded (FFPE specimens)
  • Details on the use of total nucleic acid purification for use in RNA-Seq applications and gene fusion detection


The advent of next-generation sequencing (NGS) technologies has enabled the rapid identification of unknown fusion genes. To detect gene fusions by NGS, genomic DNA can be used for whole genome or whole exome sequencing, or RNA can be used for whole transcriptome sequencing (RNA-Seq). In comparison to whole genome sequencing, which interrogates large intronic segments that likely contain biologically irrelevant fusions, whole exome sequencing only assays the exons. However, the additional exon enrichment step (hybrid capture) involved in whole exome sequencing adds to the overall cost and time to perform these assays. RNA-Seq, which interrogates only expressed fusions, is a faster, more cost-effective approach to detect biologically relevant gene fusions. Though RNA-Seq is somewhat limited in its ability to detect low expression levels of transcripts, target-enrichment strategies can be used to increase read depth over target regions of interest, thereby enhancing detection sensitivity.



Joshua Stahl
Chief Scientific Officer
ArcherDx, Inc

Josh Stahl is the Chief Scientific Officer and General Manager for ArcherDx, Inc., where he has worked since 2013. Mr. Stahl holds a Master’s in Biochemistry and an MBA from the University of Colorado at Boulder. He joined ArcherDx in the company’s infancy, specifically to be part of something that would make a lasting impact on healthcare. During his time at ArcherDx, the company has continuously developed new, innovative methods for DNA and RNA variant detection through next generation sequencing (NGS) for translational and oncology researchers.

We love to talk science.

Sign up to receive monthly invitations to our webinars.

Sign Up