Traditional methods to detect cancer-specific gene fusions are labor-intensive, subjective, not amenable to multiplexing and cannot detect novel fusions.
Join us at Molecular Medicine Tri-Conference 2015 to learn about how Archer™ FusionPlex™ Assays are bridging the gap between NGS and scalable, accurate and comprehensive gene fusion detection.
Presenter: Josh Stahl, firstname.lastname@example.org
Ryan Walters1 Josh Stahl1, Josh Haimes1, Brian Kudlow1, Brady Culver1, John A. Iafrate2, Valentina Nardi2, Kerry Lynch2, Hayley Robinson2, Yi Cao2, Jason Myers1
1 ArcherDX, Inc. Boulder, Colorado
2 Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
Understanding gene fusions in cancer biology is increasingly important and might have profound effects on future drug discovery efforts. Historical testing methods such as fluorescence in-situ hybridization (FISH) are limited by scalability and require subjective interpretation. Targeted sequencing technologies such as Anchored Multiplex PCR (AMP™) offer the ability to identify novel and known gene fusions from small amounts of input material in a single reaction. The largest hurdle to clinical validation is the use of archival RNA, which is often degraded. Here we describe the utility of the Archer™ PreSeq™ RNA QC assay to measure amplifiable RNA in archival samples used during clinical validation to predict sequencing success.
Massachusetts General Hospital sourced 26 known hematological translocation-positive and -negative samples from various cancer centers in addition to 16 in-house AML samples with unknown translocation status. Prior to AMP™ library preparation, all 42 samples were screened using the Archer™ PreSeq™ RNA QC assay to determine the amount of amplifiable RNA. Following QC, the Archer™ FusionPlex™ Assay was performed according to Enzymatics’ package insert, and samples were sequenced on the Illumina® MiSeq® platform. Sequencing analysis was performed via the Archer™ Analysis Pipeline, and reported fusion results were compared to results achieved using historical testing methods.
A strong correlation between library quality, translocation detection and the Archer™ PreSeq™ result was observed. During validation, 100% of the samples that passed PreSeq™ QC generated libraries with high complexity and successfully detected the previously reported translocation identified by orthogonal methods. Furthermore, samples that failed PreSeq™ QC failed library preparation or sequencing or were unable to report translocation status.
The Archer™ PreSeq™ RNA QC assay is a capable tool to identify RNA suitable for translocation detection during validation of Archer™ FusionPlex™ panels. This tool allows users to quickly screen historical samples prior to validation—drastically reducing sequencing failure rate. Ultimately, PreSeq™ reduces both the time and cost associated with the clinical validation of Archer™ FusionPlex™ assays.