CGI Brings the Powerful, Flexible Chemistry of ArcherDX NGS to Clinical Trials

Written by: JamieThalmann

Published on:
June 14th, 2016

Clinically relevant biomarkers are being identified at an accelerating rate, placing an ever greater premium on the importance of limited patient tissue samples. This in turn increases the already daunting complexity of clinical trial design and leads to questions that strike at the heart of successful drug development.

  • With a finite capacity to run diagnostic tests, how will I determine what signaling pathways promote or degrade the efficacy of my therapy?
  • How can I predict response and stratify my patient population?
  • What driver genes are pushing tumor growth and what direction will the cancer take to develop resistance?

Clearly, there are implications for the targets you choose to interrogate, as well as the technological platforms you choose to pursue. At Cancer Genetics, the foundation of our business is to be on the leading edge of technological innovation, regardless of platform. We have recently partnered with ArcherDX to provide the industry leading FusionPlex® and VariantPlex™ NGS assays, which are powered by Anchored Multiplex PCR (AMP™) enrichment chemistry, as part of our comprehensive package of clinical trial testing solutions for our biopharma partners.

CGI has staked a position as being technologically agnostic in order to best fit the needs of individual clinical programs and Archer’s NGS platform is no exception. The FusionPlex® and VariantPlex™ assays are equally capable of being run on either the Illumina® or Ion Torrent system. Archer’s streamlined parallel workflows allow simultaneous interrogation of DNA and RNA from any clinical sample type. The FusionPlex® workflow is designed for maximum nucleic acid recovery, capable of delivering  robust data on both known and unknown gene fusions, SNVs/indels, and isoforms from as little as 20ng of RNA from FFPE. By adding unique molecular barcodes prior to amplification and using strand specific priming the AMP™ chemistry is able to eliminate FFPE deamination artifacts and false positive results for critical biomarkers such as the NRAS 613D variation. Additionally, unique start sites opposing gene specific primers allows identification of novel gene fusions unlike traditional NGS chemistry and FISH probes.

Archer has taken on the load of manufacturing under GMP conditions and has established the regulatory acumen to develop fully validated companion diagnostic capabilities. FusionPlex® and VariantPlex assays are available off the shelf for both hematological malignancies and solid tumors. Breakpoints and fusion detection targets include receptor tyrosine kinases, MAP kinases, suppressor genes, Wnt signaling, and transcription factors. Both assays utilize a lyophilized workflow to reduce errors and RNA QC assay is included. The total turnaround time through data processing is 3-5 days, while the bioinformatics and reporting system has been designed to be an intuitive and customizable interface.

ASCCP guidelines are just a starting point in determining the testing strategy for clinical trial design. As a Certified Service Provider of ArcherDX assays CGI has a powerful new tool in our playbook of specialty diagnostics. Under the CGI umbrella you have access to any platform for any complexity of biomarker strategy. ArcherDX from CGI takes translational sequencing to the next level.