NGS assays that match the pace of discovery

By Kiri Burrow, Ph.D. on Mon Feb 26, 2018


Not all NGS assays are created equal...

  • New mutations are discovered at an increasing rate. NGS assays must evolve with the research.
  • No one gets assay content right the first time. A flexible panel that doesn’t sacrifice performance ensures an ideal assay for years to come.

AMP chemistry is modular and flexible

Modularity is one of the many advantages of Archer’s patented Anchored Multiplex PCR (AMP™) enrichment chemistry. With AMP chemistry, users can seamlessly add additional markers to an existing catalog panel without decreasing performance, or build a fully custom panel and update it as needed. This unique feature greatly increases the utility of Archer’s next generation sequencing (NGS) assays by ensuring that your personalized panel can evolve to fit the discoveries of tomorrow.

Existing panel additions or new custom panels can be designed in Assay Designer and shipped in a few weeks. Archer has hundred’s of pre-designed and functionally validated gene modules for DNA, RNA or ctDNA input. All of these are verified to work alongside any newly designed gene or in existing off-the-shelf panels, in a single tube.

Assay Designer panels have excellent performance

Archer custom panels are designed for maximum flexibility and unparalleled performance. Between cutting-edge primer design software and an expansive internal knowledge base of target designs and validated primer sets, you can be assured that your targets will achieve maximum coverage, robust panel uniformity and a high percentage of on-target reads.

Target design rate for 4 modular panel designs ranging from 12 to 914 targets.
Figure 1. Target design rate for 4 modular panel designs ranging from 12 to 914 targets.
*Target design rate is the percentage of designed primers that amplify the expected target region.

Gene modules can be added to existing panels without detriment to performance.

Given the speed at which the NGS field is advancing, assays become outdated quickly. Fortunately, the flexibility of AMP chemistry allows for new targets to be “spiked” into an existing panel without sacrificing assay performance. Therefore, any Archer panel, custom or catalog, can stay as current as the research.

Percentage of on-target reads and primer uniformity in various sized panels in which a 204-primer panel was added.
Figure 2. Percentage of on-target reads and primer uniformity in various sized panels in which a 204-primer panel was added. Percentage of on-target reads declined by <1% when the 204-primer panel was added to the 2 larger panels. Primer uniformity remained unchanged at 99.0%. Pearson correlation coefficient = 0.94.
*On-target percentage is the number of sequenced reads that map to the intended targets. This is calculated by dividing the number of on-target reads by the total number of sequenced reads and expressed as a percentage. Primer uniformity is a measure of the consistency of the coverage depth across all targeted regions and is achieved when a coverage depth of ≥20% of mean reads per GSP2 is attained.

Conclusions

The modularity of Archer’s AMP chemistry allows users to create personalized NGS panels with the utmost flexibility and confidence. With coverage, panel uniformity and on-target reads at >90%, your custom assay is guaranteed to work for your applications. Additionally, any Archer assay is future-proof. When your team decides upon an updated list of key gene targets, simply add gene targets to an existing panel, or create an entirely new custom panel, without sacrificing performance.



About Kiri Burrow, Ph.D.

Kiri earned her Ph.D. in Behavioral Genetics and Neuroscience from the University of Colorado at Boulder. Her research involved identifying novel genetic mutations associated with addictive behaviors. Her interest in cancer genomics led her to join the ArcherDX team in May, 2017. In her free time, Kiri enjoys hiking with her dog, Frankie, and spending time with her family.

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All content © 2018 ArcherDX, Inc.

For Research Use Only. Not for use in diagnostic procedures. For Research Use Only. Not for use in diagnostic procedures.