Custom Archer™ NGS assays
It is important to keep NGS panel targets relevant, but it can be a challenge to continually add biomarkers for specific cancer and disease studies. Learn how Archer NGS assays have unique flexibility to solve those challenges.
Archer NGS assay solutions
Overview
Customizable NGS assays are vital in this era of rapid discovery
Discovery of relevant biomarkers for oncology and genetic disease happens frequently, so it can be difficult for labs to keep their NGS panel content up to date. In fact, over 50,000 disease-gene associations have been identified as of 2020 [1]. Not only do labs need to add relevant biomarkers to their panels on a regular basis, but they also may need specific targets for unique oncology or genetic disease studies that may not be offered in on-market products.
Archer NGS assays have the unique flexibility to solve these challenges. Not only can targets be easily added to existing panels, but Archer panels can be built from scratch for your unique use case. Additionally, Archer Analysis software works out-of-the box with your custom panel and has several customizable settings, allowing you to get to the data you need.
How have some labs used custom Archer assays?
- Fast addition of a relevant fusion—A lab with established use of FUSIONPlex™ Pan Solid Tumor v2 was able to add LTK fusion detection within weeks of publications citing its importance in NSCLC.
- Efficient solution for thyroid neoplasms—A lab developed a 27-gene VARIANTPlex™ panel along with a 33-gene FUSIONPlex panel for the comprehensive detection of fusions, SNVs, indels, CNVs and expression levels in thyroid tumors. Customization allowed the lab to efficiently interrogate these samples by selecting only targets relevant in thyroid neoplasms, thus optimizing read depth requirements.
- Small panel optimized for deep sequencing—A 3-gene VARIANTPlex panel was developed by a lab for the detection of low-frequency SNVS, indels, and ITDs relevant for AML MRD applications. The small panel allowed the lab to sequence the panel very deeply with the available read capacity of their sequencing platform.
- Supplementary modules for lymphomas—A lab added 37 genes relevant in lymphomas along with >1,000 SNPs for the detection of chromosomal arm CNVs using supplementary modules that can be discreetly mixed with the VARIANTPlex Myeloid panel as desired, for maximum flexibility during sample interrogation.
- Multi-institution sarcoma panel with platform and target flexibility—A multi-institutional consortium developed a FUSIONPlex panel for the detection of fusions, SNVs, and indels in sarcomas. To allow for each institution to used their preferred platform, the assay was made available with both Illumina® and Ion Torrent™ chemistry reagents. Though the core FUSIONPlex panel content was developed with the consortium, individual institutions have been able to further customize it with the addition of genes using supplementary primer modules.
- High volume myeloid characterization—A high volume lab developed a VARIANTPlex panel that sequences exon regions within 50 genes associated with myeloid malignancies, including all exons for 21 genes and select exons for 29 genes. The panel was used to sequence over 24,000 samples to characterize the mutational landscape of myeloid malignancies.
How does adding targets affect assay performance?
Archer assays use patented Anchored Multiplex PCR (AMP™) chemistry for accurate and comprehensive identification of genomic alterations. AMP primers function independently, meaning gene content can be easily mixed in without compromising assay performance.
Figure 1. High performance regardless of primer pool size. Primer uniformity, coverage uniformity, and on-target percent are all high for small (n = 228 primers), medium (n = 554), and large (n = 2058) panels tested.
How is Archer Analysis flexible?
Archer Analysis settings can be adjusted in several ways based on your lab’s application and data requirements. Default variant filtering can be customized and applied across analysis jobs for efficient data review. In oncology panels assessing MSI and TMB, values for call thresholds can be changed based upon your lab’s preference. Also, outputs can be customized based on the data you want to provide. REST API access allows you to programmatically move your data in and out of Archer Analysis. Archer Analysis Unlimited autoscales without user intervention to leverage cloud computing resources according to your analysis needs.
Services
How can I get started?
To get started on customizing an existing panel or creating a new one from scratch, go to the Archer assay design tool, Assay Marketplace and sign up for an account.
Assay Marketplace leverages Archer’s ever-expanding database of predesigned, functionally tested primers optimized for the intended sample type. You can browse by disease application, sequencing platform, or nucleic acid input. You can also upload a gene list and let Assay Marketplace recommend the best catalog or custom panel that meets your lab’s need.
Though Assay Marketplace offers the fastest turnaround time and the ability to customize panels on your own, we understand that your lab may need additional customization solutions. Archer Assay Designer and Designer Pro™ services are available for more in-depth, hands-on support from our expert team of design scientists. Contact us to learn more.
Custom assay services
| Assay Marketplace | Assay Designer service | Designer Pro service | |
|---|---|---|---|
| Predesigned and functionally tested primers | Yes | Yes | Yes |
| De novo primers | No | Yes | Yes |
| In silico design review | No | Yes | Yes |
| Functional testing | No | No | Yes |
| Turnaround time for initial order | 2–4 weeks | 6–8 weeks | 12–16 weeks |
| Minimum number of reactions for initial order | 24 | 24 | 144 |
| Cost | $ | $$ | $$$ |
Can I talk to someone about a custom panel design?
Absolutely! Contact us using the form below and we’ll be happy to discuss your custom panel design.
Resources
Frequently asked questions
What does it mean for primers to be functionally tested?
Functional testing means that primer design meets predetermined thresholds for various metrics including primer and coverage uniformity. Input types and amounts used during functional testing are representative of the assay’s intended molecule type and workflow. To test functionality for FUSIONPlex™ designs, DNA input, in addition to RNA, is used to assess primer functionality in the absence of target expression variability.
References
- Chunn LM, Nefcy DC, Scouten RW, et al. Mastermind: A Comprehensive Genomic Association Search Engine for Empirical Evidence Curation and Genetic Variant Interpretation. Fron Genet. 2020; 11: 577152.