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 . 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.