Authors: Glen Bjerke, Taylor Patterson, Devin Tauber, Allison Hadjis, Ryan Rogge, Dhruti Legare, Mark Rogers, Laura Johnson, Brent Lutz
Published: 2025-04-21
DOI: 10.1158/1538-7445.am2025-4615
Source: Full article
Comprehensive Genomic Profiling (CGP) for cancer research has arisen out of the need for Next Generation Sequencing (NGS) tests that can be used across tumor types and detect both discreet genomic changes and genome-wide biomarkers. Herein, we detail IDT’s Archer CGP suite of assays, offering cutting-edge precision oncology research solutions designed to provide a thorough and accurate molecular characterization of tumors. This modular set of assays includes VARIANTPlex (DNA) and FUSIONPlex (RNA) profiling with a full range of biomarkers that offer high concordance with established orthogonal methods, ensuring both reliability and reproducibility in genomic profiling. The newest component of Archer's CGP assays is Homologous Recombination Deficiency (HRD) analysis, which is based on Archer’s tumor-only Copy Number Variation 2.0 (CNV2.0) and Allele Specific Copy Number (ASCN) calling along with an independent measure of Non-homologous End Joining (NHEJ). Archer’s HRD solution comprises a modular set of chemistry targets that can be added to any VariantPlex panel and an HRD bioinformatics workflow within Archer Analysis software. Our HRD pipeline shows high concordance with orthogonal Genomic Instability Score (GIS) methods and consistent calling across various targeted panels and input masses. Additional CGP biomarkers for DNA analyses include Microsatellite Instability (MSI) and tumor mutational burden (TMB) calling. In addition to genome-wide biomarker analysis, all VARIANTPlex panels include Single Nucleotide Variant (SNV), Insertion/Deletion (InDel), and Internal Tandem Duplication (ITD) calling with panel sizes of up to 460 genes. The RNA components of Archer’s CGP offering are FUSIONPlex panels that allow fusion calling from low purity (>= 10% tumor cellularity) samples along with RNA variant calling, which we show to be consistent with DNA allele frequencies. Furthermore, all VARIANTPlex and FUSIONPlex panels can be customized to allow users the flexibility to make a CGP solution according to their individual needs. Archer’s CGP panels offer a complete end-to-end solution including automatable chemistry workflows, Archer Analysis bioinformatics software, integration with Molecular Heath’s Guide Case Annotation Solution (CAS) tertiary analysis platform, and now include tumor-only HRD calling along with the full suite of biomarker testing for RNA and DNA panels.