Welcome aboard, B cells! Characterize isotypes, subtypes and somatic hypermutations with the new Archer® Immunoverse™ BCR kits.
Stop by booth 440 and see how both Immunoverse BCR and TCR kits enable sensitive and quantitative profiling of the expressed immune repertoire. The kits feature easy-to-use, lyophilized reagents to generate sequencing-ready libraries from RNA. Sequenced libraries are then analyzed using the Immune Repertoire pipeline in Archer Analysis, a powerful and transparent tool for clonotype identification and frequency reporting.
Jens Eberlein1, Thomas Harrison1, Jennifer Sims2, Ian McKittrick1, Megan Wemmer1, Laura M. Griffin1, Brady P. Culver1, Laura Johnson1, Brian A. Kudlow1
1ArcherDX, Inc., Boulder, CO USA; 2Q2 Solutions | EA Genomics, Morrisville NC, USA
Introduction NGS-based analysis of the immune repertoire (IR) is a powerful tool to monitor disease, adaptive immune responses to disease, vaccination and therapeutic interventions. IR characterization by NGS usually requires large primer panels, due to the extensive combinatorial diversity, and a complex system of synthetic controls to account for differential amplification efficiency across segment combinations. Anchored Multiplex PCR (AMP™) uses molecular barcoded (MBC) adapters and gene-specific primers (GSPs), enabling NGS-based immune chain mRNA interrogation from a single side. This eliminates the need for opposing primers that bind within the highly variable V-segment, eliminating clone dropout due to somatic hypermutation. Here, we describe AMP-based NGS assays for IR characterization, Immunoverse™ IGH and TCR, which utilize a minimal set of unidirectional GSPs and MBC adapters that reduce amplification bias.
Methods The quantitative reproducibility and sensitivity of our assays was validated using mRNA isolated from PBMCs of healthy donors, B-cell chronic lymphocytic leukemia donors and formalin-fixed paraffin-embedded (FFPE) tissue.
Results Both assays demonstrated high reproducibility between replicates with quantitative clone tracking down to 0.01%. The ability to determine isotype, clonotype and IGHV mutational status in a single assay was demonstrated. Preliminary TCR assay data indicates that CDR3 sequence capture is possible from FFPE tissue with clonotype calling being driven by input quantity, T-cell content, and, to a lesser degree, mRNA quality.
Conclusions AMP-based NGS with MBC quantification and error-correction is a powerful method to characterize the immune repertoire.
ArcherDX addresses the bottlenecks associated with using NGS by offering a robust platform for targeted sequencing applications.
Archer target enrichment assays utilize AMP chemistry to generate highly enriched sequencing libraries for comprehensive profiling of fusions, CNVs, SNVs and indels. Amplification from independent, unidirectional primers and universal molecular barcoded adapters permit identification of novel gene fusions and mutations with nucleotide-level resolution. Requiring only one intact primer-binding site, AMP chemistry is uniquely suited to amplify small, degraded fragments, enabling solid tumor mutation profiling from FFPE samples and liquid biopsies.
Archer’s easy-to-use, lyophilized kits generate sequencing-ready libraries from RNA, DNA, and liquid biopsy-derived ctDNA. Complemented by the Archer suite of assay design and bioinformatics analysis, Archer’s FusionPlex, VariantPlex and Reveal ctDNA assays facilitate complex mutation identification and discovery, while Immunoverse assays enable quantitative profiling of the expressed immune repertoire.
For Research Use Only. Not for use in diagnostic procedures.
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