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All corporate workshops are presented on Wednesday, October 31 in Room 302C.
Margaret Gulley, MD
Margaret Gulley, MD from the UNC School of Medicine describes her group’s method to quantify cancer mutations alongside tumor-related viral and bacterial pathogens in plasma and FFPE tissue using modified off-the-shelf Archer NGS reagents combined with Archer Analysis bioinformatics. She will discuss analytic and clinical interpretation criteria and the value of molecular barcodes and noise reduction algorithms in patient and control DNA.
Jay Brock, PhD
Jay Brock, PhD from Cleveland Clinic describes his group’s experience validating and bringing up a custom DNA-based Archer® myeloid NGS assay combined with the Archer Analysis bioinformatics platform for use in their institution.
Bob Daber, PhD, DABMG
Archer Analysis is a versatile bioinformatics platform that automates the processing of sequencing data generated from all Archer NGS assays. This versatility extends to the ability to integrate Analysis into various upstream data preparation and downstream reporting platforms. In this workshop, Aaron Berlin, Vice President of Bioinformatics and Commercial Development at ArcherDX, will introduce Archer Analysis and describe recent updates that improve accuracy in variant calling and integration. Then Bob Daber, PhD, DABMG, President and Chief Technology Officer at Genosity, will describe how his team integrated Archer Analysis into their clinical reporting software.
Friday, Nov 2, 2:30-3:30pm
Namitha M. Nair, Josh D. Haimes, Marc Bessette, Laura Johnson, Kaitlyn E. Moore, Laura M. Griffin, Abel Licon, Ryan D. Walters
ArcherDX, Boulder, CO USA
Introduction Acute Myeloid Leukemia (AML) is clinically and biologically heterogeneous, requiring the detection of mutations across multiple genes for characterization. FLT3-ITDs and CEBPA mutations represent important markers in AML, however they are difficult to detect by NGS due to the highly variable nature of ITDs, the high GC content of CEBPA, and the difficulty in mapping repeated sequences to a wild-type reference.
Methods We developed Archer® VariantPlex® myeloid assays based on Anchored Multiplex PCR (AMP™) to detect important mutations in myeloid malignancies, including FLT3-ITDs and CEBPA variants. AMP is a target enrichment strategy for NGS that uses molecular-barcoded adapters and single gene-specific primers for amplification, permitting open-ended capture of DNA fragments from a single end. This approach enables flexible and strand-specific primer design to provide better coverage of ITD-containing regions of FLT3 and GC-rich regions of CEBPA.
Results In silico FLT3-ITD datasets enabled optimization of the Archer Analysis ITD detection algorithm. This algorithm used in combination with the VariantPlex Core Myeloid assay enabled detection of FLT3-ITDs down to <0.1% AF. Furthermore, we show 100% concordance of a VariantPlex Core AML assay with other methods commonly used to detect FLT3-ITDs from 25 blood and bone marrow samples. We detected concomitant non-ITD variants in FLT3 and NPM1 in some of these samples. Finally, we show >1000x unique molecule coverage across the entire coding region of CEBPA with 2M reads and 50ng input.
Conclusions AMP provides NGS-based detection of complex mutation types that are relevant in AML, including FLT3-ITDs and CEBPA variants.
Saturday, Nov 3, 9:45am-10:45am
Verity Johnson, Kaitlyn Moore, Laura Griffin, Armin Winands, Abel Licon, Ryan Walters
ArcherDX, Boulder, CO USA
Introduction The mutational landscape of a vast array of pediatric and adult cancers is changing at a rapid pace, however targeted NGS assays typically lack the flexibility to adapt to changing mutational landscapes. For example, adding new targets to existing primer panels often requires redesign of the entire panel and expansion of panel size risks reducing the sensitivity of variant detection. Here, we describe a target enrichment method for NGS, Anchored Multiplex PCR (AMP™), which enables sensitive detection of variants regardless of panel size while permitting flexibility in panel design.
Methods AMP is a target enrichment strategy that uses unidirectional gene-specific primers and molecular barcoded (MBC) adapters ligated to DNA ends for amplification. We designed the Archer® VariantPlex® NGS assays to detect single nucleotide variants (SNVs), insertions and deletions (indels) and copy number variants (CNVs) with a customizable set of panel targets.
Results We assess the performance of the VariantPlex Solid Tumor Focus panel using reference materials titrated from 50ng to 1ng total input. We show that this panel is able to detect CNVs, as well as SNVs and indels with allele frequencies down to 5%. Furthermore, we compare per variant sensitivity and CNV sensitivity across input amounts for this panel alone and in the context of additional content that substantially increases the total targeted genomic sequence. Our data show that these assays maintain similar abilities to detect variants in small and large panels.
Conclusions Our results demonstrate that AMP-based NGS assays are sensitive while maintaining flexibility in panel design.
To address the existing bottlenecks of using NGS in translational research, we’ve created a robust platform that is purpose-built for clinical oncology research.
By combining revolutionary Anchored Multiplex PCR (AMP™) chemistry with an easy-to-use workflow and intuitive software, we are unleashing the power of translational NGS to enable accurate and scalable mutation detection.
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