Powered by Anchored Multiplex PCR (AMP™) and state-of-the-art bioinformatics, Archer® VariantPlex® Myeloid assays are expertly designed to provide unprecedented confidence in mutation detection for myeloid malignancies.
For Research Use Only. Not for use in diagnostic procedures.
Targets in bold indicate content addition from smaller panel
* CNV detection only.
** Available with Archer Assay Designer. Click the link below.
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FLT3 encodes a tyrosine kinase that is frequently mutated in hematologic malignancies. Internal tandem duplications (ITDs) in FLT3 have been detected in over 20% of acute myeloid leukemia (AML) cases and confer an aggressive phenotype. Importantly, FLT3 is the target of promising new therapeutics, yet NGS-based methods often fail to detect FLT3-ITDs, as many variant callers fail to identify these highly variable repeated sequences.
The VariantPlex myeloid kits contains independent and bi-directional probes specifically optimized for detecting ITDs of all sizes within the commonly mutated juxtamembrane domain and tyrosine kinase domain 1. The reads originating from those probes can be bioinformatically assembled using a de novo assembler to form longer consensus sequences that span the ITD. These longer sequences can then be aligned to the reference genome to identify the presence of an ITD.
The molecular landscape of leukemia and lymphoma has expanded exponentially in the last two decades, and the complexity and scope of biomarkers makes molecular analysis difficult for any single approach. Archer assays are powered by AMP target enrichment chemistry to detect multiple mutation types and gene expression profiling in a single sample.
GSPs (gene specific primers) in the region of FLT3 in which ITDs occur and simulated bi-directional reads that are then assembled and compared to the reference genome to detect the ITD. ITD information is reported in Archer Analysis, with a tiered reporting structure and event visualization in JBrowse.
De-duplication of reads allows for true coverage information – i.e. the reported coverage depth represents the number of unique input molecules that were captured and sequenced not the number of PCR duplicates that were sequenced. VariantPlex myeloid panels are designed to have superior unique molecule coverage across all targeted genes, including challenging regions like CEPBA, DNMT3A and RUNX1.
CEBPA contains 75% GC content over its coding region, making amplification and sequencing of the region challenging. AMP technology is well suited for amplification of this region due to flexible primer design strategies. Unlike opposing primer–based techniques, only one primer location needs to be designed. These primers are independent and can be moved around to give the best chance of amplification across the gene. Additionally, since Archer libraries and mutation calls are based on unique reads rather than PCR duplicates, variant calling can be made with library-specific knowledge of sensitivity.
Complete, strand-specific and bi-directional coverage of target exons, including traditionally difficult regions like CEBPA.
Powerful analysis of complex variants like CALR deletions can be detected using Archer Analysis due to the unique benefits of Anchored Multiplex PCR and extensive testing with positive samples and in-silico read generation technology.
Detecting copy number variants (CNVs) for cancer genome analysis is essential, given the frequent occurrence of these aberrations during carcinogenesis. Chromosomal arm loss is prevalent in certain myeloid malignancies (e.g., -7/7q, -5/5q, -13q, -11q and -12p/12p). The VariantPlex Myeloid panel targets key genes within these chromosomes to indicate copy loss. The CNV visualization tool within Archer Analysis was designed to detect copy number gains and losses, in addition to novel variants, with exon-level resolution.
Copy number losses in 5 key genes in chromosome 7 as visualized in Archer Analysis. Each dot represents normalized molecular barcode counts from a gene-specific primer 2 (GSP2), color-coded by gene.
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