The VariantPlex™ Solid Tumor Kit is a targeted sequencing assay that simultaneously detects and characterizes single nucleotide polymorphisms (SNVs), copy number variations (CNVs) and insertions and deletions (indels) in 67 genes associated with solid tumors. Using proprietary Anchored Multiplex PCR (AMP™)-based enrichment, input molecules are uniquely tagged and prepared for sequencing on Illumina® Platforms.
For Research Use Only. Not for use in diagnostic procedures.
Total target size
Coverage uniformity > 20% mean
Input DNA required
Recommended # of reads
Fresh frozen or FFPE
‡input recommendations for FFPE samples varies depending on Archer Preseq™ DNA QC score. 50ng input recommended in absence of PreSeq screening
Hover over or click each gene target below to see if it has Full Exon coverage, Hotspot or CNV detection.
The VariantPlex Solid Tumor Kit was designed for superior coverage across the 67 gene targets in the table above. AMP chemistry provides the flexibility of enriching using a single primer into an adapter that is ligated to fragment ends, which enables:
Exons targeted in the Solid Tumor Kit are fully and uniformly covered to enable sensitive variant calling throughout exons of interest. Full-exon coverage of genes such as TP53 means known and de novo loss of function variants can be constantly reported.
Expert primer design enables high exon coverage. Libraries were prepared from adipose, adrenal, colon and lung genomic DNA (gDNA) using the VariantPlex Solid Tumor Kit and sequenced to a depth of 1.87M reads. The read pileup shows high coverage with superior uniformity across EGFR exon 21, random start sites for high library complexity and intronic buffers for maximum exon coverage.» Click image to enlarge.
Molecular barcodes ligated to DNA post-digestion enable unique molecule counting and thus robust copy number variation detection. By counting barcodes within target regions, normalizing across the other targets in the kit (or to a tumor normal sample) and applying advanced algorithms, Archer Analysis bioinformatics software can report any copy number variations present in the sample. And CNV calls made by Archer Analysis are highly correlated with aCGH and qPCR. Forty-three relevant genes are targeted for CNV detection in the Solid Tumor Kit.
Multiple CNVs detected concurrently. PDGFRA and KIT focal amplification detected in FFPE sample using the VariantPlex Solid Tumor Kit.
» Click image to enlarge.
Archer VariantPlex Kits are NGS-based targeted sequencing kits to simultaneously detect CNVs, SNVs and indels using DNA from low-input FFPE and other clinical sample types. The VariantPlex system is powered by AMP chemistry for target amplification. Unlike traditional opposing primer techniques, AMP uses random start sites that lead to better recovery of short fragments and increased library complexity. In addition, AMP incorporates molecular barcodes to track each input molecule for read de-duplication and error correction and thus accurate mutation calling.
All VariantPlex kits include gene-targeting primers, easy-to-handle lyophilized enzymes, Illumina® or Ion Torrent™ platform-specific reagents to generate targeted sequencing libraries and an Archer PreSeq DNA QC Assay to confirm your input material quality prior to library generation. The kit incorporates an in-line, all-in-one enzymatic fragmentation step that yields DNA fragments up to 1kb in length. The complete workflow time from sample to sequence is 6 hours, which includes 2.5 hours of hands-on time. After Illumina® sequencing, the data is analyzed with Archer Analysis, the purpose built bioinformatics software to detect, visualize and report CNVs, SNVs and indels.
Archer MBCs are also required, but provided separate for customizable multiplexing and indexing flexibility.
The FusionPlex and VariantPlex Solid Tumor kits combined provide a comprehensive, targeted sequencing approach to detecting driver mutations in solid tumors. These kits can be used in parallel for the comprehensive detection of relevant fusions, CNVs, SNVs and indels from a single, low-input FFPE sample. Labs can go from sample-to-report in 3-5 days. With the FusionPlex and VariantPlex parallel workflow, Archer provides the tools for in-house, comprehensive sample analysis for all relevant mutations, reducing necessary input amounts, costly send outs and long turn-around times.
|Gene||Full Exon||Select Exon||CNV|
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