The Archer® VariantPlex® Solid Tumor Kit is a targeted sequencing assay that simultaneously detects and characterizes single nucleotide variants (SNVs), copy number variations (CNVs) and insertions and deletions (indels) in 67 genes associated with solid tumors.
For Research Use Only. Not for use in diagnostic procedures.
# of GSP2s
Total target size
Input DNA required‡
Recommended # of reads†
Coverage uniformity > 20% mean†
Fresh frozen or FFPE
†Expected coverage uniformity at the recommended read depth.
‡input recommendations for FFPE samples vary depending on Archer Preseq® DNA QC score. 50ng input recommended in absence of PreSeq screening
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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.
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 a few 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.
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