Archer VariantPlex
Solid Tumor Kit


Introduction

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.

Highlights

  • Low input requirements - greater target recovery for low-input FFPE samples
  • Quantitative - molecular barcoding enables robust and accurate CNV calling
  • Simple workflow – lyophilized reagents and in-line fragmentation for rapid turn-around time
  • Better Data – AMP chemistry produces higher-complexity libraries for superior data

For Research Use Only. Not for use in diagnostic procedures. For Research Use Only. Not for use in diagnostic procedures.



Product information

Illumina®

AB0076 - 8-reactions
AB0078 - 16-reactions - starter kit
AB0080 - 48-reactions

Archer Analysis

Local installation
Analysis Unlimited

Demo Data Get a quote

Documents

Product InsertHS ProtocolOriginal Protocol
Publications Posters

Specifications and performance

67

Gene targets

660

# of GSP2s

~51.0kb

Total target size

≥10ng

Input DNA required

2.5 million

Recommended # of reads

>94%

Coverage uniformity > 20% mean

2.5 hours

Hands-on time

1 day

Total time


Illumina

Platform

Fresh frozen or FFPE

Sample types

†Coverage uniformity and recommended number of reads expected.
‡input recommendations for FFPE samples varies depending on Archer Preseq® DNA QC score. 50ng input recommended in absence of PreSeq screening

Gene targets

ABL1
AKT1
ALK
APC
ATM
AURKA
BRAF
CCND1
CCNE1
CDH1
CDK4
CDKN2A
CSF1R
CTNNB1
DDR2
EGFR
ERBB2
ERBB3
ERBB4
ESR1
EZH2
FBXW7
FGFR1
FGFR2
FGFR3
FLT3
FOXL2
GNA11
GNAQ
GNAS
H3F3A
HNF1A
HRAS
IDH1
IDH2
JAK2
JAK3
KDR
KIT
KRAS
MAP2K1
MDM2
MET
MYC
MYCN
MLH1
MPL
NOTCH1
NPM1
NRAS
PDGFRA
PIK3CA
PIK3R1
PTEN
PTPN11
RB1
RET
RHOA
ROS1
SMAD4
SMARCB1
SMO
SRC
STK11
TERT
TP53
VHL

Need to modify this panel?

Add any of our wet lab-validated designs to this panel with Archer Assay Designer to build an assay that fits your exact requirements.

Video: VariantPlex Solid Tumor Kit

 

Expert primer design

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:

  • Flexible primer design for superior coverage of large exons
  • Inclusion of intronic buffers
  • Coverage of challenging regions of the genome

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.

The VariantPlex Solid Tumor Kit shows high coverage across EGFR exon 21

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.

Sensitive and concurrent CNV detection

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.

The VariantPlex Solid Tumor Kit detects multiple CNVs concurrently

Multiple CNVs detected concurrently. PDGFRA and KIT focal amplification detected in FFPE sample using the VariantPlex Solid Tumor Kit.
» Click image to enlarge.

VariantPlex + FusionPlex = comprehensive tumor mutation detection

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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How to contact us

Address

2477 55th Street, Suite 202

Boulder, CO 80301

Phone

Phone: (877) 771 1093

Phone: (303) 357 9001

All content © 2018 ArcherDX, Inc.

For Research Use Only. Not for use in diagnostic procedures. For Research Use Only. Not for use in diagnostic procedures.