Next-Generation
CNV-Detection

Archer VariantPlex

The 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. 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.

Highlights

  • Low Input - 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

VariantPlex Solid Tumor Kit Features

660

Targets

51.1kb

Total target size

>99%

Coverage uniformity > 20% mean

~ 1 day

Time required

10-200ng‡

Input DNA required

2M-3M

Recommended # of reads

99%

On-target

Illumina®

Platform

Fresh frozen or FFPE

Sample type

‡input recommendations for FFPE samples varies depending on Archer Preseq™ DNA QC score. 50ng input recommended in absence of PreSeq screening



Video: VariantPlex Solid Tumor Kit

 

Archer VariantPlex Solid Tumor Kit Targets


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.


About the VariantPlex System

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.


Archer's convenient VariantPlex Kit format

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 approximately 8 hours. 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.


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.


All VariantPlex Solid Tumor Kit targets

GeneFull ExonSelect ExonCNV
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
MLH1
MPL
MYC
MYCN
NOTCH1
NPM1
NRAS
PDGFRA
PIK3CA
PIK3R1
PTEN
PTPN11
RB1
RET
RHOA
ROS1
SMAD4
SMARCB1
SMO
SRC
STK11
TERT
TP53
VHL

Subscribe to stay in the loop







How to contact us

Address

2477 55th Street, Suite 202

Boulder, CO 80301

Phone

Phone: (877) 771 1093

Phone: (303) 357 9001

All content © 2017 ArcherDX, Inc.

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