Detect thyroid and lung cancer-specific variants from DNA

The Archer® VariantPlex™ Comprehensive Thyroid and Lung (CTL) Kit is an NGS-based targeted sequencing assay to detect CNVs, SNVs and indels in 31 thyroid and lung cancer-implicated genes. The kit covers entire targeted exons while maintaining high coverage uniformity (> 95%) and on-target reads (99.9%). When used alongside the RNA-based FusionPlex® CTL Kit, fusions, SNVs, CNVs and expression profiles can be analyzed from a single low-input FFPE sample.

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

Highlights

  • Expert primer design - Includes intronic buffers, superior target region coverage and high coverage uniformity
  • Orthogonal validation - Confirm relevant CNV and SNV calls when using the companion FusionPlex CTL Kit
  • Purpose-built - Optimized for low-input FFPE samples from fine needle aspirates (FNAs)
  • Molecular barcodes - Enable accurate CNV detection in relevant targets

Kit Specifications

Feature Specification‡
Input DNA Required 10-200ng*
Time Required 6 hours
Hands on Time 2.5 hours
Sample Type Fresh Frozen, FFPE
Total Target Size 19.5kb
Targets 290
Target Bases Covered >100%
On Target % >99%
Coverage Uniformity >20% of Mean >99.9%
Platform Illumina®
Recommended # Reads 1,000,000

‡ As observed with 50ng lung or adrenal genomic DNA
*Input recommendations for FFPE samples vary depending on Archer PreSeq™ DNA QC score. 50ng is recommended in absence of PreSeq screening.


Multiplexed CNV Detection

Molecular barcodes utilized in Anchored Multiplex PCR enable unique molecule counting and thus robust copy number variation detection. CNV calls made by Archer Analysis are highly correlated with aCGH and qPCR. In addition, CNV calls made in the VariantPlex CTL Kit track with expression profiles in relevant targets in the FusionPlex CTL Kit. 21 genes are enabled for CNV detection in the CTL Kit.

Figure 1 Amplification of MET in NSCLC FFPE sample

Figure 1. This figure shows 24.5x amplification of MET in an NSCLC FFPE sample. Additionally, when the sample was run with the FusionPlex CTL Kit, a 10.7x MET expression level and a MEF2D:NTRK1 fusion was identified.
» Click image to enlarge.


Accurate variant detection throughout entire exons

Primers in the CTL Kit are expertly designed to have outstanding coverage over the full exons that are targeted in the VariantPlex CTL Kit. A combination of molecular barcodes and unique start sites enable complex, deduplicated libraries for accurate variant calling.

Figure 2 Deduplicated reads over EGFR exon 21

Figure 2. This figure shows deduplicated reads over EGFR exon 21 derived from an NSCLC FFPE sample. The EGFR L858R was observed at 8% AF.
» Click image to enlarge.


Kit Targets


Gene Mutation CNV
AKT1
ALK
BRAF
CCND1
CTNNB1
DDR2
EGFR
EIF1AX
ERBB2
FGFR1
FGFR2
FGFR3
GNAS
HRAS
IDH1
IDH2
KIT
KRAS
MAP2K1
MDM2
MET
NRAS
PDGFRA
PIK3CA
PTEN
RET
ROS1
STK11
TERT
TP53
TSHR

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.