Comprehensive solid tumor profiling from low-input FFPE

The Archer Comprehensive Solid Tumor (CST) Kit is comprised of two complementary targeted NGS kits to detect gene fusions, expression, SNVs, CNVs and indels from FFPE and fresh frozen samples. CST is expertly designed to utilize both DNA and RNA in VariantPlex™ and FusionPlex® Solid Tumor kits in parallel to cover relevant exons in 40 genes associated with solid tumors.

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

Features

  • Parallel workflows - Libraries can be concurrently created from RNA and DNA from a single sample
  • In-house analysis - Comprehensive mutation detection for translational research is performed in-house, so there is no need for sample send-outs

Archer Comprehensive Solid Tumor FusionPlex and VariantPlex kits


The Comprehensive Solid Tumor Kit for Illumina®-HS comprises 48 reactions of both FusionPlex and VariantPlex assays separately targeting mutations from both RNA and DNA.

AB0110 - Comprehensive Solid Tumor Kit for Illumina®-HS, 48 reactions

FusionPlex CTL assay detects lung and thyroid cancer-specific fusions, SNVs and indels
Detect fusions,
SNVs and indels
from RNA

AB0057 - FusionPlex┬« Solid Tumor Kit, for Illumina®, 48 Reactions

VariantPlex CTL assay detects lung and thyroid cancer-specific CNVs, SNVs and indels
Detect CNVs,
SNVs and indels
from DNA

AB0080 - VariantPlex┬« Solid Tumor Kit, for Illumina®, 48 reactions



How it works

Total nucleic acid (TNA) is purified from a formalin-fixed, paraffin-embedded (FFPE) sample or a fresh frozen tissue sample. As little as 20ng TNA is then used with each kit to generate a targeted library from RNA (FusionPlex Solid Tumor) and DNA (VariantPlex Solid Tumor).

The libraries are then pooled and sequenced, and the Archer Analysis bioinformatics platform analyzes the data to identify fusions and alternative splicing events from the RNA and copy number variants (CNVs), SNVs and indels from the DNA in the 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.


Solid Tumor Kit gene targets

  •  Fusion
  •  Mutation
  •  Splicing
  •  CNV
ABL1
  
CDKN2A
  
FGFR3
 
KRAS
  
NRAS
  
RELA
   
AKT1
   
CSF1R
   
FGFR4
    
MAML2
   
NRG1
   
RET
 
AKT3
   
CTNNB1
   
FGR
   
MAP2K1
   
NTRK1
   
RHOA
   
ALK
 
DDR2
  
FLT3
  
MAP2K2
    
NTRK2
   
ROS1
  
APC
  
EGFR
FOXL2
   
MAST1
   
NTRK3
   
RSPO2
   
AR
    
ERBB2
  
GNA11
   
MAST2
   
NUMBL
   
RSPO3
   
ARAF
    
ERBB3
  
GNAQ
   
MDM2
  
NUTM1
   
SMAD4
  
ARHGAP26
   
ERBB4
  
GNAS
  
MET
PDGFRA
SMARCB1
  
ATM
  
ERG
   
H3F3A
   
MLH1
   
PDGFRB
   
SMO
  
AURKA
  
ESR1
  
HNF1A
   
MPL
   
PIK3CA
 
SRC
   
AXL
   
ETV1
   
HRAS
   
MSMB
   
PIK3R1
  
STK11
  
BRAF
 
ETV4
   
IDH1
   
MTOR
    
PKN1
   
TERT
  
BRD3
   
ETV5
   
IDH2
   
MUSK
   
PPARG
   
TFE3
   
BRD4
   
ETV6
   
INSR
   
MYB
   
PRKCA
   
TFEB
   
CCND1
   
EWSR1
   
JAK1
    
MYC
   
PRKCB
   
THADA
   
CCNE1
  
EZH2
   
JAK2
  
MYCN
   
PTEN
  
TMPRSS2
   
CDH1
  
FBXW7
  
JAK3
  
NOTCH1
 
PTPN11
   
TP53
  
CDK4
  
FGFR1
 
KDR
  
NOTCH2
   
RAF1
   
VHL
  
CDK6
    
FGFR2
 
KIT
  
NPM1
   
RB1
  

Comprehensive solid tumor profiling enables simultaneous detection of all mutation types

The FusionPlex and VariantPlex Solid Tumor kits together provide a comprehensive, targeted sequencing approach to detect all types of driver mutations in solid tumors. When used in parallel, fusions, CNVs, SNVs and indels can be detected in genes associated with an array of carcinomas, as well as some sarcomas and lymphomas.

The figure below provides an example of comprehensive mutation profiling of non-small cell lung cancer (NSCLC) FFPE samples with VariantPlex and FusionPlex Solid Tumor kits.


Distribution of mutations by class, gene and amino acid variant in 50 NSCLC FFPE samples.Archived FFPE specimens were screened by NGS for variants in DNA and RNA using Archer VariantPlex and FusionPlex assays, respectively. Fifty total driver mutations were found, some in very low-quality FFPEs. Frequency of variants is reported by class of mutation and broken down by gene within each class. KRAS and EGFR SNVs were the most frequent variants; these groups are further stratified by amino acid change. Number of samples represented by each chart is indicated (n).

Conventional methods to detect these mutations, such as karyotyping, immunohistochemistry (IHC), RT-PCR and fluorescence in situ hybridization (FISH) lack the multiplexing capability to detect mutations across multiple gene targets and cannot detect different mutation types in a single assay. This makes comprehensive mutation profiling of low-input clinical sample types (i.e. FFPE) impractical.

NGS enables comprehensive and accurate mutation profiling to fully characterize clinical tumor samples. With CST kits, unidirectional gene-specific primers and molecular barcoded adapters are used for amplification, allowing for detection of both known and unknown mutations across relevant target genes.

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.