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nCounter Vantage™ Gene Fusion Panels


Multiplexed Gene Fusion Detection Simplified

NanoString’s Vantage panels for Lung and Leukemia gene fusion detection enable a highly multiplexed assay capable of simultaneously characterizing key fusion events and selected reference genes in a single tube. Combined with direct digital counting of the nCounter® system and our patented Junction Sequence probe design, the detection of fusion genes is highly sensitive, quantitative, and easy.

Product Highlights

  • Save time and sample material with multiplexed gene fusion detection in a single tube.
  • Detect rare fusions with highly specific probes designed using patented Junction Sequence design technology.
  • Ideal for use with challenging sample types including FFPE tissue.
  • Customizable and forward compatible with our growing line of 3D Biology™ products.

Assay Details

Input Material 50–100ng Purified Total RNA (~5000–10,000 cells) 150–300ng FFPE extracted RNA
Hands on Time ~15 minutes
Time to Results <24 hours
Sample Type(s) FFPE, fresh frozen tissue, cell extracts, cell lysates
Customizable Features Add up to 24 additional genes or additional fusions with the nCounter® TagSet Extension product.
Data Analysis nSolver™ Analysis software
Required Reagents Panel CodeSet and Master Kit
Panel CodeSet and SPRINT™ Cartridge and Reagent Pack


Direct Detection and Counting of Fusion Events

No RT-PCR, No Library Prep, No more limitations with FISH assays.

nCounter Vantage™ Fusion Genes Panels: Work flow
The nCounter Analysis System utilizes a non-enzymatic protocol and novel digital color-coded barcode technology for the direct multiplexed measurement of gene expression.

Detect unique and complex fusions in the presence of abundant normal tissue

  • Junction Probes
  • 5’/3’ Expression
  • Customize
  • Data Analysis
  • Ordering Information

Junction Probes

Vantage Gene Fusion panels are created using one or more patented probe design methods.
Junction Probe Design:
NanoString’s patented Junction Probe Design enables highly specific detection of fusion junction sequences. Specificity is conferred by toehold exchange technology that utilizes an additional probe, the Protector Probe, to create a thermodynamic balance that ensures signal is only generated in the presence of a perfect match of the target sequence.1,2 This enables highly specific detection of fusions in a background of abundant normal tissue.

nCounter Vantage™ Gene Fusion Panels: Junction Probe Designs
FIGURE 1 Illustration of the junction probe design methodology. Junction probes span a unique fusion junction, using toehold exchange technology for greater specificity. For a technical explanation of toehold exchange technology, see Zhang DY, Chen SX, Tin P. (2012) Optimizing the specificity of nucleic acid hybridization. Nat Chem 4(3):208-14.

5’/3’ Positional Imbalanced Probe Gene Expression Design:

In some instances, fusion events can also be detected with a probe design that compares the ratio of gene expression upstream and downstream of a fusion junction. Each fusion partner may have promoters with different strength or activity, which will differentially affect expression of exons located 5’ or 3’ of this junction. A ratio of 5’/3’ expression that diverges from 1 is therefore indicative that a fusion event has occurred. The 5’/3’ design can be used to discover new fusions3 or to aid in the development of robust assays to support clinical research programs.4,5

Fusion Genes - 5'/3' Imbalance Designs

Diagram of a 5'/3' imbalance design with 4 probes upstream and 4 probes downstream of the fusion junction. The number of probes can be varied depending on user preferences. View the tab below for more information on 5'/3' Imbalance Designs.

  1. 1. Zhang et al. (2012) Optimizing the specificity of nucleic acid hybridization. Nat Chem 4(3):208-214.
  2. 2. Wu et al. (2015) Continuously tunable nucleic acid hybridization probes. Nat Methods 12, 1191-1196.
  3. 3. Suehara et al. (2012) Identification of KIF5B-RET and GOPC-ROS1 fusions in lung adenocarcinomas through a comprehensive mRNA-based screen for tyrosine kinase fusions. Clin Cancer Res 18(24):6599-6608.
  4. 4. Lira et al. (2013) Multiplexed gene expression and fusion transcript analysis to detect ALK fusions in lung cancer. J Mol Diagn 15(1):51-61.
  5. 5. Lira et al. (2014) A single-tube multiplexed assay for detecting ALK, ROS1, and RET fusions in lung cancer. J Mol Diagn 16(2):229-243.

Customize any Fusion Panel: nCounter Vantage Panels are available with the option to customize using our TagSet Extension product. With the additional purchase of the TagSet Extension product and custom designed probes, users can add up to 24-additional genes to any panel including:

  • Additional Fusion Genes
  • Disease or Tissue-specific genes
  • Immune response genes

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Fusion Data Analysis

Following hybridization with the nCounter Vantage Gene Fusion assay, samples are analyzed for fusion detection. Each target of interest is identified by the ‘barcode’ generated by six ordered fluorescent spots. The molecular barcode is then counted and tabulated for each target.

Detailed data analysis for Fusion panels is performed using our nSolver data analysis software. NanoString’s Field Application Scientists and Bioinformatics team can provide personalized training, data analysis and support. For more information on data analysis or to speak with one of our support scientists please contact us at: support@nanostring.com

Ordering Information

Description Format Quantity Catalog Number
nCounter Vantage Lung Fusion Panel Code Set Only 12 reactions XT-CSO-LKFU1-12
nCounter Vantage Leukemia Fusion Panel Code Set Only 12 reactions XT-CSO-XLKFU1-12
nCounter Master Kit (Max or FLEX Systems) Reagents and Cartridges 12 reactions NAA-AKIT-012
nCounter SPRINT™ Cartridge 1 Cartridge, 12 lanes 12 reactions SPRINT-CAR-1.0
nCounter SPRINT™ Reagent Pack Reagents A,B,C & Hybridization Buffer 192 reactions SPRINT-REAG-KIT

Forward-compatible nCounter Vantage assays for DNA or Protein Analysis

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