nCounter® Gene Fusion Panels and CNV Assays

Helping Your Research

Increasing numbers of actionable fusions have made traditional technologies such as PCR and FISH inefficient and costly.  NGS can profile multiple fusions in a single assay but is slow, complex, and expensive. Combined with direct digital counting on the nCounter® Analysis System and Junction Sequence probe design, the detection of fusion genes is highly sensitive, quantitative, and easy: 

  • Directly detect hundreds of fusions in one assay 
  • Gets results in less than 24 hours with less than 15 minutes of hands-on time 
  • Use challenging sample types including FFPE tissue sections                   
  • Multiplex at the price of single-plex assays 

How it Works

nCounter CNV Assays: direct and robust CNV detection with a simple workflow

Aberrations in copy number are implicated in many diseases, from genetic disorders to cancer.  FISH has traditionally been used to detect CNVs, but the growing number and importance of CNVs has made higher-plex technologies such as microarrays and NGS more attractive.  However, these approaches require cumbersome and time-consuming workflows and a significant amount of expertise.  Additionally, most microarrays are not able to resolve CNVs from FFPE samples.


NanoString’s nCounter technology makes it easy to directly quantify CNVs from up to 800 loci with:

  • Robust performance on FFPE
  • A simple assay that doesn’t require expertise
  • Minimal hands-on time and fast time-to-results
  • Lower cost than FFPE microarray assays or NGS

Additionally, the nCounter v2 Cancer Copy Number Assay offers an off-the-shelf option for multiplexed quantification of 87 genes commonly amplified or deleted in cancer including PIK3CA, AKT, PTEN, BRCA, ERBB2, and MYC.

  • Optimized for FFPE samples
  • Copy number analysis of 87 genes commonly amplified or deleted in cancer
  • Digital quantitation of highly amplified genes
  • Specific detection of bi-allelic and multi-allelic number of copies

You can choose from several options to meet your lab’s fusion detection needs:

Panel Selection Tool

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Product Information

Product Specifications 
Lung Panel Gene Fusions
Leukemia Panel Gene Fusions
Catalog Information
nCounter v2 Cancer CN Assay Gene List
Product Specifications 
Lung Panel Gene Fusions

The Vantage 3D™ Lung Fusion Panel includes 63 probes: 35 for specific fusion detection, 24 for positional gene expression imbalance detection, and 4 internal reference genes.  Specific Lung Gene Fusion Probes detect the following gene fusion families:

Lung imbalance probes detect gene expression imbalance in the following genes:

Leukemia Panel Gene Fusions

The Vantage 3D Leukemia Fusion Panel includes 42 probes in total: 27 for specific fusion detection, 12 leukemia genes, and 3 internal reference genes.

Leukemia Gene Fusion Probes detect the following gene fusion families:

Catalog Information
nCounter v2 Cancer CN Assay Gene List

Related Resources

View All Resources
Product Bulletin nCounter CNV Assay – Product Bulletin
Product Bulletin Gene Fusion Panels – Product Bulletin
App Note/Tech Note Tech Note – Analyzing FFPE Specimens with the nCounter® Copy Number Variation (CNV) Assay
App Note/Tech Note Tech Note – Optimal Thaw/Freeze Cycle Analysis for nCounter® Lung Gene Fusion Panel


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