nCounter® Gene Fusion Panels and CNV Assays

Gene Fusion Panels: The Right Balance of Plex, Turnaround Time, and Cost

Multiplexed analysis of gene fusion events

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 costly. 

Combined with direct digital counting on the nCounter 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 hrs with just 15 minutes of hands-on time
  • Use challenging sample types including FFPE tissue                  
  • Multiplex at a cost similar to single-plex assays

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

 

Feature

Specifications

Input Material

50–100 ng Purified Total RNA (~5000–10,000 cells) 150–300 ng FFPE extracted RNA

Hands On Time

~15 min

Time to Results

Approximately 24 hrs

Sample Type

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

MAX or FLEX: Panel CodeSet and Master Kit

SPRINT: Panel CodeSet and SPRINT Cartridge and Reagent Pack

 

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:

 

ALK

RET

ROS

NTRK1

EML4-ALK

CCDC6-RET

CD74-ROS1

CD74-NTRK1

HIP1-ALK

KIF5B-RET

EZR-ROS1

MPRIP-NTRK1

KIF5B-ALK

 

GOPC-ROS1

 

TFG-ALK

 

LRIG3-ROS1

 

TPR-ALK

 

SDC4-ROS1

 

 

 

SLC34A2-ROS1

 

 

 

TPM3-ROS1

 

 

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

 

ALK

RET

ROS

8 probes

8 probes

8 probes

 

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:

CML

ALL

AML

AML/APL

BCR-ABL

E2A-PBX1

AML-ETO

PML-RARA

 

MLL-AF4

CBFB-MYH11

 

 

TEL-AML1

DEK-NUP214

 

 

 

RPN1-EVI1

 

 

Leukemia Gene Expression Probes:

Genes for AML, CML, and ALL

BAALC

ERG

FLT3

MECOM

MLLT11

MN1

NRAS

PRAME

RB1

SOCS2

TP53

WT1

 

Click here to view publications.

Product

Description

Catalog Number

Unit Size

nCounter® Vantage 3D™ Lung Gene Fusion Panel 

Includes 63 probes: 35 for specific fusion detection, 24 for positional gene expression imbalance detection, and 4 internal reference genes. 

Master Kit reagents sold separately.

VRXC-LGF-12

12 reactions

nCounter® Vantage 3D™ Leukemia Gene Fusion Panel 

Includes 42 probes:  27 for specific fusion detection, 12 leukemia biomarkers, and 3 internal reference genes.

Master Kit reagents sold separately.

VRXC-LKF-12

12 reactions

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 not requiring expertise                   
  • Minimal hands-on time and fast results
  • Lower cost than FFPE microarray 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 (see table below).

  • 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

 nCounter® v2 Cancer CN Assay Gene List

nCounter® v2 Cancer CN Assay Gene List


Feature Specifications
Genomic regions analyzed in one reaction 87 genes commonly amplified or deleted in cancer (average 3 probes/region)
Recommended amount of starting material 300 ng total genomic DNA
Sample types supported
 
Human genomic DNA from FFPE samples, fresh or frozen tissue, or cell lines
Number of copies detected 0-4, multiallelic
nCounter® Prep Station throughput 12 samples < 2.5 hours
nCounter® Digital Analyzer throughput 12 samples / 2.7 hours
Controls 54 invariant genomic regions and spike-in process controls

Click here to view publications regarding CNV.

Product Description Catalog Number Unit Size

nCounter® v2 Cancer CN Assay

Enables copy number quantification for 87 genes commonly amplified or deleted in cancer. Optimized for FFPE analysis. Master Kits sold separately. XT-CSO-CAN2-12 12 reactions

nCounter® Human Karyotype Panel

Accurate monitoring of gross chromosomal abnormalities for all 24 human chromosomes. Master Kits sold separately. XT-CSO-KAR15-12 12 reactions

 

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