Clinical Research                                    Empowered by nCounter® Technology

More multiplexed than FISH and PCR…and faster, easier, and less costly than NGS

With guidelines recommending more multi-gene testing, labs are challenged with finding efficient and cost-effective approaches for testing multiple biomarkers in a single assay.  The nCounter platform is routinely run by labs around the world to quickly and easily detect fusions, CNVs, and changes in gene expression with a simple and robust workflow that generates results in less than 24 hours.   

  • Save sample, time, and money by plexing 100s of targets in a single tube 
  • Simple and fast workflow with results in less than 24 hours and 15 minutes hands-on time
  • Direct detection for more reproducible and accurate results
  • Robust performance with challenging sample types like FFPE
  • Off-the shelf or custom panels with in-house expertise for assay design and analysis


From Sample to Data in Just Three Simple Steps

Sample to data in just three simple steps workflow

Learn more about nCounter technology

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Direct Detection without Reverse Transcription or Amplification Ensures Accurate and Reproducible Results

Accurate and reproducible results are very important in clinical research, but complex workflows that rely on significant sample manipulations such as reverse transcription (RT), amplification, and library prep make this an ongoing challenge. nCounter technology cuts out these steps by direct hybridization of capture and reporter probes to target molecules, eliminating sources of bias. The nCounter platform is highly reproducible with R2 values of .97 and .98 across multiple sites and users*.

*these are typical results for the nCounter platform but will vary by assay.

Watch a video to learn more about direct detection with the nCounter.

Correlation of NanoString expression data

Robust Performance on Degraded FFPE Samples

FFPE tissue samples are a staple of clinical research, yet fragmentation and degradation make them difficult to work with.  When every sample is finite and precious, high failure rates are unacceptable.  A great demonstration of FFPE performance is achieving similar results from FFPE and matched frozen tissue. nCounter demonstrates excellent FFPE performance with highly concordant data from crude FFPE lysates and flash frozen tissues*.

*these are typical results for the nCounter platform but will vary by assay.

Learn more about FFPE performance on nCounter.

Counts from purified RNA extracted from FFPE human heart slices

The Right Balance of Plex, Turnaround Time, and Cost

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. 

NanoString’s nCounter platform allows you to:

  • Directly detect hundreds of fusions in one assay
  • Get results in less than 24 hrs with just 15 minutes of hands-on time
  • Multiplex at a cost similar to single-plex assays 

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

How it works:



Case Study

Development and Validation of a Sarcoma Fusion Assay at Vancouver General Hospital

Drs. Torsten Nielsen and Tony Ng

 Torsten Nielsen.png Tony Ng.jpg

The British Columbia Cancer Agency (BCCA) treats the whole province of British Columbia and almost all sarcoma patients get referred to Vancouver General Hospital.  Fusions play a critical role in sarcoma diagnosis and treatment, with many actionable fusions discovered to date. Pathologists Drs. Torsten Nielsen and Tony Ng were increasingly frustrated by constantly having to develop and validate additional PCR and FISH assays for every new fusion yet found NGS to be cumbersome and expensive for routine clinical research use. 

Using NanoString and nCounter technology, they were able to develop a comprehensive assay for sarcoma fusion that met their needs and was:

  • More multiplexed than PCR and FISH
  • Easy to run
  • Yielded results in less than 24 hrs
  •  Lower cost than NGS

The assay has been extensively validated and is now being requested globally by leading sarcoma researchers. Learn more about how this assay was developed, validated, and implemented:

Direct and robust CNV detection from FFPE 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


Detect CNVs with several options to meet your lab’s specific needs:

Learn more:

Democratized Access to Robust and Reliable Signature Development

Thousands of clinically relevant gene signatures have been described in the literature, but few have been developed into a standardized assay.  Implementing microarrays, qPCR, and NGS has proved to be challenging due to errors introduced during steps like library prep, RT, and amplification.

nCounter technology solves these issues with:

  • Direct digital detection with minimal sample manipulation
  • A simple workflow, eliminating error introducing steps
  • Proven reproducibility across multiple runs, users, and sites

Develop your own gene signature or implement an existing one with Custom CodeSets or Elements Reagents. If you would like a dedicated white-glove experience, take advantage of Contract Services to get expert help with assay design, validation, and implementation.


Case Study

From Gene Signature Discovery to Validated Assay

Dr. Jean Wang


The standard of care in acute myeloid leukemia (AML) is induction chemotherapy, followed by molecular and cytogenetic risk stratification. Unfortunately, many patients do not respond to chemotherapy or relapse even without adverse risk factors. The high rate of relapse has been attributed to the persistence of leukemic stem cells (LSCs). Dr. Wang at the University of Toronto and her collaborators developed a 17 gene signature for stemness that was highly prognostic and contributed greatly to accurate initial therapy resistance. The work included discovery of the signature followed by extensive validation of five cohorts comprised of 908 patient samples.

Learn more about Jean Wang's AML prognostic signature

Learn more about NanoString's gene expression signature capabilities

Each contract manufacturing services engagement is tailored to the needs of individual customers. Services offered include:

  • Reagent manufacturing: Reagents built exactly to your specifications and clinical assay needs
  • Study design consultation: Access to technical support as you prepare and conduct validation studies
  • Signature development: Optimize your algorithms prior to analytical and clinical validation studies
  • Report development: Access to third party experts who can assist in customizing your reports from nCounter data based on your unique assay specifications

Learn more about developing and validating assays for clinical research on the nCounter platform :

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

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Gene Expression

nCounter Technology