Nanostring Ncounter Gene/Protein Expression

Technology Overview

Nanostring ncounter

Reproducible, cost effective and faster than RNASeq

The nCounter is a highly robust solution for multiplex gene expression analysis of up to 800 RNA or protein targets that gets you to reproducible results faster.

Propath offers a complete service: from sample prep to data analysis, with robust QA and rapid turnaround.

Direct detection of fluorescent molecular barcodes reduces bias and increases reproducibility

How nCounter gene expression can benefit your study

  • Amplification free
    No amplification bias and no cRNA errors, giving you more reproducible results
  • Good for FFPE samples
    Flexible sample input, including FFPE, PBMCs and cell lysates
  • Highly reproducible
    Ideal for applications requiring efficient, high-precision, digital quantitation
  • Works with degraded samples
    Works with difficult samples — even severely degraded RNA can be viable
  • Broad range of panels
    Expertly curated pre-formatted panels for important pathways and research areas
  • Low sample input
    Ideal for precious samples as minimal input material is required
  • Faster than qPCR
    From samples to publication-ready data in as little as three weeks
  • Turnkey service
    A managed service available from Propath – experts in NanoString analysis

Amplification free, digital quantitation

RNASeq requires complex steps to convert RNA to cDNA, which is then amplified and quantitated as a proxy for the original RNA.

This process introduces variability which may lead to bias, error and an inability to replicate results.

Nanostring simply counts the native RNA – avoiding cDNA errors and amplification bias – which makes the assay highly reproducible, sensitive and time efficient.

Propath: an experienced service provider for NanoString analysis

Propath offers a complete nCounter gene/protein expression analysis as a turn-key service.

Simply send us your samples and receive publication ready data in as little as two weeks.

Request a quote

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Your samples

We handle them as though they are precious - with 100% traceability through our facility

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Quality of service

Professional and scientifically led, with responsive customer communication

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Rapid turnaround

Say goodbye to long waits. We can provide publication-ready data in as little as three weeks*

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Streamlined data analysis

We offer a complete data analysis service, to enable you to explore and interpret your data to discover the most meaningful insights

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Integrated histopathology support

Unlock additional insights by interpreting data in the context of histopathology

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Robust QA

From management of your sample to our people, process and facilities a strong culture of quality assurance through everything we do

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Tell us about your study

We’ll explain the complete process and provide as much support as needed to help you make key decisions and generate meaningful data that achieves your objectives.

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Select your panel

Choose from one of NanoString validated protein or mRNA panels, with the option to spike-in additional targets. Alternatively, we can help you design your own custom panel.

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Send us your samples

As little as 30ng of material per sample is sufficient. We treat all samples as though they are precious, with 100% traceability throughout our facility.

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Sample preparation

We perform all sample prep, including RNA extraction and thorough QC checks. We only proceed if samples meet QC requirements. We can also take sections from FFPE samples to enable interpretation of data in the context of histopathology.

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Hybridisation of RNA with molecular barcodes

RNA is hybridised with NanoString’s proprietary molecular probes. Once hybridised, the probes are immobilised and aligned on cartridges ready for counting.

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Digital counting

Hybridised molecular barcodes are then digitally counted using NanoString’s nCounter platform. Counts are precise and highly reproducible.

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Data analysis

We perform comprehensive data analysis, with outputs tailored to your specific requirements. Or we send back data files for you to perform your own analysis.

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QA review and audits

We perform comprehensive data analysis, with outputs tailored to your specific requirements. Or we send back data files for you to perform your own analysis.

How nCounter gene expression can benefit your study

Over 35 years experience

in Molecular Pathology and Histopathology

Over 35 years experience

in Molecular Pathology and Histopathology

Over 35 years experience

in Molecular Pathology and Histopathology

Over 35 years experience

in Molecular Pathology and Histopathology

Over 35 years experience

in Molecular Pathology and Histopathology

Over 35 years experience

in Molecular Pathology and Histopathology
* Turnaround times depends on sample numbers and complexity, but most projects are completed within three weeks.

Applications

Challenging FFPE samples

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Challenging FFPE samples

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Challenging FFPE samples

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Data Analysis

We provide a range of data analysis packages, leaving you free to focus on the biology, without waiting months for bioinformatic reports.

We provide an interactive one-on-one review of data with rich visualisations and publication ready figures.

Data analysis packages can be tailored to meet your requirements.

Our Data Analysis service enables you to:

  • Discover gene signatures and create gene lists
  • Explore pathway, disease and drug knowledge bases
  • Collaboration in real time and share results
  • Import NCBI Short Read Archive Public Data
  • Find patterns across datasets with Meta-Analyses
  • Download publication-ready figures and plot

Advanced analysis options include contamination detection, covariate correction, batch correction and multi-omic analyses

Discover more: Advanced data analysis options

Through our partnership with NanoString, we offer a range of advanced analytical options, including the Tumor Inflammation Signature, which quantifies the magnitude of a peripherally suppressed, adaptive immune response in the tumour microenvironment.

PanCancer IO 360™ Data Analysis Report

Data analysis report for the nCounter® PanCancer IO 360™ Gene Expression Panel offers the following:
  • Unique 360 view of gene expression for the tumor, microenvironment and immune response
  • Interactive reports prepared by NanoString expert scientists
  • 48 signatures including TIS, 14 signatures measuring immune cell populations and 34 novel signatures measuring important tumor and immune activities
  • Tumor Inflammation Score (TIS) provided for each sample to determine “hot” and “cold” tumors
  • Analysis includes sample signature score in relation to immune response
  • All data undergoes QC and normalization
  • Flexibility to include up to 5 additional user-defined signatures based on IO 360 or Panel Plus genes
  • Standard report currently available for human only

Breast Cancer 360™ Data Analysis Report

Data analysis report for the nCounter Breast Cancer 360 Gene Expression Panel offers the following:
  • Interactive report provides a 360-degree view of gene expression for the breast tumor microenvironment and immune response
  • 48 signatures across 13 categories of breast cancer tumor biology
  • PAM50 intrinsic subtype provided for each sample to determine luminal A, luminal B, HER2-enriched, or basal-like subtypes
  • Tumor Inflammation Signature (TIS) score provided for each sample to determine “hot” and “cold” tumors
  • Signature scores as a function of response, treatment, and survival where annotations are provided
  • Time series analysis available to determine how signatures are changing through time

PanCancer IO 360™ Data Analysis Report

Tumor Inflammation Signature analysis:
  • Quantifies the magnitude of a peripherally suppressed, adaptive immune response in the tumor microenvironment.
  • The algorithm has been trained and validated by Merck to correlate response to single agent Pembrolizumab, independent of tumor cell of origin.
  • 48 signatures including TIS, 14 signatures measuring immune cell populations and 34 novel signatures measuring important tumor and immune activities
  • Tumor Inflammation Score (TIS) provided for each sample to determine “hot” and “cold” tumors
  • Analysis includes sample signature score in relation to immune response
  • All data undergoes QC and normalization
  • Flexibility to include up to 5 additional user-defined signatures based on IO 360 or Panel Plus genes
  • Standard report currently available for human only

PAM50

  • PAM50 intrinsic breast cancer subtypes used in this analysis defines 4 prototypical subtypes: Basal, Her2-Enriched, Luminal B and Luminal A.
  • The clinical and prognostic characteristics of these subtypes are extensively studied.
  • If clinical tumor size is provided, the PAM50 report will also include the Risk of Recurrence (ROR) score.
  • Tumor Inflammation SIf the number of positive nodes is provided, the PAM50 report will also include Risk Category.core (TIS) provided for each sample to determine “hot” and “cold” tumors

LST

  • The Lymphoma Subtyping Test Signature is based on the Leukemia and Lymphoma Molecular Profiling Project Lymph2Cx assay and provides cell of origin data for diffuse large B-cell lymphomas.
  • The LST report includes the Linear Predictor Score (LPS) and the DLBCL cell of origin subtype: GCB, ABC, or Unclassified.

Publications & Resources

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FAQs

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