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Vantage 3D™ Assays

Vantage 3D™ Assays

Prosigna Score / ROR Score:

The ROR Score has been validated to predict the risk of recurrence of disease in ER+ breast cancer after surgery and treatment with 5 years of endocrine therapy. The ROR score depends upon the biology of the intrinsic subtypes, the proliferation score of the tumor, and the tumor size as shown in the equation below:

ROR = aRLumA + bRLumB + cRHer2 + dRBasal + eP + fT

Each of the R variables in the equation above indicate the Pearson correlation coefficient of the PAM50 expression profile for the tumor compared to each of the prototypical centroids for the intrinsic subtypes shown in the heatmap below. P is the proliferation score, which is the average gene expression profile of genes associated with cell-cycle progression and T is the tumor stage.

Figure: Heatmap of PAM50 genes by subtype. Red is higher expression and green is lower expression

Vantage 3D™ Assays
  • NanoString is pioneering the field of 3D Biology to accelerate the rate of research and maximize the amount of information that can be generated from a single sample.

  • 3D Biology™ Technology is the ability to analyze combinations of RNA and protein simultaneously in a single experiment.

  • This approach eliminates the need for sequential testing and removes potential bias arising from splitting samples and merging data from different platforms, which allows for biological discrepancies between analytes to be directly identified.

GeoMx DSP COVID-19 Protein and RNA Analysis

  • Rapidly perform high-plex spatial analyses of the host response in FFPE or fresh frozen tissue using the  GeoMx Digital Spatial Profiler (DSP). NanoString’s GeoMx DSP platform enables high-plex protein and RNA experiments in key areas of biology such as molecular response, cellular (immune) response, tissue damage, and drivers of individual susceptibility to severe forms of disease.

  • The GeoMx COVID-19 Immune Response Atlas, a ~1,850-plex RNA assay, enables spatial studies of the SARS-CoV-2 virus and host response. RNA targets include COVID-19 receptors and proteases, pulmonary alveolar type I and II markers, lung biology markers, viral response markers, and SARS-CoV-2 probes. RNA targets are profiled simultaneously using the GeoMx DSP and an Illumina next-generation sequencer (NGS) for readout. Users can run ACD RNAscope™ probes alongside GeoMx RNA probes to identify regions of interest.

  • A five-antibody custom, ready-to-go protein panel, with receptor, protease, and viral markers is available through the GeoMx Technology Access Program or for order through Abcam. This  COVID-19 GeoMx-formatted Antibody  is run with the 20-plex GeoMx Immune Cell Profiling Core (plus controls) with readout on the nCounter Analysis System. Users can add up to six 10-plex modules including the Immune Activation Status, Immune Cell Typing, and/or Cell Death modules to more deeply profile proteins involved in T cell activation and cell death. NanoString scientists can recommend commercially-available markers for lung epithelium, nasal epithelium, immune response markers, and the viral spike protein.

Organized-workflow and data analysis

Based on the proven nCounter digital molecular barcoding technology, 3D Biology Technology simplifies your workflow and data analysis by comparing gene and protein expression in a single view.

Flexible in nature

The nCounter Vantage 3D portfolio is designed for flexibility.

Flexible Data Generation

Each panel can also be run as a stand-alone assay so you can generate the data you need.

Provides a deeper view of cancer and immune biology and can be mixed and matched to answer a wide variety of biological questions.

The eight essential components of stem cell biology

Stemness
Pluripotency
Regulatory Signaling
Epigenetics
Mechano-Signaling
Metabolism
Differentiation Signaling
Lineage Specification

Stem Cell Renewal:

  • Stem Cell Prolifiration

  • Cell Cycle

  • Senescence/Quiescence

  • Autophagy

  • Apoptosis

  • Anti-Apoptosis

  • PSC Pluripotency Markers and Regulators

  • Naive State/Primed State

Regulatory Pathways:​

  • Wnt/B-catenin Pathway

  • Hedgehog Signaling

  • AP-1 Signaling

  • PI3K-AKTmTOR Pathway

  • MAPK Pathway

  • JAK/STAT Pathway

  • Notch Signaling

Epigenetic Mechanism:

  • DNA Methylation

  • Histone Acetylation & Methylation

Mechano-Signaling:

  • Rho/ROCK Signaling

  • integrin/Cadherin Signaling

  • Hippo Pathway

Metabolism:

  • Oxidative Stress Response

  • Hypoxia Response

  • Amino Acid Metabolism

  • Fatty Acid Metabolism

  • Glutamine Metabolism

  • Glucose Metabolism

Differentiation Signaling and Pathways:

  • TGFB Signaling

  • Cytoskeletal Reorganization

  • MET/EMT Signaling

  • HOX Gene Activation

Differentiation Lineage:

  • Endodermal /Ectodermal /Mesodermal Lineage Markers

  • Key Somatic Cell Types

Custom & Clinical Products

Assay Type
Product
Maximum Targets
Daily Sample Throughput
Analytes Offered
Common Applications

Custom codeSets

Elements TagSets

PlexSet Reagents

Self-assembled, interchangeable probes, optimized for smaller validation projects with maximum flexibility

Self-assembled, interchangeable probes for high-throughput, sample multiplexing projects

User-designed, turn-key solution that comes ready-to-use

216

96

800

24-96

24-96

192-1152

mRNA, CNV, Fusions

mRNA, Fusions

mRNA, miRNA, CNV, Fusions

Cell line drug screen, biomarker development, infectious disease

Gene Signature Development

Model Organism, Microbes, Agriculture

VANTAGE 3D RNA HEME PANEL Gene Expression CodeSet profiling (192 genes) 180 hematologic oncology related human genes + 12 internal reference controls. CodeSet Only.

Description

12 Reactions

Pack Size

VRXC-HEME-12

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nCounter® Vantage 3D™ Protein Immune Cell Profiling Panel for cell suspensions (D) + Universal Cell Capture Kit Contains Antibody Mix for 30 Extracellular immunology protein targets. Protein TagSet (D) (ERCC) for protein target detection. Universal Cell Capture Kit—Cell Surface Compatible, which contains universal cell capture beads, Buffer W, and Buffer LH. To be used as a stand-alone protein assay. Compatible with cell suspensions.

Description

12 Reactions

Pack Size

VPODC-B2M-HIPS-12

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nCounter® Vantage 3D™ Protein Immune Cell Profiling Panel for cell suspensions (R) + Universal Cell Capture Kit Contains Antibody Mix for 30 Extracellular immunology protein targets. Protein TagSet (R) (no ERCC) for protein target detection. Universal Cell Capture Kit—Cell Surface Compatible, which contains universal cell capture beads, buffer W, and buffer LH. To be used with custom CodeSets, PanCancer RNA Panels, and nCounter® Vantage 3D RNA Panels. Compatible with cell suspensions.

Description

12 Reactions

Pack Size

VPRXC-B2M-HIPS-12

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VANTAGE 3D RNA-DNA DAMAGE AND REPAIR PANEL Gene Expression CodeSet profiling (192 genes) 180 DNA Damage and Repair-related human genes + 12 internal reference controls. CodeSet Only.

Description

12 Reactions

Pack Size

VRXC-DNA1-12

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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.

Description

12 Reactions

Pack Size

VRXC-LGF-12

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VANTAGE 3D RNA CELLULAR SIGNALING PANEL Gene Expression CodeSet profiling (192 genes) 180 Cellular signaling-related human genes + 12 internal reference controls. CodeSet Only.

Description

12 Reactions

Pack Size

VRXC-CS1-12

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Vantage 3D Protein Heme Panel (R) for FFPE Contains: Antibody Mix and Protein TagSet (R) reagent (no ERCC) for protein target detection. Buffer W and Buffer T for protein sample preparation. To be used with custom CodeSets, PanCancer RNA Panels, and nCounter Vantage 3D RNA Panels. Compatible with FFPE samples.

Description

12 Reactions

Pack Size

VPRXC-HHMF-12

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Vantage 3D Protein Heme Panel (D) for FFPE Contains: Antibody Mix and Protein TagSet (D) reagent (ERCC) for protein target detection. Buffer W and Buffer T for protein sample preparation. To be used as a stand-alone protein assay or with nCounter Vantage 3D DNA assays. Compatible with FFPE samples

Description

12 Reactions

Pack Size

VPODC-HHMF-12

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VANTAGE 3D RNA CANCER METABOLISM PANEL Gene Expression CodeSet profiling (192 genes) 180 metabolism-related human genes + 12 internal reference controls. CodeSet Only.

Description

12 Reactions

Pack Size

VRXC-CM1-12

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VANTAGE 3D RNA MAPK-PI3K PATHWAYS PANEL Gene Expression CodeSet profiling (192 genes) 180 MAPK-PI3K related human genes + 12 internal reference controls. CodeSet Only.

Description

12 Reactions

Pack Size

VRXC-MAPK1-12

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nCounter Vantage 3D Protein Solid Tumor Panel for FFPE (R) + FFPE Sample Prep Kit Contains: Antibody Mix for 26 solid tumor signaling protein targets. Protein TagSet (R) (no ERCC) for protein target detection. Protein FFPE Sample Prep Kit, which contains Buffer W and Buffer T. To be used with custom CodeSets, PanCancer RNA Panels, and nCounter Vantage 3D RNA Panels. Compatible with FFPE sample

Description

12 Reactions

Pack Size

VPRXC-SPKP-HSTF-12

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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.

Description

12 Reactions

Pack Size

VRXC-LKF-12

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Vantage 3D Protein Solid Tumor Panel for FFPE (D) + FFPE Sample Prep Kit Contains: Antibody Mix for 26 solid tumor signaling protein targets. Protein TagSet (D) (ERCC) for protein target detection. Protein FFPE Sample Prep Kit, which contains Buffer W and Buffer T. To be used as a stand-alone protein assay. Compatible with FFPE samples.

Description

12 Reactions

Pack Size

VPODC-SPKP-HSTF-12

SKU

VANTAGE 3D RNA ADAPTIVE IMMUNITY PANEL Gene Expression CodeSet profiling (192 genes) 180 immune-related human genes + 12 internal reference controls. CodeSet Only.

Description

12 Reactions

Pack Size

VRXC-AI1-12

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VANTAGE 3D RNA INNATE IMMUNITY PANEL Gene Expression CodeSet profiling (192 genes) 180 immune-related human genes + 12 internal reference controls. CodeSet Only.

Description

12 Reactions

Pack Size

VRXC-II1-12

SKU

VANTAGE 3D RNA WNT PATHWAYS PANEL Gene Expression CodeSet profiling (192 genes) 180 Wnt pathway-related human genes + 12 internal reference controls. CodeSet Only.

Description

12 Reactions

Pack Size

VRXC-Wnt1-12

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VANTAGE 3D RNA CELLULAR PROFILING PANEL Gene Expression CodeSet profiling (192 genes) 180 cell marker-related human genes + 12 internal reference controls. CodeSet Only.

Description

12 Reactions

Pack Size

VRXC-CP1-12

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SKU
Description
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