RUO PAM50
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RUO PAM50 Code Set

RUO PAM50 Code Set

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

RUO PAM50 Code Set

The PAM50 Signature

  • The RUO PAM50 CodeSetcontains probes for the 50 genes within the PAM50 signature as well as 8 reference genes. The 50 genes were selected to optimize the accuracy of identification of all 4 subtypes and the development of the signature was performed using more than 500 archived FFPE samples (Wallden BMC Med Gen, 2015). Customers interested in obtaining a PAM50 data analysis report must purchase the report separately.

PAM50 Subtypes:

  • Luminal A: Typically ER+ and characterized by lower proliferation and lower risk of recurrence after primary treatment

  • Luminal B: Typically ER+, but characterized by higher proliferation and higher risk of recurrence after primary treatment

  • HER2-Enriched: Majority Her2+, but can be ER+ or ER- and characterized by a higher risk of recurrence

  • Basal-like: Typically ER-/Her2- and characterized by a higher risk of recurrence

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.

Difficult Sample Type

Cancer researchers are often faced with the challenge of maximizing biological information from small and difficult sample types. The Nanostring RUO PAM50 CodeSet is compatible with RNA extracted from FFPE breast carcinoma samples.

PAM50 Subtyping Analysis

The 50-gene PAM50 signature measures a gene expression profile that allows for the classification of breast cancer into four biologically distinct intrinsic subtypes and determination of a prognostic Risk Of Recurrence (ROR) score.

Customizable

Add up to 55 unique genes with Panel-Plus

The RUO PAM50 Assay At Work

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

RUO PAM50 codeset: Includes 58 genes total; 8 internal reference genes for data normalization

Description

12 Reactions

Pack Size

RUO-PAM50-12

SKU

nCounter Master Kit:

Reagents, cartridges, and consumables necessary for sample processing on nCounter MAX and FLEX Systems

Description

12 Reactions

Pack Size

NAA-AKIT-012

SKU

nCounter Sprint Cartridge:

Sample Cartridge for nCounter SPRINT System

Description

12 Reactions

Pack Size

SPRINT-CAR-1.0

SKU

nCounter SPRINT Reagent Pack containing Reagents A, B, C, and Hybridization Buffer

Description

192 Reactions

Pack Size

SPRINT-REAG-KIT

SKU
SKU
Description
Pack Size

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