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Lymphoma Subtyping Test (LST) CodeSet – RUO
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
The LST CodeSet contains probes for the 20 genes within the LST signature, 15 target genes and 5 reference genes.
The signature was originally identified by performing gene expression profiling of DLBCL samples using microarrays (Alizadeh et al, 2000). The gene expression profiles indicated two different stages of B-cells differentiation: germinal center (GCB) and activated B cell based (ABC) based on the cell of origin and distinct mechanisms of oncogenesis. This signature was later refined to 20 genes using the FFPE tissues on the nCounterAnalysis system (Scott et al, 2014).
NanoString developed a multiplex gene expression assay on the nCounter Analysis System that can identify the cell of origin (COO) subtypes (ABC-type or GCB-type) of DLBCL: the 20-gene assay was trained using 51 FFPE biopsies; the locked assay was validated using an independent cohort of 68 FFPE biopsies. Comparisons were made with COO assignment using the original COO model on matched frozen tissue. A linear predictor score (LPS) calculated as the weighted sum of the 15 normalized target genes compared to pre-defined thresholds determine the DLBCL cell-of-origin subtype.
GeoMx DSP COVID-19 Protein and RNA Analysis
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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.
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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.
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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.
Lymphoma Subtyping
The RUO version of the NanoString Lymphoma Subtyping Test (LST) determines the Cell-of-Origin (COO) molecular subtype of samples run on the RUO LST CodeSet. Samples are reported as one of the two molecular subtypes, Activated-B-Cell (ABC), Germinal Center-B-Cell (GCB), or Unclassified. The Linear Predictor Score (LPS) is also reported.
Minimum Input and difficult Sample Type
50-300 ng without amplification and compatible with FFPE-derived RNA, total RNA, and cell lysates
Rapid Turnaround Time
Time required for result is approximately 24 hours
Customizable
Add up to 55 unique genes with Panel-Plus
LST RUO 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:
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Stem Cell Prolifiration
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Cell Cycle
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Senescence/Quiescence
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Autophagy
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Apoptosis
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Anti-Apoptosis
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PSC Pluripotency Markers and Regulators
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Naive State/Primed State
Regulatory Pathways:
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Wnt/B-catenin Pathway
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Hedgehog Signaling
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AP-1 Signaling
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PI3K-AKTmTOR Pathway
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MAPK Pathway
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JAK/STAT Pathway
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Notch Signaling
Epigenetic Mechanism:
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DNA Methylation
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Histone Acetylation & Methylation
Mechano-Signaling:
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Rho/ROCK Signaling
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integrin/Cadherin Signaling
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Hippo Pathway
Metabolism:
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Oxidative Stress Response
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Hypoxia Response
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Amino Acid Metabolism
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Fatty Acid Metabolism
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Glutamine Metabolism
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Glucose Metabolism
Differentiation Signaling and Pathways:
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TGFB Signaling
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Cytoskeletal Reorganization
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MET/EMT Signaling
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HOX Gene Activation
Differentiation Lineage:
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Endodermal /Ectodermal /Mesodermal Lineage Markers
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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 LST CodeSet:
Includes 20 genes total; 5 reference genes
Description
12 Reactions
Pack Size
RUO-LST-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