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GeoMx® Cancer Transcriptome Atlas
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 GeoMx® Cancer Transcriptome Atlas (CTA) is designed for comprehensive profiling of tumor biology, the tumor microenvironment, and the immune response. Profile RNA expression of over 1,800 genes simultaneously with spatial resolution from distinct regions of interest with a single tissue section using the GeoMxDigital Spatial Profiler.
Spatial Profiling with High Reproducibility
Comprehensive RNA content designed for cancer biology research
Over 50 pathways to explore all aspects of cancer and tumor biology
Compatible with RNAscope® and antibody visualization markers
Supplement with up to 30 additional targets of interest
Curated Content for Cancer Biology
Profile the global immune response
Assess microenvironment immune activity
Quantify tumor reactivity to the immune response and therapeutic treatments
Measure clinically-derived gene sets including the 18-gene Tumor Inflammation Signature (TIS) known to be associated with response to PD-1/PD-L1 inhibitor pathway blockade, and the 50-gene Prediction Analysis of Microarray 50 signature (PAM50) known to be associated with breast cancer metastasis.
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.
Comprehensive RNA Content
Coverage of the immune response, tissue microenvironment, tumor biology, and genes from clinically relevant genes sets such as the Tumor Inflammation Signature and PAM50
Explore Tumor Biology
Over 100 pathways to explore all aspects of cancer
Supplement with up to 60 additional targets of interest
Targets critical to oncology and immuno-oncology research on the GeoMx Digital Spatial Profiler.
The eight essential components of stem cell biology
Stem Cell Renewal:
Stem Cell Prolifiration
PSC Pluripotency Markers and Regulators
Naive State/Primed State
Histone Acetylation & Methylation
Oxidative Stress Response
Amino Acid Metabolism
Fatty Acid Metabolism
Differentiation Signaling and Pathways:
HOX Gene Activation
Endodermal /Ectodermal /Mesodermal Lineage Markers
Key Somatic Cell Types
Custom & Clinical Products
Daily Sample Throughput
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
mRNA, CNV, Fusions
mRNA, miRNA, CNV, Fusions
Cell line drug screen, biomarker development, infectious disease
Gene Signature Development
Model Organism, Microbes, Agriculture
GeoMx Cancer Transcriptome Atlas Human RNA for Illumina Systems RNA panel including over 1,800 targets plus controls for human immune response, tumor biology, and microenvironment. Includes RNA probes for Illumina NGS readout.
GeoMx Solid Tumor TME Morphology Kit Human RNA Compatible Morphology kit for visualization of human solid tumors and the tumor microenvironment. For use with RNA assays. Includes fluorescent antibodies against Pan-CK, CD45, and a nuclear stain.
GeoMx Melanoma TME Morphology Kit Human RNA Compatible Morphology kit for visualization of human melanoma and the tumor microenvironment. For use with RNA assays. Includes fluorescent antibodies against S100B/Pmel17, CD45, and a nuclear stain.
GeoMx Seq Code Pack Compatible with Illumina Systems NGS readout reagents for GeoMx DSP RNA and proteinanalysis. Includes two Seq Code primer plates (choice of A&B, C&D, E&F, or G&H) and two universal enzyme master mixes
GeoMx RNA Slide Prep Kit for FFPE Sample prep reagents for GeoMx DSP RNA analysis. Includes Buffer W, Buffer S, and Buffer R.
GeoMx DSP Collection Plate Barcoded collection plates for use on the GeoMx DSP. Required for AOI tracking. Kit includes 12 plates covering 1,152 AOI.
GeoMx DSP Instrument Buffer Kit for the GeoMx DSP. Includes Buffer S and Buffer H. Sufficient for ~48 samples with ~18 AOI each. Volume requirements may vary based on experimental design.
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AUTOIMMUNE DISEASE AND CHRONIC INFLAMMATORY DISEASE COVERAGE
Chronic inflammatory disorder that impacts the lining of joints.
Chronic inflammatory of the digestive tract.
Autoimmune disease is where the immune system mistakenly attacks the insulin-producing cells of the pancreas
Demyelinating disease that disrupts communication with the nervous system.
Immune-mediated disease that causes skin cells to rapidly build up on the surface of the skin
Certain treatments and infections have been reported to interfere with the immune system and induce a series of autoimmune disease or adverse immune-related events.
Chronic inflammatory disease that manifests systematically throughout the body.
Inflammatory Bowel Disease
Type 1 Diab
Type 1 Diabetes
Systematic Lupus Erythematosus
Induced Adverse Immune Events
Immune Checkpoint Coverage
Pathways Regulating Glia
(178/180 Hs/Mm Genes)
Inflammation & Peripheral Immune Invasion
(187/188 Hs/Mm Genes)
Cell Stress & Damage Response
(127/134 Hs/Mm Genes)
NO Metabolism and Signaling
Oxidative & Nitrosative Stress
MAPK & PI3K
Antigen Processing & Presentation