nCounter® Breast Cancer 360™ Panel

The human nCounter Breast Cancer 360 panel and data analysis service provides a unique 360 degree view of gene expression for the breast tumor microenvironment and immune response. Now researchers can more quickly decode the complexities of breast cancer biology, develop novel breast cancer gene signatures, and categorize disease heterogeneity using 48 biological signatures including signatures based upon the validated PAM50 and Tumor Inflammation Signature* (TIS) assays.

Product Highlights:

  • Breast Cancer 360 Subtype, Signatures, and Biology tableExpertly curated, comprehensive content includes 776 genes across 23 key breast cancer pathways and processes
  • Provides a unique 360 degree view of gene expression for the breast tumor microenvironment and immune response
  • Interactive Breast Cancer 360 data analysis report available to expedite analysis to insight
    • 48 signatures across 13 categories measuring biological variables crucial to breast cancer tumor biology
    • Access to validated signatures: PAM50, Tumor Inflammation Signature (TIS), Risk of Recurrence (ROR)/Genomic Risk
    • Expanded evaluation of breast cancer subtypes including: PAM50 Signature, TNBC, and Claudin-Low Signature
    • Publication ready figures and statistical methods included for speed to presentation

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Learn about our nCounter Analysis System and nSolver™ Analysis Software.

*Ayers, Mark, et al. "IFN-y-related mRNA profile predicts clinical response to PD-1 blockade." The Journal of Clinical Investigation 127.8 (2017).

Breast Cancer Prognosis Genomic Risk / Risk of Recurrence              
Breast Cancer Subtyping PAM50 Molecular Subtypes Luminal A Correlation Value (PAM50) Luminal B Correlation Value (PAM50) HER2-Enriched Correlation Value (PAM50) Basal-like Correlation Value (PAM50) Claudin-Low Subtype Score Triple Negative Subtype  
Breast Cancer Receptors ESR1 Gene Expression PGR Gene Expression ERBB2 Gene Expression AR Gene Expression        
Breast Cancer Signaling Pathways ER Signaling PTEN Gene Expression CDK4 Expression CDK6 Expression        
Tumor Mutational Response HRD BRCA p53          
Tumor Regulation Proliferation (PAM50) Apoptosis Differentiation FOXA1 Gene Expression Cell Adhesion Mammary Stemness RB1 Gene Expression SOX2 Gene Expression
Tumor Immunogenicity APM (Antigen Processing Machinery)              
Stromal Factors Endothelial Cells Stromal Abundance            
Inhibitory Metabolism Hypoxia              
Inhibitory Immune Mechanisms IDO1 Expression PD-L1 Gene Expression B7-H3 TGF-Beta        
Anti-Tumor Immune Activity Tumor Inflammation Signature (TIS) Interferon Gamma Signaling MHC Class II Antigen Presentation Cytotoxicity        
Inhibitory Immune Signaling Inflammatory Chemokines TIGIT Gene Expression PD-L2 Gene Expression PD-1 Gene Expression        
Immune Cell Abundance Cytoxic Cell CD-8+ T Cell Macrophage Mast Cell Treg      

 

Signatures Based Upon Validated PAM50 and TIS Signatures
Risk of Recurrence The Risk of Recurrence score (ROR) is an integer value on a 0–100 scale that is related to an individual patient’s probability of distant recurrence within 10 years of diagnosis, with 0 being lowest risk and 100 being highest risk. The ROR score is calculated by comparing the expression profiles of 46 genes in the sample with the four PAM50 centroids, to calculate four different correlation values. These correlation values are then combined with the PAM50 proliferation score and the tumor size to calculate the ROR score. When nodal status is provided, these scores can be classified into low, intermediate, and high-risk categories.
Genomic Risk The Genomic Risk of Recurrence score (Genomic Risk) is calculated by comparing the expression profiles of 46 genes in the sample with the four PAM50 centroids, to calculate four different correlation values. These correlation values are then combined with the PAM50 proliferation score to estimate the genomic risk of distant recurrence. The results are reported on a scale of 0 to 100, with 0 being lowest risk and 100 being highest risk. This score is distinct from the Risk of Recurrence (ROR) score, as it does not include the tumor size included in the score calculation – it is solely based on the genomic data.
PAM50 Molecular Subtypes This 50-gene signature measures a gene expression profile that allows for the classification of breast cancer into four biologically distinct subtypes (Luminal A, Luminal B, HER2-Enriched, Basal-like).
Luminal A Correlation Value Luminal A tumors are typically characterized by high expression of estrogen receptor (ER), progesterone receptor (PR), and genes associated with ER activation1. These tumors are low-grade, tend to grow slowly, exhibit low expression of genes associated with cell cycle activation and have the best prognosis.
Luminal B Correlation Value Luminal B tumors are typically characterized by high expression of estrogen receptor (ER), progesterone receptor (PR), and genes associated with ER activation1. These tumors tend to grow slightly faster than Luminal A tumors, exhibit high expression of genes associated with cell cycle activation and proliferation, and have a slightly worse prognosis than Luminal A tumors.
HER2-Enriched Correlation Value HER2-Enriched tumors are typically characterized as clinically HER2 positive breast cancer as defined by traditional IHC/FISH criteria. Some studies have indicated that the HER2-Enriched molecular subtype may be a better predictor of response to HER2-targeted therapies when compared with IHC and FISH.
Basal-like Correlation Value Basal-like tumors are typically characterized as having low expression of ER, PR, and HER2. Most clinically triple negative tumors are Basal-like subtype by molecular profiling. These tumors are poorly differentiated invasive high-grade ductal carcinomas that by have metastatic properties.
Proliferation (PAM50) This signature outputs the PAM50 proliferation score by measuring key genes involved in breast tumor proliferation. In some cases, a highly proliferative breast tumor may correlate with an increase in disease progression or metastasis.
Tumor Inflammation Signature (TIS) Tumor Inflammation Signature. TIS measures the abundance of a peripherally suppressed adaptive immune response within the tumor.
  • This signature is trained to predict response to anti-PD1 therapy (pembrolizumab). It consists of genes related to Interferon gamma signaling (IFNγ), antigen presentation, natural killer (NK) and T cells and inhibitory pathways. It also consists of normalization genes that have been selected to give consistent expression levels across most tissue or tumor types.
  • This signature is useful for predicting response to anti-PD1 therapy and determining hot and cold immune status across multiple cancer types.

 

Research Signatures
Claudin-Low Signature This molecular subtype is characterized by low levels of luminal differentiation markers, high enrichment for epithelial-to-mesenchymal transition markers, immune response and cancer stem cell-like genes.
TNBC Signature This signature identifies four distinct TNBC subtypes: Luminal/AR subtype 1, characterized by AR, ER, prolactin and ErbB4 signaling; Mesenchymal subtype 2, characterized by cell cycle, mismatch repair, and DNA damage networks; Basal-like Immune-Suppressed subtype 3, characterized by downregulation of B, T and NK-cells immune-regulating and cytokine pathways; Basal-like Immune Activated subtype 4, characterized by upregulation of B, T and NK cells immune-regulating pathways, and activation of STAT.
CDK4 Expression Cyclin-dependent kinases 4 and 6 (CDK4/6) play a key role in the regulation of proliferation in normal breast tissue and breast tumors. CDK4/6 inhibitors have been indicated in hormone receptor (HR) positive metastatic breast cancer. Cyclin-dependent kinase 4 (CDK4) is an enzyme encoded by the CDK4 gene, mutations in this gene as well as in its related proteins have been shown to be associated with tumorigenesis.
CDK6 Expression Cyclin-dependent kinases 4 and 6 (CDK4/6) play a key role in the regulation of proliferation in normal breast tissue and breast tumors. CDK4/6 inhibitors have been indicated in hormone receptor (HR) positive metastatic breast cancer. CDK6, as well as CDK4, has been shown to phosphorylate and regulate the activity of the tumor suppressor protein Retinoblastoma and indicating a role in cancer development.
Differentiation This signature assigns a score of differentiation to the sample. Well-differentiated tumors that is phenotypically more similar to normal cells or tissue will grow and spread at a slow rated compared with poorly differentiated tumors, these present with abnormal cells that often grow rapidly.
Breast Cancer p53 Signature This signature categorizes p53 status by mutant-like vs wild-type-like in breast cancer and the signature is significantly associated with overall survival in breast cancer, identifying a group with high unmet need.
BRCAness Signature This signature captures breast cancer biology that is informative as to defects in the DNA damage repair-genes BRCA1 and BRCA2. Similar to the Homologous Recombination Deficiency signature this captures breakdown in DNA damage repair, however, these are specific to BRCA-related mutations and more heavily weighted to BRCA1 mutants.
HRD Signature This signature is used to functionally assess Homologous Recombination Repair status, with potential to predict sensitivity to DNA-damage repair inhibitors such as PARP inhibitors. This captures cell cycle regulation, DNA damage, DNA replication, and DNA recombination and repair pathways. Additionally, this signature is also used to predict overall survival in breast cancer.
ER Signaling Signature Estrogen-binding systems associate with various proteins that direct cell cycle signaling, proliferation and survival. This signature captures ER-mediated signaling pathways to elucidate how ER modulates activity of key transcription factors through stabilizing DNA-protein complexes and recruiting co-activators. This signature also captures the impact to other signaling pathways induced by the binding of estrogens in the nuclear causing conformational changes in the receptors.
PTEN/AKT Phosphatase and tensin homolog gene expression. PTEN is a tumor suppressor gene that functions through the regulation of the Akt/PKB signaling pathway. Mutations or loss of PTEN expression are common across a range of cancer types, including breast cancer.

 

Tumor/Immune Activity Signatures
ESR1 PGR ERBB2 AR Apoptosis
FOXA1 Cell Adhesion Mammary Stemness Rb1 SOX2
APM Endothelial Cells Stroma Hypoxia IDO1
PD-L1 B7-H3 TGF-Beta IFN Gamma MHC2
Cytotoxicity Inflammatory Chemokines TIGIT PD-L2 PD-1
Cytotoxic Cells CD8 T-Cells Macrophages Mast Cells Treg

Includes expertly curated 776 genes across 23 categories of breast cancer tumor biology to support the evaluation of pathways and process, as well as novel signature development. 

Pathways
Cell Cycle ER Signaling Chromatin Modification Hedgehog MAPK Wnt
Notch STAT PI3K TGFβ RAS  

 

Processes
Tumor Microenvironment Immune
Breast Cancer Subtypes Cancer Progression EMT Immune Cell Marker
Triple Negative Tumor Biology Microenvironment Tissue Marker Immune Infiltration
Tumor Metabolism Cancer Progression Immune Response
Tumor Proliferation Angiogenesis  
Tumor Suppression    

Content included in the Breast Cancer 360 panel allows for a more comprehensive measurement of biological variables crucial to tumor progression and response to a wide-range of treatments. Research signatures are enriched with potentially predictive genes involved in proliferation, endothelial, angiogenesis, cytotoxicity, stroma, inflammatory chemokines, and apoptosis.

  • 48 signatures including two analytically validated signatures- PAM501,2 and Tumor Inflammation Signature3
  • 10 research focused signatures and 30 novel signatures measuring important tumor and immune activities
  • adapted to decode breast cancer biology in concert 

 

Analytically Validated Signatures

PAM50 Signature1,2

Included with the Breast Cancer 360 panel is the PAM50 Signature.  This 50-gene signature measures a gene expression profile that allows for the classification of breast cancer into four biologically distinct subtypes and a prognostic score.

  • PAM50 Subtype
    • Luminal A
    • Luminal B
    • HER2-Enriched
    • Basal-like
  • Prosigna Score / Risk of Recurrence

PAM50 gene expression signature heatmap subtypes

 

Tumor Inflammation Signature3

Included with the Breast Cancer 360 panel is the Tumor Inflammation Signature. This 18-gene signature measures activity known to be associated with response to PD-1/PD-L1 inhibitors pathway blockade3.

  • Includes 4 Areas of immune biology used to determine peripherally suppressed immune response and the identification of “hot” or “cold” tumors
    • Antigen Presenting Cells
    • T Cell/NK presence
    • IFNγ Biology
    • T Cell Exhaustion
  • Tissue-of-origin agnostic (Pan-cancer)
  • Potential surrogate for PD-L1 and mutational load in research setting4

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View publication and video.

 

18-gene Tumor Inflammation Signature
CCL5 CD8A STAT1 PD-L2/PDCD1LG2 HLA-DQA1 HLA-DRB1
CXCL9 CXCR6 TIGIT PD-L1/CD274 HLA-E CMKLR1
CD27 IDO1 LAG3 CD276 PSMB10 NKG7

 

Feature Specifications
Number of Targets 776 (Human), Including internal reference genes
Sample Input – Standard (No amplification required) 50 – 300 ng
Sample Input – Low Input As little as 10 ng with nCounter RNA Low Input Kit and Panel specific primer pools (sold separately)
Breast Cancer 360 Panel Standard Synthetic oligonucleotide pool corresponding to all panel gene targets used for normalization
Sample Type(s) FFPE-derived RNA, total RNA, and cell lysates
Customizable Add up to 55 unique genes with Panel-Plus
Time to Results Approximately 24 hours
Data Analysis nSolver Analysis software, BC 360 Data Analysis Service

 

For Research Use Only. Not for use in diagnostic procedures.