Analyze the immune pathway, including low-expressing genes, from clinical research samples with as little as 10 ng FFPE RNA

The Oncomine™ Immune Response Research Assay is a targeted, next-generation sequencing (NGS) gene expression assay that enables immuno-oncology research through the quantitative evaluation of the expression of markers associated with different leukocyte subsets, antigen presentation, checkpoint pathways, and tumor progression. The assay measures the expression of genes involved in tumor-immune interactions, including the low-expressing genes involved in inflammatory signaling.

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Using an NGS gene expression assay in your biomarker identification research

Designed with comprehensive coverage of targets associated with key genes relevant to immune response biomarker research, the Oncomine Immune Response Research Assay achieves superior performance in the detection of low-expressing genes from as little as 10 ng input RNA from FFPE research samples.

The assay offers:

  • Highly curated content—assess tumor microenvironment and identify predictive markers for drug response
  • High sensitivity—achieve improved detection for low expressing genes over similar competitor products
  • Excellent reproducibility—a broad dynamic range with a clear signal-to-noise ratio increases confidence in the calls made by the optimized analysis software
  • Minimal sample input—save precious FFPE samples with as little as 10 ng total RNA input required by leveraging proven Ion AmpliSeq™ technology
  • Automation— enable fast turn-around time using the NGS workflow on Ion Chef™ System with Ion S5™ System sequencing

Figure 1. The Oncomine Immune Response Research Assay is intended for biomarker profiling applications. Signatures you detect with the assay may lead to separate clinical trial assay and companion diagnostic development efforts in the future.

Key genes to enable mechanistic studies and identification of predictive biomarkers

The Oncomine Immune Response Research Assay features content designed for future clinical trial research cohorts.

  • Simultaneous detection of 395 genes relevant to immune response research across multiple cancer types
  • High-sensitivity detection of low-expressing signaling molecules such as interleukins and interferon gamma (IFNG)
  • Content driven by the Oncomine™ Knowledgebase, current research publications, and global experts in pharmaceutical and research organizations

Functional annotation group

Number of genes

Functional annotation group

Number of genes

Antigen presentation

3

B cell marker

11

Antigen processing

19

Dendritic cell

7

Innate immune response

11

Dendritic cell, macrophage

6

Leukocyte inhibition

2

Helper T cells

8

Leukocyte migration

5

Macrophage

5

Lymphocyte activation

2

Myeloid marker

7

Lymphocyte development

3

Neutrophil

5

Lymphocyte infiltrate

46

NK activation

8

B cell receptor signaling

3

NK cell marker

4

T cell receptor signaling

6

T cell differentiation

2

T cell regulation

9

 

TCR coexprssion

19

Checkpoint pathway

30

 

PD-1 signaling

<9>

Chemokine signaling

10

Drug target

21

Cytokine signaling

15

 

Interferonsignaling

8

Adhesion, migration

14

Type I interferon signaling

8

Apoptosis

4

Type II interferon signaling

23

Proliferation

10

 

Tumor antigen

<17>

Housekeeping

11

Tumor marker

27

Table 1. Oncomine Immune Response Research Assay content includes 395 genes across 36 functional annotation groups comprised of genes associated with lymphocyte regulation, cytokine signaling, lymphocyte markers, checkpoint pathways, and tumor characterization. 

The Oncomine Immune Response Research Assay contains key clinical cancer research targets including cytokine signaling genes like IFNG, drug target genes like CTLA4, and PD-1 signaling genes like MTOR and PTEN.

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A targeted NGS approach to immunotherapy research improves detection among low-expressing genes

Figure 2. Range of expression across 10 pancancer research samples. The Oncomine Immune Response Research Assay demonstrates improved detection over the competitor N assay when interrogating key immune response research gene subsets including low-expression genes associated with both T cell receptor signaling and checkpoint pathways.

Providing solutions to address current immunotherapy research challenges: predictive biomarkers and stratification of clinical research samples

Current PD-1 and PD-L1 assays may miss important genes that can indicate immune response. Further, throughput and reproducibility challenges with IHC make it difficult to conduct robust studies. The Oncomine Immune Response Research Assay addresses these challenges.

Part of a comprehensive solution including automation with the Ion Chef System and Ion S5 System, the assay contains the reagents for library construction and a single pool of primers used to perform multiplex PCR for preparation of amplicon libraries from formalin-fixed paraffin-embedded (FFPE) samples. Achieving 4, 8, or 32 samples per run depending on your throughput needs, the workflow gives you the flexibility to run small or large retrospective or prospective profiling research studies.

Figure 3. Current immunotherapy research with IHC lacks reproducibility and does not scale beyond 1–2 assays per tumor sample (left). The Oncomine Immune Response Research Assay can provide insights about the composition of the tumor microenvironment that may improve stratification of samples (right).

Figure 4. Preliminary indicator that may aid in improved stratification of samples. The Oncomine Immune Response Research Assay achieves better stratification of samples compared to the competitor N assay evident in the clearer distinction between cancer types when clustered by all genes shared by each panel.

Workflow, analysis and local support help you focus on results

Supported on Ion S5 and Ion PGM™ Sequencers, the Oncomine Immune Response Research Assay enables your lab to efficiently run small- and large-scale studies.

The optimized informatics and visualization software minimizes the complexity of data analysis. The analysis workflow consists of a data exploration component automated by the Immune Response Torrent Suite™ Plug-in, and a two-group differential analysis provided by the Affymetrix™ Transcriptome Analysis Console (TAC). Together these tools offer a streamlined process for common gene expression analyses and exportable data files that are amenable to further exploration with other third-party software.

These tools enable:

  • QC metrics and expression of housekeeping genes to qualify data
  • Hierarchical clustering of samples with user-defined gene sets or by all genes on the panel
  • Visualization with PCA, heat maps, and gene expression distribution plots
  • Sample correlation using rich correlation plots
  • Fold-change estimates in easy-to-use tabular data format (TAC)
  • Volcano plots to visualize differentially genes (TAC)

Figure 5. The Oncomine Immune Response Research Assay includes reagents for library construction, primers for library preparation, and analysis software for interpretation of results. *Two-day workflow requires overnight template preparation.

The tools you need for targeted NGS gene expression immune response research