Oncomine Immune Response Research Assay

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.

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

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.

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.

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.