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Next-Generation Sequencing Solutions Enable Deeper Insights into the Tumor Microenvironment
Immuno-oncology (I/O) therapies are considered to be promising anti-cancer treatments and are generating hope and excitement among researchers, clinicians, and patients. The Ion Torrent portfolio of immuno-oncology next-generation sequencing (NGS) assays enables an innovative, multi-dimensional approach to understanding the tumor microenvironment. Each genomic assay uses the sensitivity of NGS to decipher the hidden biology within precious samples, and can be implemented independently or together for a more holistic view to enhance clinical research study design and positively impact study outcomes.
- TCR beta assays for deeper insights in clonality and convergence
- BCR IgH assays to quantify somatic hypermutations and study isotypes
- Immune response assay to monitor the tumor microenvironment
- Tumor mutation load assay for accurate quantification of TMB
For mouse studies:
- Sequencing assays to interrogate CDR3 for TCR beta and for BCR IgH, enabling deeper insights in repertoire analysis
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Human research assays
Oncomine TCR Beta-SR Assay
The Ion Torrent Oncomine TCR Beta-SR Assay specifically interrogates the CDR3 region of the TCR beta chain. Compatible with both FFPE DNA and RNA, this short-read sequencing assay enables characterization of the immune status and detection of T cell minimal residual disease (MRD) in peripheral blood. Requiring low sample input, this assay offers a two-day turnaround time complete with superior informatics for accurate clonality and CDR3 TCR beta chain sequence assessment without interference from primer bias.
Oncomine TCR Beta-LR Assay
Utilizing a newly developed long-read sequencing technology, the Ion Torrent Oncomine TCR Beta-LR Assay is designed to efficiently capture all three complementarity-determnining regions of the TCR beta chain (CDR1, CDR2, CDR3) with high accuracy. This approach may enable key applications, such as predictive or prognostic biomarker discovery, T cell characterization, and identification of variable gene polymorphisms from samples such as RNA extracted from whole blood, fresh-frozen tissue, or FACS-sorted cells. The identification of rare and abundant clones can be achieved with as little as 10 ng RNA input. The use of an RNA template allows sequencing of productive and relevant variable (V), diversity (D), and joining (J) rearrangements—improving the identification of rare clones.
Oncomine BCR IGH LR Assay
The Ion Torrent Oncomine BCR IGH LR Assay uses the long read sequencing capabilities of Ion Torrent to interrogate all complementarity determining regions of the BCR immunoglobulin heavy chain (IgH). High sequencing accuracy enables you to quantify somatic hypermutation and provide insights into B cell development and malignant transformation research. The frequency of hypermutation in biomarker research may have future prognostic value for some cancers, such as chronic lymphocyte leukemia (CLL). Assessing clonal expansion, evaluating clonal evolution and isotype abundance can be performed from either DNA or RNA samples. The identification of rare clones can be performed using as little as 10 ng of RNA sample material.
Oncomine BCR IGH SR Assay
The Ion Torrent Oncomine BCR IGH SR Assay allows you to interrogate the CDR3 region of the BCR immunoglobulin heavy chain (IgH) from research samples such as formalin-fixed, paraffin-embedded (FFPE) tissue or circulating free nucleic acid in blood. The assay can identify somatic hypermutations in the diverse CDR3 region, allowing you to study clonal evolution and isotype abundance with deeper insight. High sensitivity means the assay may be used to evaluate potential biomarkers of measurable residual disease (MRD) with a limit of detection that is equivalent or better than current practice, thus providing potential future prognostic value for myeloma and other cancer research studies.
Oncomine Immune Response Research Assay
The Ion Torrent Oncomine Immune Response Research panel was carefully selected to monitor the tumor microenvironment (TME). The assay can be used for identification of biomarkers, and to study the mechanism of action and other interactions emanating from combination therapy experiments. In a head-to-head comparison with its competitors, the assay detected lower expressors associated with T-cell receptor (TCR) signaling and check-point inhibitors, thereby allowing researchers to focus on the correct TCR and the most-suited immunotherapy.
Oncomine Tumor Mutation Load Assay
Tumor Mutation Load or Tumor Mutational Burden (TMB) is rapidly becoming an independent predictor for patient stratification for response to immunotherapy. The Ion Torrent Oncomine Tumor Mutation Load Assay covers 1.7 Mb across 409 cancer-related genes relevant across major cancer types and requires as little as 20 ng of tumor DNA with a three-day workflow and streamlined analysis. The assay highly correlates with exome mutation counts, thereby obviating the need for whole-exome sequencing, allowing for a higher percentage of samples to be evaluated and conserving precious samples for additional biomarker assessment.
Mouse assays
Ion AmpliSeq Mouse TCR Beta SR Assay
The Ion AmpliSeq Mouse TCR Beta SR Assay is designed to accurately identify and measure the clonal expansion of T cell lymphocytes from mouse models. The panel identifies T cell clones by targeting the complementarity-determining region 3 (CDR3) using either DNA or RNA from a variety of samples such as blood, PBLs, PBMCs, and FFPE samples. High sequencing accuracy of the diverse CDR3 region allows you to assess clonal expansion, convergence, and identify T cells that are responding to antigen challenge, thus expanding your study designs in immuno-oncology research and biomarker discovery.
Ion AmpliSeq Mouse BCR IGH SR Assay
The Ion AmpliSeq Mouse BCR IGH SR Assay is designed to interrogate the CDR3 region of the BCR immunoglobulin heavy chain (IgH). The high sequencing accuracy achieved with the panel and Ion Torrent technology enables deeper insights in several research areas. Clonal expansion can be assessed, advancing the understanding of B cell response in cancer and immunotherapy research. Accurately identified somatic hypermutations enable repertoire biomarker research analysis that is useful for effective vaccine research. A low limit of detection enables improved monitoring of disease state and response within your model system.
Workflow overview
The Ion Torrent immuno-sequencing solution is designed to help identify markers relevant to research using our streamlined sequencing platform and fully integrated informatics solutions to analyze and interpret results. This sample-to-results approach is a superior solution, bringing accuracy, sensitivity, and ease of use to your immuno-oncology research.
• Blood
• Fresh-frozen tissue
• Sorted cells
• Formalin-fixed, paraffin-embedded (FFPE) tissue
Prepare libraries from either DNA or RNA input depending on your assay requirements
Sequence samples using the Ion GeneStudio S5 System and appropriate Ion 5 Series Chip
Perform downstream data analysis with Ion Reporter Software
• Blood
• Fresh-frozen tissue
• Sorted cells
• Formalin-fixed, paraffin-embedded (FFPE) tissue
Prepare libraries from either DNA or RNA input depending on your assay requirements
Sequence samples using the Ion GeneStudio S5 System and appropriate Ion 5 Series Chip
Perform downstream data analysis with Ion Reporter Software
How does Ion AmpliSeq technology work?
How does the Ion S5 System work?
For Research Use Only. Not for use in diagnostic procedures.