OncomineTCR-Beta-LR-Assay
Harness the power of the immune repertoire with an Ion Torrent long-read NGS assay

Studies aimed at leveraging an individual’s own immune system as a potential strategy toward the advancement of precision oncology has been a shared goal of scientists for many years. However, the complexities of tumor–immune interactions warrant a multidimensional approach to facilitate well-designed translational research studies and interpretation of results. Genomic analysis solutions based on next-generation sequencing (NGS) can be powerful tools to help gain significant insights in translational and clinical research.

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Investigate the immune repertoire by interrogating all regions of the TCR beta chain – CDR1, CDR2 and CDR3 with one assay

Analyzing the immune repertoire to capture the diversity of T cell receptor (TCR) rearrangements can help you make significant progress in immuno-oncology research. The Oncomine TCR Beta-LR Assay, provides researchers with a rapid, long-read NGS tool for studying the complexity of cellular immunology. This comprehensive solution enables you to:

immuno-oncology research

Discover immune response biomarkers—accurately measure T cell repertoire diversity and clonal expansion, and identify antigen-specific T cells to accelerate translational research

immunotherapy research

Investigate markers for immune-mediated adverse events (IMAEs)—analyze all three complementarity-determining regions (CDR1, 2, and 3) for allele-specific polymorphisms that may be linked to autoimmune diseases and IMAEs

manufacture and function

Optimize the function and manufacture of potentially therapeutic T cells—characterize TCR beta chain sequences and optimize the manufacture of genetically engineered T cells

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Immuno-oncology webinar series

Deciphering the cancer immunity cycle through next generation sequencing

  • Dr. Simon Cawley, Head of Software and Bioinformatics for the Ion Torrent NGS platform, discusses current challenges in precision immunotherapy today and the impacts on immunotherapy translational research
  • Learn about the advantages of Ion Torrent’s full immuno-oncology NGS portfolio to help decipher the immunity cycle

View webinar ›

Dr. Simon Cawley
Looney_profile

Advancing precision immunotherapy through next-generation sequencing of T cell receptors, Part I

  • Dr. Timothy Looney, Staff Scientist, Bioinformatics, at Thermo Fisher Scientific, reviews the current applications of T cell receptor sequencing to immunotherapy translational research
  • Explore the advantages of long-amplicon TCRB sequencing via Ion Torrent solutions for immunotherapy biomarker discovery from peripheral blood

View webinar ›

Advancing precision immunotherapy through next-generation sequencing of T cell receptors, Part II

  • Dr. Looney returns to further explore the recent advancements in the application of NGS of TCRB chain repertoires to precision immunotherapy
  • Data is presented that suggests short-amplicon TCRB repertoire sequencing of FFPE samples may be used to characterize T cell responses to tumor antigens through the assessment of T cell expansion, diversity, and receptor convergence

View webinar ›

Video: Can T-cell receptor (TCR) repertoire sequencing be a missing piece of the immuno-oncology puzzle?

Dr. Prof. Jose Carlos Machado Ipatimup, Medical Faculty Porto, Portugal
The concept that the immune system plays a critical role in anti-tumor responses has been demonstrated and, more recently, immune checkpoint therapy has started a revolution in the field of oncology research. Several research studies are ongoing to identify appropriate biomarkers, and a multi-biomarker approach is seen as the only path to advance immunotherapy research.


Workflow overview

Manual library construction is followed by automated template preparation using the Ion Chef System. Sequencing is performed on the Ion S5 System with data analysis using Ion Reporter Software.

48 Hours
RNA Extraction

• Blood

• Fresh-frozen tissue

• Sorted cells

Ion AmpliSeq library

Prepare libraries from 10ng to 1ug RNA input

48 Hours

Sequence 1 to 16 samples using the Ion GeneStudio S5 System and the Ion 530 Chip

Ion reporter software

Perform downstream data analysis using Ion Reporter Software 5.6 or later

RNA Extraction

• Blood

• Fresh-frozen tissue

• Sorted cells

Ion AmpliSeq library

Prepare libraries from 10ng to 1ug RNA input

48 Hours

Sequence 1 to 16 samples using the Ion GeneStudio S5 System and the Ion 530 Chip

Ion reporter software

Perform downstream data analysis using Ion Reporter Software 5.6 or later

 

From complex to comprehensible—in just two days

Based on robust, highly referenced Ion AmpliSeq technology, our NGS solution has been carefully designed to significantly improve your turnaround time—go from sample to analysis in as little as 48 hours (Figure 1). The Oncomine TCR Beta-LR Assay, is comprehensive with up to 400 bp read-length amplicons for complete characterization of CDR1, CDR2, and CDR3 (Figure 2). It is highly accurate with mRNA-based sequencing and exerts extremely low PCR-driven primer bias.

data privacy

Data security—you have full control of your data (with no service model or additional fees) and full transparency in analysis, and your TCR sequences stay with you

data privacy

Accuracy—with RNA as a starting point, you can interrogate productive rearrangement of TCR beta chain genes and benefit from low substitution error rates achieved on the Ion S5 System

data privacy

Low input requirement—create your Ion AmpliSeq library from a range of input amounts (10 ng–1 μg), depending on your sample constraints and application preferences

Figure 2. Stacked barplot indicating the representation of variable genes among clones identified in a sample. Color segments within each bar indicate the frequency of particular variable gene alleles. IMGT annotation of identified alleles is indicated on the x-axis.

Resources

 Poster: TCRB chain convergence in chronic cytomegalovirus infection and cancer
 Download flyer
 Flyer-Ion AmpliSeq Immune Repertoire Assay Plus, TCR β
 Poster: Peripheral blood TCRB repertoire convergence and clonal expansion predict response to anti-CTLA-4 monotherapy for cancer
 Poster: Peripheral blood TCRB chain convergence predicts response to immunotherapy in advanced melanoma
 Poster: TRBV polymorphism predicts adverse events during checkpoint blockade immunotherapy
 Poster: Evaluation of therapeutic T cell manufacture using long amplicon TCRβ immune repertoire sequencing
 Flyer: Multidimensional NGS solutions enable tumor-immune insights within IO research
 Poster: Targeted T-cell receptor beta immune repertoire sequencing in several FFPE tissue types
 Poster: Peripheral Blood TCRB Chain Convergence Predicts Response to Dendritic Cell-Based Immunotherapy in Advanced-Stage Melanoma Patients
 Poster: Peripheral blood TCRB repertoire convergence and clonal expansion predict response to anti-CTLA-4 monotherapy for cancer