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Oncomine TCR Beta-SR Assay
Interrogate the tumor microenvironment with an Ion Torrent short-read NGS assay
The identification of T-cell clones in tumors and the measurement of clonal expansion is important to characterize tumors, design cancer vaccines, and assess the utility for researching minimal residual disease (MRD). The CD3 region on the beta (β) chain of the T-cell receptor is most responsible for antigen recognition.
The sequence coding for the CDR3 region is extremely diverse and is unique for every T-cell clonotype. Hence, in immune repertoire sequencing, the CDR3 sequences are used to identify a T-cell clonotype. The Oncomine TCR Beta-SR Assay targets the CDR3 region, enabling such investigations.
Analyzing the immune repertoire to capture the diversity of T-cell receptor (TCR) rearrangements can help you make significant progress in immuno-oncology research. While the Oncomine TCR Beta-LR Assay interrogates complementarity-determining regions (CDRs) 1, 2, and 3, the Oncomine TCR Beta-SR Assay specifically interrogates CDR3 with short-amplicon TCR sequencing to characterize the immune status.
Featured products
Characterize T cell response—measure response to tumor antigens through clonal assessment of T lymphocytes
Identify low frequency clones—detect T-cell malignancies with a LOD of 1 in 104 to 1 in 105
Sequence the beta chain of the T-cell receptor with genomic DNA or RNA—interrogate the tumor microenvironment with 100 ng DNA or 50 ng RNA from FFPE samples
Featured webinar series: Advancements in immunotherapy
Deciphering the cancer immunity cycle through next-generation sequencing
Simon Cawley, PhD
Head of Software and Bioinformatics for the Ion Torrent next-generation sequencing (NGS) platform, Thermo Fisher Scientific
Advancing precision immunotherapy through next-generation sequencing of T cell receptors: Parts I, II
Timothy Looney, PhD
Staff Scientist, Bioinformatics, Thermo Fisher Scientific
Oncomine TCR Beta-SR Assay performance
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Figure 1. Testing of three different FFPE tissues. (A) Tonsil RNA, high T-cell content; (B) thymus RNA, medium T-cell content; (C) spleen RNA, low T-cell content. T-cell content for each tissue was previously established using a qPCR assay that probes for a gene that is common to all T cells. The TCR beta sequencing data is consistent with what was previously measured with this qPCR assay.
Oncomine TCR Beta-SR Assay DNA & RNA workflow
- FFPE tissue
- Fresh-frozen (FF) tissue
- Sorted T cells
- PBMCs/whole blood
- cfDNA
- For DNA preparation, libraries require 100 ng to 1 µg DNA input
- For RNA preparation, libraries require 50 ng to 1 µg RNA input
- Sequence samples using the Ion GeneStudio S5 System and the Ion 540 Chip or the Ion 550 Chip
- Perform downstream data analysis with Ion Reporter Software 5.10 and up
- FFPE tissue
- Fresh-frozen (FF) tissue
- Sorted T cells
- PBMCs/whole blood
- cfDNA
- For DNA preparation, libraries require 100 ng to 1 µg DNA input
- For RNA preparation, libraries require 50 ng to 1 µg RNA input
- Sequence samples using the Ion GeneStudio S5 System and the Ion 540 Chip or the Ion 550 Chip
- Perform downstream data analysis with Ion Reporter Software 5.10 and up
From sample to report—in just two days
Data security—retain full control of your data (with no service model or additional fees), full transparency in analysis, and ownership of your TCR sequences since they stay with you
Accuracy—with either DNA or RNA as a starting point, you can interrogate only the productive rearrangement of the TCR beta chain for clonality data on the Ion GeneStudio S5 System
Low input requirement—create your Ion AmpliSeq library from a range of input amounts (50 ng–1 μg), depending on your sample constraints and application preferences
Resources
For Research Use Only. Not for use in diagnostic procedures.