T-Cell Receptor Profiling

National Jewish Health is a preferred provider of ThermoFisher TCRb-Seq providing full data sets, custom reports and access to interactive data analysis tools to work with your TCR data in ThermoFisher’s powerful Ion Reporter Cloud. Standard and Deep Sequencing options are available. Through our Center for Genes, Environment and Health Data Science Group at National Jewish Health we can assist with experiment design, sample preparation, study design and custom analysis.

TCRb-seq provides a solution for traditionally hard-to-determine questions. These could include questions such as:

Observing specific (clonal) vs. non-specific cellular activation within a diverse sample set (i.e. Human subjects)
Examining the contributions of pathogen driven inflammation to disease models or human disease
Identifying unique TCRb populations comparing specific T cell populations
Observing TCR-selection and/or evolution over time in the course of autoimmune development, vaccine studies, pathogen-host interactions, or cancer models.

Ion Ampliseq™ TCR Beta Next Gen Sequencing (TCRb-Seq) is used to track the activity of specific groups of immune cells (at a semi-clonal level) in the T cell compartment of the adaptive immune system. It is a more specific and selective indication of adaptive immune activation vs. traditional activation assays, such as cytokine production or cell surface activation marker expression. Importantly, it does not require prior knowledge of an activating antigen as with Tetramer-Flow assays.

Ion TCRb-seq is also much more cost effective vs. single-cell(sc) TCR-seq. TCRb-seq provides TCR usage data for large T cell populations vs. the few thousand cells typically profiled with scTCR-seq. After sequencing on the Thermo Ion platform, the analysis pipeline for TCRb-seq has been designed to be easy to use, easy to compare data across samples, and easy to generate figures for presentations, grants, or publications. Thus, you can analyze your TCRb-seq without access to extensive bioinformatic resources.

TCRb Sequencing

Clonal Expansion Profiling of TCR’s

Get a detailed visual of clonal expansion from your experiments.

See how diverse or targeted the expansion activity is within your samples.

Sample Prep

Please refer to instructions in the extraction kit. If you have further questions, reach out to the core for clarification. For DNA, we can help match your samples to a workflow and kit that has previously performed well for us.

Sample Prep Guidance

We have had success with the Qiagen kits for RNA and DNA. Please contact us for more information to match your sample sources and amounts.

FFPE – Both RNA and DNA from the same sample- Recover Total Nucleic Acid Isolation kit for FFPE. Please contact the core to confirm your extraction method matches your sequencing needs.
MagMax FFPE DNA/RNA Ultra kit works well for low genomic amounts

For RNA extraction and sample prep, we have had success using RNeasy Mini or RNeasy Micro kit (Qiagen). We highly recommend performing all of the optional steps including the DNAse treatment in RNA extraction.

RNeasy Mini kit – elution at 30uL. Client must provide 5uL of QC aliquot, and the RNA stock. It is ok to do an internal QC.
RNeasy Micro kit – elution at 13uL. Send the RNA stock. We prefer you NOT perform internal QC when using this kit to preserve RNA amounts.
We highly recommend performing all of the optional steps including the DNAse treatment.
For the RNeasy mini kit, please provide concentration.
Store and submit samples using DNA LoBind tubes (1.5 uL) – Eppendorf Tubes Cat# 022431021.

Submission Resources

Sample Submission Form

New TCRb Project Request Form

Labeling

Black permanent marker for labeling
Top tube label – 1A+Pi initials, 2A+Pi initials (i.e. 1AKW). We will determine initials.
Side of the tube = Sample name