TCRb Sequencing

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-seq can be used to interrogate both human and mouse samples, to address questions from basic science to clinical research. To get started you need the ability to isolate RNA from a cell sample. After that, the workflow requires DNA and RNA processing, access to Thermo Ion Sequencers, and standard computing resources to run the highly automated analysis pipeline. If access to Ion sequencing is not readily available, send your RNA samples for TCRb-seq to a preferred service provider. A Thermo preferred academic partner for NGS, the National Jewish Health Genomics core at the Center for Genes Environment and Health, provides expert access to the TCRb-seq technology. The Genomics Core and faculty at NJH have helped pioneer development of TCR sequencing and can help design experiments and studies to get the information you need.

  • Anyone whose research can benefit from identifying or analyzing T cell activation at the specificity and granularity of specific TCR usage, should consider TCRb-seq.

  • Immunologists who need more specificity than provided by Flow Cytometry activation markers, better population representation than scRNA-seq TCR profiling, or human clinical studies

  • Cancer researchers who need a tool to examine T cell activity

  • Microbiologists who want to examine/track host response dynamics

  • Clinicians who desire a research tool to examine the connection be disease etiology and specific T cell/immune activation.

  • Infectious Disease researchers/clinicians who need a tool to track or identify specific immune cell activation in response to a pathogen

  • Identify specific T-cell populations involved in immune activation, clonal expansion, and immune response evolution in the context of human disease or animal models.

  • T cell activation and/or clonal expansion with respect to a specific disease, pathogen, or antigen.

  • Longitudinal analysis of T-cell activation, expansion, and/or memory function

  • Monitoring immune response and T cell activation in the context of vaccines, drug therapy, and/or infectious pathogens.

  • Clinical identification and tracking of T-Cell involvement during disease progression

  • Indication of specific vs. diverse pathogenic drivers of disease and/or progression.

  • Interrogating T-cell activation, clonal expansion, immune response evolution in the context of human disease or animal models

  • Requiring only an ability to collect RNA from a sample, TCRb-seq can be utilized at any stage of a research project

  • Ideal for investigating potential inflammation or immune response questions

  • Data reveals specific T-cell activation as a signal for unique antigen or pathogen involvement.

  • Analysis pipeline is streamlined and provides figure-ready PDF’s displaying a wide range of information regarding T-cell activation.

    • TCR clone percentages

    • Shannon Diversity

    • Cross-sample comparisons

    • CDR3 identities

  • Include flow cytometry to more finely subset the activated T cell population; compliments immune system activation profiles.

  • Include single cell RNA-seq to provide a more comprehensive analysis of TCR usage within the T cell compartment; profile millions of T-cells with TCRb-seq vs. a few thousand with scRNA-seq TCR profiling.

  • Include RNA-seq to provide specific analysis of TCR clonal expansion and understand associated actively transcribed activation pathways.

  • Include standard clinical tests, such as cell diff (CBC), to provide a closer look at the adaptive immune activation; Easily identify specific populations of activated T cells as evidence for a specific disease mechanism such as for cancer immunology, infectious disease, or autoimmunity.

  • Include as a companion to other NGS-based approaches, such as RNA-seq, ChIP-seq, ATAC-seq, etc., to compliment mechanism studies, biomarker discovery, or target validation.


Key Features

  • Clonal Expansion Profiling of TCR’s
  • T-Cell Repertoire Comparison
  • T-Cell Convergence
  • TCRb targeted primer kits


Other Features

  • Competitive Pricing
  • 5-10 days turnaround time based on sample drop off days
  • Re-run guarantee* (we re-run samples one extra time for no additional cost if we see poor results)
  • Expert analysis available
  • Study Design available from PhD Biostatisticians
  • Partnerships on larger projects
  • Interactive Data Report AND sequencing files for further analysis


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

  • T-Cell Repertoire Comparison
    •  Compare genomic sequences easily
    • Visually compare clonal expansion between experiments
  • T-Cell Convergence
    • Elucidate similar antigen binding TCR’s with different sequences
    • Easily determine DNA and AA sequences of expanded T-cell clones from tumors and other samples
    • Identify antigen specific sequences of TCR’s
  • TCRb targeted primer kits
    • Targeted primers help target important regions for better insights
    • Targeted primers help deliver consistent measurements across experiments


Expert Assistance

ThermoFisher Product Resources

TCR Beta-SR Assay

TCR Beta-SR Assay - DNA

TCR Beta-LR Assay


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

1) TCRb
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

2) DNA
There are many kits and applications for different cell sources. Please contact the core to confirm that your extraction method matches the sequencing technique being requested.

  • FFPE and low abundance samples will need a consult prior to submission.

3) RNA
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

Download Sample Submission Form
Download New TCRb Project Request Form



  • 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


  • Parafilm tubes
  • Biohazard Ziploc® filled with Kimwipes or napkins/tissues
  • Sandwiched between dry ice
  • Include sample sheet in the box in Ziploc® back
  • Put QC tubes and Stock RNA in two separate Ziploc® bags

Attn: Fatjon Leti, A642
National Jewish Health
1400 Jackson St
Genomics Facility CGEH
Denver, CO 80206


Supporting Papers

Comparative analysis of murine T-cell receptor repertoires, M Izraelson et al, Immunology. 2018 Feb;153(2):133-144

Quantifiable predictive features define epitope specific T cell receptor repertoires, P Dash et al., Nature. 2017 Jul 6;547(7661):89-93

Identifying specificity groups in the T cell receptor repertoire, J Glanville et al., Nature. 2017 Jul 6;547(7661):94-98

IMGT, the international ImMunoGeneTics database, M-P Lefranc et al., Nucleic Acids Res. 1999 Jan 1;27(1):209-12

VDJdb: a curated database of T-cell receptor sequences with known antigen specificity, M Shugay et al., Nucleic Acids Res. 2018 Jan 4;46(D1):D419-D427