Multiplex Identification of Antigen-Specific T Cell Receptors Using a Combination of Immune Assays and Immune Receptor Sequencing

PLoS One. 2015 Oct 28;10(10):e0141561. doi: 10.1371/journal.pone.0141561. eCollection 2015.


Monitoring antigen-specific T cells is critical for the study of immune responses and development of biomarkers and immunotherapeutics. We developed a novel multiplex assay that combines conventional immune monitoring techniques and immune receptor repertoire sequencing to enable identification of T cells specific to large numbers of antigens simultaneously. We multiplexed 30 different antigens and identified 427 antigen-specific clonotypes from 5 individuals with frequencies as low as 1 per million T cells. The clonotypes identified were validated several ways including repeatability, concordance with published clonotypes, and high correlation with ELISPOT. Applying this technology we have shown that the vast majority of shared antigen-specific clonotypes identified in different individuals display the same specificity. We also showed that shared antigen-specific clonotypes are simpler sequences and are present at higher frequencies compared to non-shared clonotypes specific to the same antigen. In conclusion this technology enables sensitive and quantitative monitoring of T cells specific for hundreds or thousands of antigens simultaneously allowing the study of T cell responses with an unprecedented resolution and scale.

MeSH terms

  • Clonal Evolution / genetics
  • Clonal Evolution / immunology
  • Enzyme-Linked Immunospot Assay* / methods
  • Enzyme-Linked Immunospot Assay* / standards
  • Epitopes, T-Lymphocyte / immunology*
  • High-Throughput Nucleotide Sequencing*
  • Humans
  • Receptors, Antigen, T-Cell / genetics*
  • Receptors, Immunologic / genetics*
  • Reproducibility of Results
  • T-Cell Antigen Receptor Specificity / genetics*
  • T-Cell Antigen Receptor Specificity / immunology*


  • Epitopes, T-Lymphocyte
  • Receptors, Antigen, T-Cell
  • Receptors, Immunologic

Grants and funding

The authors received no specific funding for this work. Authors are employees and stockholders of Adaptive Biotechnologies Corporation. Adaptive Biotechnologies provided support in the form of salaries for all authors, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.