ArticleFrontiers in immunology2019
A Framework for Annotation of Antigen Specificities in High-Throughput T-Cell Repertoire Sequencing Studies.
Article in Frontiers in immunology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 51 citations in OpenAlex.
- Towards high-quality large-scale T cell receptor antigen specificity data: challenges and promises.Nature methods · 2026Article
- T Cell Thoughts.Immunological reviews · 2026Review
- Integrated transcriptomic and TCR profiling reveals local immune dysregulation of T cells in Gl aGvHD.Bone marrow transplantation · 2026Article
- Biophysical modeling for accurate T cell specificity prediction of viral and tumor antigens.Nature communications · 2026Article
- Inference of SARS-CoV-2 exposure biomarkers using large-scale T-cell repertoire profiling.Genome medicine · 2026Article
- Neighborhood enrichment for the identification of antigen-specific T-cell receptors.Briefings in bioinformatics · 2025Article
- Comprehensive analysis of αβT-cell receptor repertoires reveals signatures of thymic selection.Frontiers in immunology · 2025Article
- Limits on inferring T cell specificity from partial information.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Convergence, plasticity, and tissue residence of regulatory T cell response via TCR repertoire prism.eLife · 2024Article
- Local Enrichment with Convergence of Enriched T-Cell Clones Are Hallmarks of Effective Peptide Vaccination against B16 Melanoma.Vaccines · 2024Article
- Aberrant adaptive immune response underlies genetic susceptibility to tuberculosis.Frontiers in immunology · 2024Article
- A transfer-learning approach to predict antigen immunogenicity and T-cell receptor specificity.eLife · 2023Article
- Human adipose tissue as a major reservoir of cytomegalovirus-reactive T cells.Frontiers in immunology · 2023Article
- The landscape of the immunoglobulin repertoire in endemic pemphigus foliaceus.Frontiers in immunology · 2023Article
- Reference-based comparison of adaptive immune receptor repertoires.Cell reports methods · 2022Article
- TCR-L: an analysis tool for evaluating the association between the T-cell receptor repertoire and clinical phenotypes.BMC bioinformatics · 2022Article
- Article
- Progress in kidney transplantation: The role for systems immunology.Frontiers in medicine · 2022Review
- Inactivated tick-borne encephalitis vaccine elicits several overlapping waves of T cell response.Frontiers in immunology · 2022Article
- Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recently developed molecular methods allow large-scale profiling of T-cell receptor (TCR) sequences that encode for antigen specificity and immunological memory of these cells. However, it is well-known that the even unperturbed TCR repertoire structure is extremely complex due to the high diversity of TCR rearrangements and multiple biases imprinted by VDJ rearrangement process. The latter gives rise to the phenomenon of "public" TCR clonotypes that can be shared across multiple individuals and non-trivial structure of the TCR similarity network. Here, we outline a framework for TCR sequencing data analysis that can control for these biases in order to infer TCRs that are involved in response to antigens of interest. We apply two previously published methods, ALICE and TCRNET, to detect groups of homologous TCRs that are enriched in samples of interest. Using an example dataset of donors with known HLA haplotype and CMV status, we demonstrate that by applying HLA restriction rules and matching against a database of TCRs with known antigen specificity, it is possible to robustly detect motifs of epitope-specific responses in individual repertoires. We also highlight potential shortcomings of TCR clustering methods and demonstrate that highly expanded TCRs should be individually assessed to get the full picture of antigen-specific response.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.