ArticlePloS one2013
Combining next-generation sequencing and immune assays: a novel method for identification of antigen-specific T cells.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 38 citations in OpenAlex.
- T-cell receptor sequencing demonstrates persistence of virus-specific T cells after antiviral immunotherapy.British journal of haematology · 2019Trial
- V-J combinations of T-cell receptor predict responses to erythropoietin in end-stage renal disease patients.Journal of biomedical science · 2017Trial
- NeoTCRseek: an integrated platform for high-sensitivity identification of neoantigen-specific TCR clonotypes to track clinical T-cell dynamics.Frontiers in immunology · 2026Article
- A large-scale database of T-cell receptor beta sequences and binding associations from natural and synthetic exposure to SARS-CoV-2.Frontiers in immunology · 2025Article
- T-cell immunity induced and reshaped by an anti-HPV immuno-oncotherapeutic lentiviral vector.NPJ vaccines · 2024Article
- Barcoding intracellular reverse transcription enables high-throughput phenotype-coupled T cell receptor analyses.Cell reports methods · 2023Article
- SARS-CoV-2-specific T cell responses in patients with multisystem inflammatory syndrome in children.Clinical immunology (Orlando, Fla.) · 2022Article
- Impaired humoral immunity is associated with prolonged COVID-19 despite robust CD8 T cell responses.Cancer cell · 2022Article
- Tumor-induced double positive T cells display distinct lineage commitment mechanisms and functions.The Journal of experimental medicine · 2022Article
- In chronic infection, HIV gag-specific CD4+ T cell receptor diversity is higher than CD8+ T cell receptor diversity and is associated with less HIV quasispecies diversity.Journal of virology · 2021Article
- Advances in identification and selection of personalized neoantigen/T-cell pairs for autologous adoptive T cell therapies.Oncoimmunology · 2021Review
- A Framework to Identify Antigen-Expanded T Cell Receptor Clusters Within Complex Repertoires.Frontiers in immunology · 2021Article
- Ultra-efficient sequencing of T Cell receptor repertoires reveals shared responses in muscle from patients with Myositis.EBioMedicine · 2020Article
- A large-scale database of T-cell receptor beta (TCRβ) sequences and binding associations from natural and synthetic exposure to SARS-CoV-2.Research square · 2020Article
- Characterization and Monitoring of Antigen-Responsive T Cell Clones Using T Cell Receptor Gene Expression Analysis.Frontiers in immunology · 2020Article
- TCR Convergence in Individuals Treated With Immune Checkpoint Inhibition for Cancer.Frontiers in immunology · 2019Article
- Immunosequencing identifies signatures of cytomegalovirus exposure history and HLA-mediated effects on the T cell repertoire.Nature genetics · 2017Article
- T cell receptor repertoire usage in cancer as a surrogate marker for immune responses.Seminars in immunopathology · 2017Review
- 3D: diversity, dynamics, differential testing - a proposed pipeline for analysis of next-generation sequencing T cell repertoire data.BMC bioinformatics · 2017Article
- T-cell receptor profiling in cancer.Molecular oncology · 2015Review
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In this study, we combined a novel sequencing method, which can identify individual clonotypes based on their unique T cell receptor (TCR) rearrangement, with existing immune assays to characterize antigen-specific T cell responses. We validated this approach using three types of assays routinely used to measure antigen-specific responses: pentamers which enable identification of T cells bearing specific TCRs, activation marker expression following antigen stimulation and antigen-induced proliferation to identify cytomegalovirus (CMV) specific clonotypes. In one individual, 8 clonotypes were identified using a pentamer reagent derived from the CMV pp65 protein. The same 8 clonotypes were also identified following sequencing of cells that upregulated an activation marker following incubation with an identical peptide derived from pp65. These 8 and an additional 8 clonotypes were identified using a more sensitive CFSE-based proliferation assay. We found clear sequence homology among some of the clonotypes identified, and the CDR3 region in one clonotype was identical to a previously published pp65-specific clonotype sequence. Many of these CMV-specific clonotypes were present at frequencies below 10(-5) which are undetectable using standard flow-cytometric methods. These studies suggest that an immune response is comprised of a diverse set of clones, many of which are present at very low frequencies. Thus, the combination of immune assays and sequencing depicts the richness and diversity of an immune response at a level that is not possible using standard immune assays alone. The methods articulated in this work provide an enhanced understanding of T cell-mediated immune responses at the clonal level.
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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.