ArticleeLife2021
TCR meta-clonotypes for biomarker discovery with
Article in eLife, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 141 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
141 citing papers in PubMed, 184 citations in OpenAlex.
- Article
- T cell immunomonitoring: a comparative analysis of traditional and novel methods to quantify and characterize human antigen-specific T cells.Nature protocols · 2026Review
- Entering the Age of Specificity in T Cell Immunity.Immunological reviews · 2026Review
- Predicting specificity of TCR-pMHC interactions using machine-learning and biophysical models.Cell systems · 2026Article
- Unsupervised identification of low-frequency antigen-specific TCRs using distance-based anomaly scoring.Briefings in bioinformatics · 2026Article
- Structural T-Cell Receptor Analysis in the Age of Machine Learning.Immunological reviews · 2026Review
- Potential Role of Prebiotics and Probiotics on Oocyte Quality, Embryo Development, Endometrial Health, and Fertility Outcomes in Assisted Reproductive Technologies.Probiotics and antimicrobial proteins · 2026Review
- Clonal overlap and convergent clustering of T cell receptor signatures in Crohn's disease in monozygotic twins.Inflammatory bowel diseases · 2026Article
- Machine Learning of Personal Repertoires From Public T Cell Receptors.Immunological reviews · 2026Review
- TcrDesign: de novo design of epitope-specific full-length T cell receptors.Science China. Life sciences · 2026Article
- The Role of the T Cell Receptor Sequence in Shaping T Cell Functional Fate.Immunological reviews · 2026Review
- Computational identification of antigen-specific T cell groups through generative epitope modeling.iScience · 2026Article
- A cell-based kinetic framework enables TCR specificity prediction.Signal transduction and targeted therapy · 2026Article
- The challenge and promise of studying human antigen-specific T cells.Nature reviews. Immunology · 2026Review
- TCR-FramePose: a local-frame representation for decomposing global docking and CDR3 loop geometry in TCR-pMHC recognition.bioRxiv : the preprint server for biology · 2026Article
- DUET: a graph-based workflow for TCR-epitope prioritization and tumor-reactive T-cell identification.Briefings in bioinformatics · 2026Article
- Machine Learning for TCR Repertoire Epitope Annotation and Pattern Discovery.Immunological reviews · 2026Review
- Modeling TCR-Epitope Recognition Specificity: What We Should Learn to Succeed.Immunological reviews · 2026Review
- VDJ-REMIX: REpertoire Module Identification and eXploration.Bioinformatics (Oxford, England) · 2026Article
- The T Cell Receptor: Molecular Sensor, Therapeutic Mediator and Probabilistic Driver of Adaptive Immunity.Immunological reviews · 2026Review
81 more citing papers are in PubMed but not listed here.
Corrections and comments
- Update of
Authors and funding
10 authors at 4 institutions in 3 countries.
Funding
Abstract
T-cell receptors (TCRs) encode clinically valuable information that reflects prior antigen exposure and potential future response. However, despite advances in deep repertoire sequencing, enormous TCR diversity complicates the use of TCR clonotypes as clinical biomarkers. We propose a new framework that leverages experimentally inferred antigen-associated TCRs to form meta-clonotypes - groups of biochemically similar TCRs - that can be used to robustly quantify functionally similar TCRs in bulk repertoires across individuals. We apply the framework to TCR data from COVID-19 patients, generating 1831 public TCR meta-clonotypes from the SARS-CoV-2 antigen-associated TCRs that have strong evidence of restriction to patients with a specific human leukocyte antigen (HLA) genotype. Applied to independent cohorts, meta-clonotypes targeting these specific epitopes were more frequently detected in bulk repertoires compared to exact amino acid matches, and 59.7% (1093/1831) were more abundant among COVID-19 patients that expressed the putative restricting HLA allele (false discovery rate [FDR]<0.01), demonstrating the potential utility of meta-clonotypes as antigen-specific features for biomarker development. To enable further applications, we developed an open-source software package,
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What OpenQuestion holds
Registered trials
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.