ArticlePLoS computational biology2025
Learning predictive signatures of HLA type from T-cell repertoires.
Article in PLoS computational biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- T Cell Thoughts.Immunological reviews · 2026Review
- Shared CD4+ T cell receptor specificity groups in Crohn's disease and ulcerative colitis.JCI insight · 2026Article
- Computational prediction of TCR cross-reactivity: principles, challenges and translational opportunities.Journal of translational medicine · 2026Review
- Identification of a type 1 diabetes-associated T cell receptor repertoire signature from the human peripheral blood.Science advances · 2026Article
- Quantitative V gene-targeted T cell receptor sequencing as a biomarker in type 1 diabetes.JCI insight · 2026Article
- TCR representation learning with protein language models: a comprehensive review.International immunology · 2026Review
- T cell receptor clonotypes predict human leukocyte antigen allele carriage and antigen exposure history.Communications biology · 2026Article
- CORSA study finds spike-specific blunted immune responses in lymphoma patients after SARS-CoV-2 vaccine.Frontiers in immunology · 2026Article
- TCR2HLA: Calibrated inference of HLA genotypes from TCR repertoires enables identification of immunologically relevant metaclonotypes.PLoS computational biology · 2026Article
- Machine learning in AIRR diagnostics: Advances and applications.Immunoinformatics (Amsterdam, Netherlands) · 2025Article
- Quantitative and large-scale investigation of human TCR-HLA cross-reactivity.Science advances · 2025Article
- Challenges and future directions of AIRR-seq-based diagnostics.Immunoinformatics (Amsterdam, Netherlands) · 2025Article
- Breast cancer is detectable from peripheral blood using machine learning over T cell receptor repertoires.NPJ systems biology and applications · 2025Article
- TCR2HLA: calibrated inference of HLA genotypes from TCR repertoires enables identification of immunologically relevant metaclonotypes.bioRxiv : the preprint server for biology · 2025Article
- Circulating T-cell receptor repertoire for cancer early detection.NPJ precision oncology · 2025Article
- Probing TCR Specificity Using Artificial In Vivo Diversification of CDR3 Regions.European journal of immunology · 2025Article
- Large-scale statistical mapping of T-cell receptorFrontiers in immunology · 2025Article
- Quantifying conformational changes in the TCR:pMHC-I binding interface.Frontiers in immunology · 2024Article
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6 authors.
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Abstract
T cells recognize a wide range of pathogens using surface receptors that interact directly with peptides presented on major histocompatibility complexes (MHC) encoded by the HLA loci in humans. Understanding the association between T cell receptors (TCR) and HLA alleles is an important step towards predicting TCR-antigen specificity from sequences. Here we analyze the TCR alpha and beta repertoires of large cohorts of HLA-typed donors to systematically infer such associations, by looking for overrepresentation of TCRs in individuals with a common allele.TCRs, associated with a specific HLA allele, exhibit sequence similarities that suggest prior antigen exposure. Immune repertoire sequencing has produced large numbers of datasets, however the HLA type of the corresponding donors is rarely available. Using our TCR-HLA associations, we trained a computational model to predict the HLA type of individuals from their TCR repertoire alone. We propose an iterative procedure to refine this model by using data from large cohorts of untyped individuals, by recursively typing them using the model itself. The resulting model shows good predictive performance, even for relatively rare HLA alleles.
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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.