ArticleGenome medicine2022
T cell receptor beta germline variability is revealed by inference from repertoire data.
Article in Genome medicine, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Thymic selection of the T cell receptor repertoire is biased toward autoimmunity in females.eLife · 2026Article
- T-cell receptor repertoires against HLA class I-restricted minor histocompatibility antigens are highly diverse with a small subset of public clonotypes.Journal for immunotherapy of cancer · 2026Article
- gAIRR-wgs: high-resolution T cell receptor allele typing in biobank-scale whole-genome sequencing data.Briefings in bioinformatics · 2026Article
- Modeling TCR-Epitope Recognition Specificity: What We Should Learn to Succeed.Immunological reviews · 2026Review
- A multi-ethnic reference map of T cell receptor germline diversity reveals evidence of natural selection on alpha chain genes.Nature communications · 2026Article
- Inference of SARS-CoV-2 exposure biomarkers using large-scale T-cell repertoire profiling.Genome medicine · 2026Article
- The current landscape of adaptive immune receptor genomic and repertoire data: OGRDB and VDJbase.Nucleic acids research · 2026Article
- Challenges and future directions of AIRR-seq-based diagnostics.Immunoinformatics (Amsterdam, Netherlands) · 2025Article
- TRAIT: A Comprehensive Database for T-cell Receptor-antigen Interactions.Genomics, proteomics & bioinformatics · 2025Article
- Enhancing sequence alignment of adaptive immune receptors through multi-task deep learning.Nucleic acids research · 2025Article
- Simulation of adaptive immune receptors and repertoires with complex immune information to guide the development and benchmarking of AIRR machine learning.Nucleic acids research · 2025Article
- Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR.Genome research · 2024Article
- Interpretable GWAS by linking clinical phenotypes to quantifiable immune repertoire components.Communications biology · 2024Article
- An unbiased comparison of immunoglobulin sequence aligners.Briefings in bioinformatics · 2024Article
- Novel insights into TCR-T cell therapy in solid neoplasms: optimizing adoptive immunotherapy.Experimental hematology & oncology · 2024Review
- The complete and fully-phased diploid genome of a male Han Chinese.Cell research · 2023Article
- IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data.Nucleic acids research · 2023Article
- Contribution of the TCRβ Repertoire to Marek's Disease Genetic Resistance in the Chicken.Viruses · 2023Article
- Adaptive immune receptor genotyping using theFrontiers in immunology · 2023Article
- A template for multitudes: Germline immune polymorphism of the T cell receptor loci.Cell genomics · 2022Article
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8 authors.
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Abstract
backgroundT and B cell receptor (TCR, BCR) repertoires constitute the foundation of adaptive immunity. Adaptive immune receptor repertoire sequencing (AIRR-seq) is a common approach to study immune system dynamics. Understanding the genetic factors influencing the composition and dynamics of these repertoires is of major scientific and clinical importance. The chromosomal loci encoding for the variable regions of TCRs and BCRs are challenging to decipher due to repetitive elements and undocumented structural variants.
methodsTo confront this challenge, AIRR-seq-based methods have recently been developed for B cells, enabling genotype and haplotype inference and discovery of undocumented alleles. However, this approach relies on complete coverage of the receptors' variable regions, whereas most T cell studies sequence a small fraction of that region. Here, we adapted a B cell pipeline for undocumented alleles, genotype, and haplotype inference for full and partial AIRR-seq TCR data sets. The pipeline also deals with gene assignment ambiguities, which is especially important in the analysis of data sets of partial sequences.
resultsFrom the full and partial AIRR-seq TCR data sets, we identified 39 undocumented polymorphisms in T cell receptor Beta V (TRBV) and 31 undocumented 5
conclusionsWe reveal a rich picture of germline variability and demonstrate how a single nucleotide polymorphism dramatically affects the composition of the whole repertoire. Our findings provide a basis for annotation of TCR repertoires for future basic and clinical studies.
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