ArticlePLoS computational biology2017
Identifying T Cell Receptors from High-Throughput Sequencing: Dealing with Promiscuity in TCRα and TCRβ Pairing.
Article in PLoS computational biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
What it found
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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.
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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.
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Who cites it
25 citing papers in PubMed, 41 citations in OpenAlex.
- T-cell receptor alpha to beta chains binding prediction.Briefings in bioinformatics · 2026Article
- circVDJ-seq for T cell clonotype detection in single-cell and spatial multi-omics.Genome medicine · 2026Article
- TIRTL-seq: deep, quantitative and affordable paired TCR repertoire sequencing.Nature methods · 2026Article
- CD4+ mucosal-associated invariant T cells express highly diverse T cell receptors.Journal of immunology (Baltimore, Md. : 1950) · 2025Article
- Identifying T-cell clubs by embracing the local harmony between TCR and gene expressions.Molecular systems biology · 2024Article
- Cell activation-based screening of natively paired human T cell receptor repertoires.Scientific reports · 2023Article
- TCR sequencing: applications in immuno-oncology research.Immuno-oncology technology · 2023Review
- Longitudinal analysis reveals age-related changes in the T cell receptor repertoire of human T cell subsets.The Journal of clinical investigation · 2022Article
- T-Cell Receptor Repertoire Sequencing and Its Applications: Focus on Infectious Diseases and Cancer.International journal of molecular sciences · 2022Review
- Machine Learning Approaches to TCR Repertoire Analysis.Frontiers in immunology · 2022Review
- Expansion of Unique Hepatitis C Virus-Specific Public CD8Journal of immunology (Baltimore, Md. : 1950) · 2021Article
- High-throughput and single-cell T cell receptor sequencing technologies.Nature methods · 2021Review
- T cell receptor sequencing in autoimmunity.Journal of life sciences (Westlake Village, Calif.) · 2020Article
- Article
- Identification of Disease-associated Traits and Clonotypes in the T Cell Receptor Repertoire of Monozygotic Twins Affected by Inflammatory Bowel Diseases.Journal of Crohn's & colitis · 2020Article
- Comprehensive analysis of structural and sequencing data reveals almost unconstrained chain pairing in TCRαβ complex.PLoS computational biology · 2020Article
- Determinants governing T cell receptor α/β-chain pairing in repertoire formation of identical twins.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Selected before selection: A case for inherent antigen bias in the T cell receptor repertoire.Current opinion in systems biology · 2019Article
- A Bayesian framework for high-throughput T cell receptor pairing.Bioinformatics (Oxford, England) · 2019Article
- Single T Cell Sequencing Demonstrates the Functional Role ofFrontiers in immunology · 2019Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 3 countries.
Funding
Abstract
Characterisation of the T cell receptors (TCR) involved in immune responses is important for the design of vaccines and immunotherapies for cancer and autoimmune disease. The specificity of the interaction between the TCR heterodimer and its peptide-MHC ligand derives largely from the juxtaposed hypervariable CDR3 regions on the TCRα and TCRβ chains, and obtaining the paired sequences of these regions is a standard for functionally defining the TCR. A brute force approach to identifying the TCRs in a population of T cells is to use high-throughput single-cell sequencing, but currently this process remains costly and risks missing small clones. Alternatively, CDR3α and CDR3β sequences can be associated using their frequency of co-occurrence in independent samples, but this approach can be confounded by the sharing of CDR3α and CDR3β across clones, commonly observed within epitope-specific T cell populations. The accurate, exhaustive, and economical recovery of TCR sequences from such populations therefore remains a challenging problem. Here we describe an algorithm for performing frequency-based pairing (alphabetr) that accommodates CDR3α- and CDR3β-sharing, cells expressing two TCRα chains, and multiple forms of sequencing error. The algorithm also yields accurate estimates of clonal frequencies.
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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.