ArticleBriefings in bioinformatics2018
High-throughput sequencing of the T-cell receptor repertoire: pitfalls and opportunities.
Article in Briefings in bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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Who cites it
64 citing papers in PubMed, 102 citations in OpenAlex.
- Plasticity of the Immune System in Children Following Treatment Interruption in HIV-1 Infection.Frontiers in immunology · 2021Trial
- Therapeutic strategy for cervical gastric-type adenocarcinoma by targeting CLU to relieve CLU-associated stress and sensitize chemotherapy.Precision clinical medicine · 2026Article
- Decoding adaptive immunity: advanced strategies in T and B cell repertoire analysis.Journal of translational medicine · 2026Review
- A multi-branch ensemble learning framework for detection of non-small cell lung cancer via T-cell receptor sequencing.BMC cancer · 2026Article
- Stable global repertoire architecture masks short-term clonal remodeling in intratumoral TCR repertoires.Frontiers in immunology · 2026Article
- HELP-TCR: Harmonized Explainable Language Processing Toolkit for T Cell Antigen Receptor Repertoires.Computational and structural biotechnology journal · 2026Article
- Disrupting explicit encoding paradigms: property-interactive transformers decode T-cell receptor specificity beyond dataset biases.Briefings in bioinformatics · 2025Article
- T-cell receptor/CD28-targeted immunotherapeutics selectively drive naive T-cell expansion to generate functional HIV-specific responses.Journal of virology · 2025Article
- The differential immunological impact of photon vs proton radiation therapy in high-grade lymphopenia in patients with gastrointestinal tumors.Clinical and experimental immunology · 2025Article
- Significance and challenges of immunopharmacogenomics.Frontiers in immunology · 2025Review
- Pep2TCR: Accurate prediction of CD4 T cell receptor binding specificity through transfer learning and ensemble approach.iMetaOmics · 2024Article
- Deciphering Abdominal Aortic Diseases Through T-Cell Clonal Repertoire of Perivascular Adipose Tissue.Journal of the American Heart Association · 2024Article
- T-cell immunity induced and reshaped by an anti-HPV immuno-oncotherapeutic lentiviral vector.NPJ vaccines · 2024Article
- A Paratope-Enhanced Method to Determine Breadth and Depth TCR Clonal Metrics of the Private Human T-Cell Vaccine Response after SARS-CoV-2 Vaccination.International journal of molecular sciences · 2023Article
- Review
- Measures of epitope binding degeneracy from T cell receptor repertoires.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Inferring the T cell repertoire dynamics of healthy individuals.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Immune repertoire analysis of normal Chinese donors at different ages.Cell proliferation · 2022Article
- Stitchr: stitching coding TCR nucleotide sequences from V/J/CDR3 information.Nucleic acids research · 2022Article
- A roadmap for translational cancer glycoimmunology at single cell resolution.Journal of experimental & clinical cancer research : CR · 2022Review
4 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
T-cell specificity is determined by the T-cell receptor, a heterodimeric protein coded for by an extremely diverse set of genes produced by imprecise somatic gene recombination. Massively parallel high-throughput sequencing allows millions of different T-cell receptor genes to be characterized from a single sample of blood or tissue. However, the extraordinary heterogeneity of the immune repertoire poses significant challenges for subsequent analysis of the data. We outline the major steps in processing of repertoire data, considering low-level processing of raw sequence files and high-level algorithms, which seek to extract biological or pathological information. The latest generation of bioinformatics tools allows millions of DNA sequences to be accurately and rapidly assigned to their respective variable V and J gene segments, and to reconstruct an almost error-free representation of the non-templated additions and deletions that occur. High-level processing can measure the diversity of the repertoire in different samples, quantify V and J usage and identify private and public T-cell receptors. Finally, we discuss the major challenge of linking T-cell receptor sequence to function, and specifically to antigen recognition. Sophisticated machine learning algorithms are being developed that can combine the paradoxical degeneracy and cross-reactivity of individual T-cell receptors with the specificity of the overall T-cell immune response. Computational analysis will provide the key to unlock the potential of the T-cell receptor repertoire to give insight into the fundamental biology of the adaptive immune system and to provide powerful biomarkers of disease.
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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.