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IMGT/HighV QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling
Open accessAbstract
T cell repertoire diversity and clonotype follow-up in vaccination, cancer, infectious and immune diseases represent a major challenge owing to the enormous complexity of the data generated. Here we describe a next generation methodology, which combines 5′RACE PCR, 454 sequencing and, for analysis, IMGT, the international ImMunoGeneTics information system (IMGT), IMGT/HighV-QUEST web portal and IMGT-ONTOLOGY concepts. The approach is validated in a human case study of T cell receptor beta (TRB) repertoire, by chronologically tracking the effects of influenza vaccination on conventional and regulatory T cell subpopulations. The IMGT/HighV-QUEST paradigm defines standards for genotype/haplotype analysis and characterization of IMGT clonotypes for clonal diversity and expression and achieves a degree of resolution for next generation sequencing verifiable by the user at the sequence level, while providing a normalized reference immunoprofile for human TRB. Dynamic changes in T cell repertoire underlie immune responses during infection, allergy, autoimmunity and cancer. Here, Li et al. present a workflow for high throughput sequencing and analysis of T cell receptor sequences, and use it to monitor the T cell response to influenza vaccination in a human patient.
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Seddiki, N., Santner-Nanan, B., Martinson, J., Zaunders, J., Sasson, S., Landay, A., Solomon, M., Selby, W., Alexander, S. I., Nanan, R., et al. (2006) · The Journal of Experimental Medicine · doi:10.1084/jem.20060468 · Cited by 1,512
A Direct Estimate of the Human αβ T Cell Receptor Diversity
Arstila, T. P., Casrouge, A., Baron, V., Even, J., Kanellopoulos, J., & Kourilsky, P. (1999) · Science · doi:10.1126/science.286.5441.958 · Cited by 931
Cited by
Overview of methodologies for T-cell receptor repertoire analysis
Rosati, E., Dowds, C. M., Liaskou, E., Henriksen, E. K. K., Karlsen, T. H., & Franke, A. (2017) · BMC Biotechnology · doi:10.1186/s12896-017-0379-9 · Cited by 322
Loss of the HVEM Tumor Suppressor in Lymphoma and Restoration by Modified CAR-T Cells
Boice, M., Salloum, D., Mourcin, F., Sanghvi, V., Amin, R., Oricchio, E., Jiang, M., Mottok, A., Denis-Lagache, N., Ciriello, G., et al. (2016) · Cell · doi:10.1016/j.cell.2016.08.032 · Cited by 257
Bioinformatic and Statistical Analysis of Adaptive Immune Repertoires
Greiff, V., Miho, E., Menzel, U., & Reddy, S. T. (2015) · Trends in Immunology · doi:10.1016/j.it.2015.09.006 · Cited by 210
Greiff, V., Bhat, P., Cook, S. C., Menzel, U., Kang, W., & Reddy, S. T. (2015) · Genome Medicine · doi:10.1186/s13073-015-0169-8 · Cited by 181
Hanke, L., Sheward, D. J., Pankow, A., Vidakovics, L. P., Karl, V., Kim, C., Urgard, E., Smith, N. L., Astorga-Wells, J., Ekström, S., et al. (2022) · Science Advances · doi:10.1126/sciadv.abm0220 · Cited by 38
Metadata
- Authors
- Li, S., Lefranc, M.-P., Miles, J. J., Alamyar, E., Giudicelli, V., Duroux, P., Freeman, J. D., Corbin, V. D. A., Scheerlinck, J.-P., Frohman, M. A., Cameron, P. U., Plebanski, M., Loveland, B., Burrows, S. R., Papenfuss, A. T., & Gowans, E. J.
- Venue
- Nature Communications
- Published
- 2013-09-02
- Volume
- 4
- Issue
- 1
- Pages
- 2333-2333
- ISSN
- 2041-1723 (ISSN-L)
- OpenAlex
- W2009125186
- Cited by
- 222
- References
- 2
- FWCI
- 10.70
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Li, S., Lefranc, M.-P., Miles, J. J., Alamyar, E., Giudicelli, V., Duroux, P., Freeman, J. D., Corbin, V. D. A., Scheerlinck, J.-P., Frohman, M. A., Cameron, P. U., Plebanski, M., Loveland, B., Burrows, S. R., Papenfuss, A. T., & Gowans, E. J. (2013). IMGT/HighV QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling. Nature Communications. https://doi.org/10.1038/ncomms3333
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
