1. De Simone, M., Rossetti, G., and Pani, M. Single cell T cell receptor sequencing: techniques and future challenges. Front. Immunol. (2018)18: 2000-2021.
  2. Rosati, E., Dowds, C.M., Liaskou, E., Henriksen, E.K., Karlsen, T. and Franke, A. Overview of methodologies for T-cell receptor repertoire analysis. BMC Biotech. (2017) 17: 61-77.
  3. Teraguchi, S., Saputri, D., et al. Methods for sequence and structural analysis of B and T cell receptor repertoire. Comput. Struct. Biotechn. (2020) 18: 2000-2011.
  4. Pai, J.A., and Satpathy, A.T. High-throughput and single-cell T cell receptor sequencing technologies. Nat. Methods (2021) 18: 881-892.
  5. Stubbintgton, M.J.T., Rozenblatt-Rosen, O., Regev, A., and Teichmann, S.A. Single-cell transcriptomics to explore the immune system in health and disease. Science (2017) 358: 58-63.
  6. Joglekar, A.V., and Li, G. T cell antigen discovery. Nat. Methods (2021) 18: 873-880.
  7. Zvyagin, I.V., Tsvetkov, V.O., Chudakov, D.M. and Shugay, M. An overview of immunoinformatics approaches and databases linking T cell receptor repertoires to their antigen specificity. Immunogenetics (2020) 72: 77-84.
  8. Barennes, P., Quiniou, V., Shugay, M., Egorov, E.S., Davydov, A.N., Chudakov, D.M., et al. Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases. Nat. Biotech. (2021) 39: 236-245.
  9. Yamawaki, T.M., Lu, D.R., Ellwanger, D.C., Bhatt, D. et al. Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling. BMC Genomics (2021) 22: 66-84.
  10. Monaco, G., Lee, B., Xu, W. et al. RNA-seq signatures normalized by mRNA abundance allow absolute deconvolution of human immune cell types. Cell Reports (2019) 26: 1627-1640.
  11. Bolotin, D.A., Poslavsky, S., Mitrophanov, I., Shugay, M., et al. MiXCR: software for comprehensive adaptive immunity profiling. Nat. Methods (2015) 12: 380-381.
  12. Brodin, P., Duffy, D., and Quintana-Murchi, L. A call for blood – in human immunology. Immunity (2019) 50: 1335-1336.
  13. Minervina, A., Pogorelyy, M., and Mamedov, I. T-cell receptor and B-cell receptor repertoire profiling in adaptive immunity. Transplant Intern. (2019) 32: 1111-1123.
  14. Truck, J., Eugster, A., Barennes, P., Tipton, C.M. et al. Biological controls for standardization and interpretation of adaptive immune receptor repertoire profiling. eLife (2021) 10: e66274.
  15. Soto, C., Bombardi, M.K., Gujral, M., Mallal, S., and Crowe, J. High frequency of shared clonotypes in human T cell receptor repertoire. Cell Reports (2020) 32: 107882.
  16. Briney, B., Inderbitzin, A., Joyce, C. and Burton, D.R. Commonality despite exceptional diversity in the baseline human antibody repertoire. Nature (2019) 566: 393-399.
  17. Soto, C., Bpmbardi, R.G., Branchizio, A., Kose, N., .. Crowe Jr, J.E. High frequency of shared clonotypes in human B cell receptor repertoires. Nature (2019) 566: 398-402.
  18. Aversa, I., Malanga, D., Fiume, G. and Palmiere, C. Molecular T-cell repertoire analysis as source of prognostic and predictive biomarkers for checkpoint blockade immunotherapy. Int. J. Mol. Sci. (2020) 21: 2378-2397.
  19. Wu, M., Zhao, M., Wu, H. and Lu, Q. Immune repertoire: Revealing the real time adaptive immune response in autoimmune diseases. Autoimmunity (2021) 54: 61-75.
  20. Sudmeier, L. J., Hoang, K. B., Nduom, E. K., Wieland, A., Neill, S. G., Schniederjan, M. J., Ramalingam, S. S., Olson, J. J., Ahmed, R., & Hudson, W. H. Distinct phenotypic states and spatial distribution of CD8+ T cell clonotypes in human brain metastases.(2022) Cell Reports. Medicine, 3(5), 100620.
  21. Martini, S., Nielsen, M., Peters, B. and Sette, A. The Immune epitope database and analysis resource program 2013-2018: reflection and outlook. Immunogenetics (2020)72: 57-76.
  22. Kosaloglu-Yalcin, Blazeska, N. et al. The cancer epitope database and analysis resource: a blueprint for the establishment of a new bioinformatics resource for use by the cancer immunology community. Front. Immunology (2021) 12: article 735609.
  23. Fairfax, B.P., Taylor, C.A. et al. Peripheral CD8+ T cell characteristics associated with durable responses to immune checkpoint blockade in patients with metastatic melanoma. Nat. Medicine (2020) 26: 193-199.
  24. Aoki, H., Shigeyuki, S., Matsushima, K. and Ueha, S. Revealing clonal responses of tumor-reactive T-cells through T cell receptor repertoire analysis. Front. Immunology (2022) 13: article 807696.
Last modified: 23 January 2024

Need more help with this?
Contact Us

Thanks for your feedback.