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References

  • 1
    Arstila, T. P., Casrouge, A., Baron, V., Even, J., Kanellopoulos, J. and Kourilsky, P., A direct estimate of the human alphabeta T cell receptor diversity. Science 1999. 286: 958961.
  • 2
    Douek, D. C., Betts, M. R., Brenchley, J. M., Hill, B. J., Ambrozak, D. R., Ngai, K. L., Karandikar, N. J. et al., A novel approach to the analysis of specificity, clonality, and frequency of HIV-specific T cell responses reveals a potential mechanism for control of viral escape. J. Immunol. 2002. 168: 30993104.
  • 3
    Naylor, K., Li, G., Vallejo, A. N., Lee, W. W., Koetz, K., Bryl, E., Witkowski, J. et al., The influence of age on T cell generation and TCR diversity. J. Immunol. 2005. 174: 7446.
  • 4
    Baum, P. D. and McCune, J. M., Direct measurement of T-cell receptor repertoire diversity with AmpliCot. Nat. Methods 2006. 3: 895901.
  • 5
    Shen, D. F., Doukhan, L., Kalams, S. and Delwart, E., High-resolution analysis of T-cell receptor beta-chain repertoires using DNA heteroduplex tracking. J. Immunol. Methods 1998. 215: 113121.
  • 6
    Gorski, J., Piatek, T., Yassai, M. and Maslanka, K., Improvements in repertoire analysis by CDR3 size spectratyping. Bifamily PCR. Ann. NY Acad Sci. 1995. 756: 99102.
  • 7
    Pannetier, C., Cochet, M., Darche, S., Casrouge, A., Zoller, M. and Kourilsky, P., The sizes of the CDR3 hypervariable regions of the murine T-cell receptor beta chains vary as a function of the recombined germ-line segments. Proc. Natl. Acad Sci. USA 1993. 90: 43194323.
  • 8
    Freeman, J. D., Warren, R. L., Webb, J. R., Nelson, B. H. and Holt, R. A., Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing. Genome Res. 2009. 19: 18171824.
  • 9
    Warren, R. L., Freeman, J. D., Zeng, T., Choe, G., Munro, S., Moore, R., Webb, J. R. et al., Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes. Genome Res. 2011. 21: 790797.
  • 10
    Venturi, V., Quigley, M. F., Greenaway, H. Y., Ng, P. C., Ende, Z. S., McIntosh, T., Asher, T. E. et al., A mechanism for TCR sharing between T cell subsets and individuals revealed by pyrosequencing. J. Immunol. 2011. 186: 42854294.
  • 11
    Robins, H. S., Campregher, P. V., Srivastava, S. K., Wacher, A., Turtle, C. J., Kahsai, O., Riddell, S. R. et al., Comprehensive assessment of T-cell receptor beta-chain diversity in alphabeta T cells. Blood 2009. 114: 40994107.
  • 12
    Robins, H. S., Srivastava, S. K., Campregher, P. V., Turtle, C. J., Andriesen, J., Riddell, S. R., Carlson, C. S. and Warren, E. H., Overlap and effective size of the human CD8+ T cell receptor repertoire. Sci. Transl. Med. 2010. 2: 4764.
  • 13
    Weinstein, J. A., Jiang, N., White, R. A., Fisher, D. S. and Quake, S. R., High-throughput sequencing of the zebrafish antibody repertoire. Science 2009. 324: 807810.
  • 14
    Boyd, S. D., Marshall, E. L., Merker, J. D., Maniar, J. M., Zhang, L. N., Sahaf, B., Jones, C. D. et al., Measurement and clinical monitoring of human lymphocyte clonality by massively parallel VDJ pyrosequencing. Sci. Transl. Med. 2009. 1: 1223.
  • 15
    Wang, C., Sanders, C. M., Yang, Q., Schroeder, H. W., Wang, E., Babrzadeh, F., Gharizadeh, B. et al., High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets. Proc. Natl. Acad Sci. USA 2010. 107: 15181523.
  • 16
    Alamyar, E., Giudicelli, V., Li, S., Duroux, P. and Lefranc, M. P., IMGT/HighV-QUEST: the IMGT® web portal for immunoglobulin (IG) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing. Immunome Res. 2012. 8: 26.
  • 17
    Bolotin, D. A., Mamedov, I. Z., Britanova, O. V., Zvyagin, I. V., Shagin, D., Ustyugova, S. V., Turchaninova, M. A. et al., Next generation sequencing for TCR repertoire profiling: platform-specific features and correction algorithms. Eur. J. Immunol. 2012. 42: 30733083.
  • 18
    Loman, N. J., Misra, R. V., Dallman, T. J., Constantinidou, C., Gharbia, S. E., Wain, J. and Pallen, M. J., Performance comparison of benchtop high-throughput sequencing platforms. Nat. Biotechnol. 2012. 30: 434439.
  • 19
    Nakamura, K., Oshima, T., Morimoto, T., Ikeda, S., Yoshikawa, H., Shiwa, Y., Ishikawa, S. et al., Sequence-specific error profile of Illumina sequencers. Nucleic Acids Res. 2011. 39: e90.
  • 20
    Miles, J. J., Douek, D. C. and Price, D. A., Bias in the αβ T-cell repertoire: implications for disease pathogenesis and vaccination. Immunol. Cell Biol. 2011. 89: 375387.
  • 21
    Zagordi, O., Klein, R., Däumer, M. and Beerenwinkel, N., Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies. Nucleic Acids Res. 2010. 38: 74007409.
  • 22
    Nguyen, P., Ma, J., Pei, D., Obert, C., Cheng, C. and Geiger, T. L., Identification of errors introduced during high throughput sequencing of the T cell receptor repertoire. BMC Genomics 2011. 12: 106.
  • 23
    Krueger, F., Andrews, S. R. and Osborne, C. S., Large scale loss of data in low-diversity illumina sequencing libraries can be recovered by deferred cluster calling. PLoS One 2011. 6: e16607.
  • 24
    Warren, R. L., Nelson, B. H. and Holt, R. A., Profiling model T-cell metagenomes with short reads. Bioinformatics 2009. 25: 458464.
  • 25
    Gras, S., Chen, Z., Miles, J. J., Liu, Y. C., Bell, M. J., Sullivan, L. C., Kjer-Nielsen, L. et al., Allelic polymorphism in the T cell receptor and its impact on immune responses. J. Exp. Med. 2010. 207: 15551567.
  • 26
    Li, H., Ye, C., Ji, G., Wu, X., Xiang, Z., Li, Y., Cao, Y. et al., Recombinatorial biases and convergent recombination determine interindividual TCRβ sharing in murine thymocytes. J. Immunol. 2012. 189: 24042413.
  • 27
    Benichou, J., Ben-Hamo, R., Louzoun, Y. and Efroni, S., Rep-Seq: uncovering the immunological repertoire through next-generation sequencing. Immunology 2012. 135: 183191.
  • 28
    Price, D. A., Asher, T. E., Wilson, N. A., Nason, M. C., Brenchley, J. M., Metzler, I. S., Venturi, V. et al., Public clonotype usage identifies protective Gag-specific CD8+ T cell responses in SIV infection. J. Exp. Med. 2009. 206: 923936.
  • 29
    Chen, H., Ndhlovu, Z. M., Liu, D., Porter, L. C., Fang, J. W., Darko, S., Brockman, M. A. et al., TCR clonotypes modulate the protective effect of HLA class I molecules in HIV-1 infection. Nat. Immunol. 2012. 13: 691700.
  • 30
    Wu, D., Sherwood, A., Fromm, J. R., Winter, S. S., Dunsmore, K. P., Loh, M. L., Greisman, H. A. et al., High-throughput sequencing detects minimal residual disease in acute T lymphoblastic leukemia. Sci. Transl. Med. 2012. 4: 134163.