The methods described herein have been implemented in software and are available as a Microsoft Windows installer at http://www.bu.edu/ computationalimmunology/research/software.
Source code is available at Codeplex, at https://lplib.codeplex.com.
This work was supported by the National Institute of Immunology, Allergy, and Transplantation under cooperative agreement 1 U19 AI117892-01.
1. J. A. Weinstein, N. Jiang, R. A. White, D. S. Fisher, and S. R. Quake. High- throughput sequencing of the zebrafish antibody repertoire. Science 324, 807810 (2009).
2. J. Glanville, W. Zhai, J. Berka, D. Telman, G. Huerta, G. R. Mehta, I. Ni, et al. Precise determination of the diversity of a combinatorial antibody library gives insight into the human immunoglobulin repertoire. Proceedings of the National Academy of Sciences 106, 20216-20221 (2009).
3. J. A. Finn, and J. E. Crowe, Jr. Impact of new sequencing technologies on studies of the human B cell repertoire. Current Opinion in Immunology 25, 613-618 (2013).
4. H. Robins. Immunosequencing: Applications of immune repertoire deep sequencing. Current Opinion in Immunology 25, 646-652 (2013).
5. P. Mathonet, and C. Ullman. The application of next generation sequencing to the understanding of antibody repertoires. Frontiers in Immunology 4, 265 (2013).
6. G. Georgiou, G. C. Ippolito, J. Beausang, C. E. Busse, H. Wardemann, and S. R. Quake. The promise and challenge of high-throughput sequencing of the antibody repertoire. Nature Biotechnology 32, 158-168 (2014).
7. S. D. Boyd, Y. Liu, C. Wang, V. Martin, and D. K. Dunn-Walters. Human lymphocyte repertoires in ageing. Current Opinion in Immunology 25, 511515 (2013).
8. W. H. Robinson. Sequencing the functional antibody repertoire—Diagnostic and therapeutic discovery. Nature Reviews Rheumatology 11, 171-182 (2015).
9. A. C. Logan, H. Gao, C. Wang, B. Sahaf, C. D. Jones, E. L. Marshall, I. Buno, et al. High-throughput VDJ sequencing for quantification of minimal residual disease in chronic lymphocytic leukemia and immune reconstitution assessment. Proceedings of the National Academy of Sciences 108, 21194-21199 (2011).
10. N. Jiang, J. He, J. A. Weinstein, L. Penland, S. Sasaki, X.-S. He, C. L. Dekker, et al. Lineage structure of the human antibody repertoire in response to influenza vaccination. Science Translational Medicine 5, 171ra119 (2013).
11. J. D. Galson, A. J. Pollard, J. Truck, D. F. Kelly. Studying the antibody repertoire after vaccination: Practical applications. Trends in Immunology 35, 319-331 (2014).
12. X. Wu, T. Zhou, J. Zhu, B. Zhang, I. Georgiev, C. Wang, X. Chen, et al. Focused evolution of HIV-1 neutralizing antibodies revealed by structures and deep sequencing. Science 333, 1593-1602 (2011).
13. H. X. Liao, R. Lynch, T. Zhou, F. Gao, S. M. Alam, S. D. Boyd, A. Z. Fire, et al. Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus. Nature 496, 469-476 (2013).
14. G. M. Edelman. Antibody structure and molecular immunology. Science 180, 830-840 (1973).
15. F. Trepel. Number and distribution of lymphocytes in man. A critical analysis. Klinische Wochenschrift 52, 511-515 (1974).
16. R. Somasundaram, M. A. Prasad, J. Ungerback, and M. Sigvardsson. Transcription factor networks in B-cell differentiation link development to acute lymphoid leukemia. Blood 126, 144-152 (2015).
17. E. ten Boekel, F. Melchers, and A. Rolink. The status of Ig loci rearrangements in single cells from different stages of B cell development. Internal Immunology 7, 1013-1019 (1995).
18. E. Meffre, and M. C. Nussenzweig. Deletion of immunoglobulin beta in developing B cells leads to cell death. Proceedings of the National Academy of Sciences of the United States of America 99, 11334-11339 (2002).
19. M. S. Naradikian, J. L. Scholz, M. A. Oropallo, and M. P. Cancro. Drugs Targeting B-Cells in Autoimmune Diseases. (Springer, New York, 2014), pp. 11-35.
20. D. Gay, T. Saunders, S. Camper, and M. Weigert. Receptor editing: An approach by autoreactive B cells to escape tolerance. Journal of Experimental Medicine 177, 999-1008 (1993).
21. H. Wardemann, S. Yurasov, A. Schaefer, J. Young, E. Meffre, and M. Nussenzweig. Predominant autoantibody production by early human B cell precursors. Science 301, 1374-1377 (2003).
22. E. Gaudin, Y. Hao, M. M. Rosado, R. Chaby, R. Girard, and A. A. Freitas. Positive selection of B cells expressing low densities of self-reactive BCRs. Journal of Experimental Medicine 199, 843-853 (2004).
23. A. G. Rolink, J. Tschopp, P. Schneider, and F. Melchers. BAFF is a survival and maturation factor for mouse B cells. European Journal of Immunology 32, 20042010 (2002).
24. Y. X. Fu, and D. D. Chaplin. Development and maturation of secondary lymphoid tissues. Annual Review of Immunology 17, 399-433 (1999).
25. M. Nishana, and S. C. Raghavan. Role of recombination activating genes in the generation of antigen receptor diversity and beyond. Immunology 137, 271-281 (2012).
26. D. G. Schatz, and Y. Ji. Recombination centres and the orchestration of V(D)J recombination. Nature Reviews Immunology 11, 251-263 (2011).
27. J. M. den Haan, R. Arens, and M. C. van Zelm. The activation of the adaptive immune system: Cross-talk between antigen-presenting cells, T cells and B cells. Immunology Letters 162, 103-112 (2014).
28. C. A. Janeway, Jr., P. Travers, M. Walport, and M. Schlomchik. Immunobiology: The Immune System in Health and Disease. 6th edn. (Garland Science, New York, 2005), pp. 369-383.
29. N. S. De Silva, and U. Klein. Dynamics of B cells in germinal centres. Nature Reviews Immunology 15, 137-148 (2015).
30. G. D. Victora, and M. C. Nussenzweig. Germinal centers. Annual Review of Immunology 30, 429-457 (2012).
31. A. Tanaka, H. M. Shen, S. Ratnam, P. Kodgire, and U. Storb. Attracting AID to targets of somatic hypermutation. Journal of Experimental Medicine 207,405-415 (2010).
32. S. D. Wagner, C. Milstein, and M. S. Neuberger. Codon bias targets mutation. Nature 376, 732-732 (1995).
33. T. B. Kepler. Codon bias and plasticity in immunoglobulins. Molecular Biology and Evolution Society 14, 637-643 (1997).
34. J. Tan, K. Pieper, L. Piccoli, A. Abdi, M. Foglierini, R. Geiger, C. M. Tully, et al. A LAIR1 insertion generates broadly reactive antibodies against malaria variant antigens. Nature 529, 105-109 (2016).
35. M. Seifert, M. Przekopowitz, S. Taudien, A. Lollies, V. Ronge, B. Drees, M. Lindemann, et al. Functional capacities of human IgM memory B cells in early inflammatory responses and secondary germinal center reactions. Proceedings of the National Academy of Sciences of the United States of America 112, E546-555 (2015).
36. L. J. Mcheyzer-Williams, P. J. Milpied, S. L. Okitsu, and M. G. Mcheyzer- Williams. Class-switched memory B cells remodel BCRs within secondary germinal centers. Nature Immunology 16, 296-305 (2015).
37. H. Morbach, E. M. Eichhorn, J. G. Liese, and H. J. Girschick. Reference values for B cell subpopulations from infancy to adulthood. Clinical & Experimental Immunology 162, 271-279 (2010).
38. M. P. Cancro. The persistence of memory: A unique niche for IgG memory B cells. Proceedings of the National Academy of Sciences of the United States of America 107, 12737-12738 (2010).
39. R. A. Manz, A. Thiel, and A. Radbruch. Lifetime of plasma cells in the bone marrow. Nature 388, 133-134 (1997).
40 . X . Yu, T . Tsibane, P . A . McGraw, F . S. House, C . J . Keefer, M . D . Hicar, T . M. Tumpey, et al. Neutralizing antibodies derived from the B cells of 1918 influenza pandemic survivors. Nature 455, 532-536 (2008).
41. M. K. Slifka, R. Ahmed. Long-lived plasma cells: A mechanism for maintaining persistent antibody production. Current Opinion in Immunology 10, 252-258 (1998).
42. J. A. Weinstein, X. Zeng, Y. H. Chien, and S. R. Quake. Correlation of gene expression and genome mutation in single B-cells. PLoS One 8, e67624 (2013).
43. C. E. Busse, I. Czogiel, P. Braun, P. F. Arndt, and H. Wardemann. Single-cell based high-throughput sequencing of full-length immunoglobulin heavy and light chain genes. European Journal of Immunology 44, 597-603 (2014).
44. B. J. DeKosky, G. C. Ippolito, R. P. Deschner, J. J. Lavinder, Y. Wine, B. M. Rawlings, N. Varadarajan, et al. High-throughput sequencing of the paired human immunoglobulin heavy and light chain repertoire. Nature Biotechnology 31, 166-169 (2013).
45. J. L. Duke, C. Lind, K. Mackiewicz, D. Ferriola, A. Papazoglou, O. Derbeneva, D. Wallace, and D. S. Monos. Towards allele-level human leucocyte antigens genotyping—Assessing two next-generation sequencing platforms: Ion Torrent Personal Genome Machine and Illumina MiSeq. International Journal of Immunogenetics 42, 346-358 (2015).
46. M. Schirmer, U. Z. Ijaz, R. D'Amore, N. Hall, W. T. Sloan, and C. Quince. Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform. Nucleic Acids Research 43, e37 (2015).
47. J. J. Kozich, S. L. Westcott, N. T. Baxter, S. K. Highlander, and P. D. Schloss. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Applied and Environmental Microbiology 79, 5112-5120 (2013).
48. M. Quail, M. E. Smith, P. Coupland, T. D. Otto, S. R. Harris, T. R. Connor, A. Bertoni, H. P. Swerdlow, and Y. Gu. A tale of three next generation sequencing platforms: Comparison of Ion torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 13, 1 (2012).
49. M. Jain, I. T. Fiddes, K. H. Miga, H. E. Olsen, B. Paten, and M. Akeson. Improved data analysis for the MinION nanopore sequencer. Nature Methods 12, 351-356 (2015).
50. World Health Organization. (2016, November) HIV/AIDS [Fact Sheet]. Retrieved from http://www.who.int/mediacentre/factsheets/fs360/
51. L. M. Mansky, and H. M. Temin. Lower in-vivo mutation-rate of human- immunodeficiency-virus type-1 than that predicted from the fidelity of purified reverse-transcriptase. Journal of Virology 69, 5087-5094 (1995).
52. J. F. Koellhoffer, C. D. Higgins, and J. R. Lai. Protein engineering strategies for the development of viral vaccines and immunotherapeutics. FEBS Letters 588, 298-307 (2013).
53. D. R. Burton, R. Ahmed, D. H. Barouch, S. T. Butera, S. Crotty, A. Godzik, D. E. Kaufmann, et al. A blueprint for HIV vaccine discovery. Cell Host and Microbe 12, 396-407 (2012).
54. N. A. Doria-Rose, R. M. Klein, M. G. Daniels, S. O'Dell, M. Nason, A. Lapedes, T. Bhattacharya, et al. Breadth of human immunodeficiency virus-specific neutralizing activity in sera: Clustering analysis and association with clinical variables. Journal of Virology 84, 1631-1636 (2010).
55. L. M. Walker, M. D. Simek, F. Priddy, J. S. Gach, D. Wagner, M. B. Zwick, S. K. Phogat, P. Poignard, and D. R.Burton. A limited number of antibody specificities mediate broad and potent serum neutralization in selected HIV-1 infected individuals. PLoS Pathogens 6, e1001028 (2010).
56. M. D. Simek, W. Rida, F. H. Priddy, P. Pung, E. Carrow, D. S. Laufer, J. K. Lehman, et al. Human immunodeficiency virus type 1 elite neutralizers: Individuals with broad and potent neutralizing activity identified by using a high-throughput neutralization assay together with an analytical selection algorithm. Journal of Virology 83, 7337-7348 (2009).
57. J. R. Mascola, and B. F. Haynes. HIV-1 neutralizing antibodies: Understanding nature's pathways. Immunological Reviews 254, 225-244 (2013).
58. A. J. Hessell, P. Poignard, M. Hunter, L. Hangartner, D. M. Tehrani, W. K. Bleeker, P. W. Parren, P. A. Marx, and D. R. Burton. Effective, low-titer antibody protection against low-dose repeated mucosal SHIV challenge in macaques. Nature Medicine 15, 951-954 (2009).
59. A. J. Hessell, E. G. Rakasz, P. Poignard, L. Hangartner, G. Landucci, D. N. Forthal, W. C. Koff, D. I. Watkins, and D. R. Burton. Broadly neutralizing human anti-HIV antibody 2G12 is effective in protection against mucosal SHIV challenge even at low serum neutralizing titers. PLoS Pathogens 5, e1000433 (2009).
60. B. F. Haynes, J. Fleming, E. W. St Clair, H. Katinger, G. Stiegler, R. Kunert, J. Robinson, et al. Cardiolipin polyspecific autoreactivity in two broadly neutralizing HIV-1 antibodies. Science 308, 1906-1908 (2005).
61. R. Diskin, J. F. Scheid, P. M. Marcovecchio, A. P. West, F. Klein, H. Gao, P. N. P. Gnanapragasam, et al. Increasing the potency and breadth of an HIV antibody by using structure-based rational design. Science 334, 1289-1293 (2011).
62. J. Zhu, G. Ofek, Y. Yang, B. Zhang, M. K. Louder, G. Lu, K. McKee, et al. Mining the antibodyome for HIV-1-neutralizing antibodies with next-generation sequencing and phylogenetic pairing of heavy/light chains. Proceedings of the National Academy of Sciences of the United States of America 110, 6470-6475 (2013).
63. J. Zhu, X. Wu, B. Zhang, K. McKee, S. O'Dell, C. Soto, T. Zhou, et al. De novo identification of VRC01 class HIV-1-neutralizing antibodies by next-generation sequencing of B-cell transcripts. Proceedings of the National Academy of Sciences of the United States of America 110, E4088-4097 (2013).
64. J. Zhu, S. O'Dell, G. Ofek, M. Pancera, X. Wu, B. Zhang, Z. Zhang, et al. Somatic populations of PGT135-137 HIV-1-neutralizing antibodies identified by 454 pyrosequencing and bioinformatics. Frontiers in Microbiology 3, 315 (2012).
65. B. F. Haynes, G. Kelsoe, S. C. Harrison, and T. B. Kepler. B-cell-lineage immunogen design in vaccine development with HIV-1 as a case study. Nature Biotechnology 30, 423-433 (2012).
66. A. Escolano, J. M. Steichen, P. Dosenovic, D. W. Kulp, J. Golijanin, D. Sok, N. T. Freund, et al. Sequential immunization elicits broadly neutralizing anti-HIV-1 antibodies in Ig knockin mice. Cell 166, 1445-1458. e12 (2016).
67. Z. Yang. Molecular Evolution: A Statistical Approach. (Oxford University Press, Oxford, UK, 2014).
68. M. Kimura. Estimation of evolutionary distances between homologous nucleotide sequences. Proceedings of the National Academy of Sciences 78, 454-458 (1981).
69. Ramesh A. Immunogenetics of the Rhesus Macaque, an Animal Model for HIV Vaccine Development (Doctoral dissertation, Boston University School of Medicine), (2017).