메뉴 건너뛰기




Volumn 4, Issue , 2014, Pages

Toward a more accurate view of human B-cell repertoire by next-generation sequencing, unbiased repertoire capture and single-molecule barcoding

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBODY; IMMUNOGLOBULIN HEAVY CHAIN; IMMUNOGLOBULIN LIGHT CHAIN; NEUTRALIZING ANTIBODY;

EID: 84961289824     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep06778     Document Type: Article
Times cited : (78)

References (46)
  • 1
    • 39649117755 scopus 로고    scopus 로고
    • The impact of next-generation sequencing technology on genetics
    • Mardis, E. R. The impact of next-generation sequencing technology on genetics. Trends Genet. 24, 133-141, doi:10.1016/j.tig.2007.12.007 (2008).
    • (2008) Trends Genet. , vol.24 , pp. 133-141
    • Mardis, E.R.1
  • 2
    • 52949096084 scopus 로고    scopus 로고
    • Next-generation DNA sequencing methods
    • Mardis, E. R. Next-generation DNA sequencing methods. Annu. Rev. Genom. Hum. Genet. 9, 387-402, doi:10.1146/annurev.genom.9.081307.164359 (2008).
    • (2008) Annu. Rev. Genom. Hum. Genet. , vol.9 , pp. 387-402
    • Mardis, E.R.1
  • 3
    • 72849144434 scopus 로고    scopus 로고
    • Sequencing technologies - The next generation
    • Metzker, M. L. Sequencing technologies - the next generation. Nat. Rev. Genet. 11, 31-46, doi:10.1038/nrg2626 (2010).
    • (2010) Nat. Rev. Genet. , vol.11 , pp. 31-46
    • Metzker, M.L.1
  • 4
    • 53649106195 scopus 로고    scopus 로고
    • Next-generation DNA sequencing
    • Shendure, J. & Ji, H. Next-generation DNA sequencing. Nat. Biotechnol. 26, 1135-1145, doi:10.1038/nbt1486 (2008).
    • (2008) Nat. Biotechnol. , vol.26 , pp. 1135-1145
    • Shendure, J.1    Ji, H.2
  • 5
    • 79960940363 scopus 로고    scopus 로고
    • Systems analysis of adaptive immunity by utilization of high-throughput technologies
    • Reddy, S. T. & Georgiou, G. Systems analysis of adaptive immunity by utilization of high-throughput technologies. Curr. Opin. Biotechnol. 22, 584-589, doi:10.1016/j.copbio.2011.04.015 (2011).
    • (2011) Curr. Opin. Biotechnol. , vol.22 , pp. 584-589
    • Reddy, S.T.1    Georgiou, G.2
  • 6
    • 78651390679 scopus 로고    scopus 로고
    • Sequencing antibody repertoires the next generation
    • Fischer, N. Sequencing antibody repertoires The next generation. Mabs 3, 17-20, doi:10.4161/mabs.3.1.14169 (2011).
    • (2011) Mabs , vol.3 , pp. 17-20
    • Fischer, N.1
  • 7
    • 84893831480 scopus 로고    scopus 로고
    • The promise and challenge of high-throughput sequencing of the antibody repertoire
    • Georgiou, G. et al. The promise and challenge of high-throughput sequencing of the antibody repertoire. Nat. Biotechnol. 32, 1-11, doi:10.1038/nbt.2782 (2014).
    • (2014) Nat. Biotechnol. , vol.32 , pp. 1-11
    • Georgiou, G.1
  • 8
    • 65649122270 scopus 로고    scopus 로고
    • High-throughput sequencing of the zebrafish antibody repertoire
    • Weinstein, J. A., Jiang, N., White, R. A., III, Fisher, D. S. & Quake, S. R. High-Throughput Sequencing of the Zebrafish Antibody Repertoire. Science 324, 807-810, doi:10.1126/science.1170020 (2009).
    • (2009) Science , vol.324 , pp. 807-810
    • Weinstein, J.A.1    Jiang, N.2    White, R.A.3    Fisher, D.S.4    Quake, S.R.5
  • 9
    • 77956688921 scopus 로고    scopus 로고
    • Monoclonal antibodies isolated without screening by analyzing the variable-gene repertoire of plasma cells
    • Reddy, S. T. et al. Monoclonal antibodies isolated without screening by analyzing the variable-gene repertoire of plasma cells. Nat. Biotechnol. 28, 965-969, doi:10.1038/nbt.1673 (2010).
    • (2010) Nat. Biotechnol. , vol.28 , pp. 965-969
    • Reddy, S.T.1
  • 10
    • 77954601328 scopus 로고    scopus 로고
    • Measurement and clinical monitoring of human lymphocyte clonality by massively parallel V-D-J pyrosequencing
    • Boyd, S. D. et al. Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing. Sci. Transl. Med. 1, 12ra23, doi:10.1126/scitranslmed.3000540 (2009).
    • (2009) Sci. Transl. Med. , vol.1 , pp. 12ra23
    • Boyd, S.D.1
  • 11
    • 80052942203 scopus 로고    scopus 로고
    • Focused evolution of HIV-1 neutralizing antibodies revealed by structures and deep sequencing
    • Wu, X. et al. Focused Evolution of HIV-1 Neutralizing Antibodies Revealed by Structures and Deep Sequencing. Science 333, 1593-1602, doi:10.1126/science.1207532 (2011).
    • (2011) Science , vol.333 , pp. 1593-1602
    • Wu, X.1
  • 12
    • 84882589754 scopus 로고    scopus 로고
    • Multidonor analysis reveals structural elements, genetic determinants, and maturation pathway for HIV-1 neutralization by VRC01-class antibodies
    • Zhou, T. et al. Multidonor analysis reveals structural elements, genetic determinants, and maturation pathway for HIV-1 neutralization by VRC01-class antibodies. Immunity 39, 245-258, doi:10.1016/j.immuni.2013.04.012 (2013).
    • (2013) Immunity , vol.39 , pp. 245-258
    • Zhou, T.1
  • 13
    • 84872616030 scopus 로고    scopus 로고
    • Somatic populations of PGT135-137HIV-1-neutralizing antibodies identified by 454 pyrosequencing and bioinformatics
    • Zhu, J. et al. Somatic Populations of PGT135-137HIV-1-Neutralizing Antibodies Identified by 454 Pyrosequencing and Bioinformatics. Front. Microbiol. 3, 315-315, doi:10.3389/fmicb.2012.00315 (2012).
    • (2012) Front. Microbiol. , vol.3 , pp. 315-315
    • Zhu, J.1
  • 14
    • 84876272159 scopus 로고    scopus 로고
    • Mining the antibodyome for HIV-1-neutralizing antibodies with next-generation sequencing and phylogenetic pairing of heavy/light chains
    • Zhu, J. et al. Mining the antibodyome for HIV-1-neutralizing antibodies with next-generation sequencing and phylogenetic pairing of heavy/light chains. Proc. Natl. Acad. Sci. USA 110, 6470-6475, doi:10.1073/pnas.1219320110 (2013).
    • (2013) Proc. Natl. Acad. Sci. USA , vol.110 , pp. 6470-6475
    • Zhu, J.1
  • 15
    • 84886430146 scopus 로고    scopus 로고
    • De novo identification of VRC01 class HIV-1-neutralizing antibodies by next-generation sequencing of B-cell transcripts
    • Zhu, J. et al. De novo identification of VRC01 class HIV-1-neutralizing antibodies by next-generation sequencing of B-cell transcripts. Proc. Natl. Acad. Sci. USA 110, E4088-E4097, doi:10.1073/pnas.1306262110 (2013).
    • (2013) Proc. Natl. Acad. Sci. USA , vol.110 , pp. E4088-E4097
    • Zhu, J.1
  • 16
    • 84888251984 scopus 로고    scopus 로고
    • The effects of somatic hypermutation on neutralization and binding in the PGT121 family of broadly neutralizing HIV antibodies
    • Sok, D. et al. The Effects of Somatic Hypermutation on Neutralization and Binding in the PGT121 Family of Broadly Neutralizing HIV Antibodies. PLoS Pathog. 9, e1003754, doi:10.1371/journal.ppat.1003754 (2013).
    • (2013) PLoS Pathog. , vol.9 , pp. e1003754
    • Sok, D.1
  • 17
    • 84866493348 scopus 로고    scopus 로고
    • Broad and potent neutralization of HIV-1 by a gp41-specific human antibody
    • Huang, J. et al. Broad and potent neutralization of HIV-1 by a gp41-specific human antibody. Nature 491, 406-412, doi:10.1038/nature11544 (2012).
    • (2012) Nature , vol.491 , pp. 406-412
    • Huang, J.1
  • 18
    • 70349887757 scopus 로고    scopus 로고
    • Broad and potent neutralizing antibodies from an African donor reveal a new HIV-1 vaccine target
    • Walker, L. M. et al. Broad and Potent Neutralizing Antibodies from an African Donor Reveal a New HIV-1 Vaccine Target. Science 326, 285-289, doi:10.1126/science.1178746 (2009).
    • (2009) Science , vol.326 , pp. 285-289
    • Walker, L.M.1
  • 19
    • 80053132436 scopus 로고    scopus 로고
    • Broad neutralization coverage of HIV by multiple highly potent antibodies
    • Walker, L. M. et al. Broad neutralization coverage of HIV by multiple highly potent antibodies. Nature 477, 466-470, doi:10.1038/nature10373 (2011).
    • (2011) Nature , vol.477 , pp. 466-470
    • Walker, L.M.1
  • 20
    • 77954943648 scopus 로고    scopus 로고
    • Structural basis for broad and potent neutralization of HIV-1 by antibody VRC01
    • Zhou, T. et al. Structural Basis for Broad and Potent Neutralization of HIV-1 by Antibody VRC01. Science 329, 811-817, doi:10.1126/science.1192819 (2010).
    • (2010) Science , vol.329 , pp. 811-817
    • Zhou, T.1
  • 21
    • 84884874778 scopus 로고    scopus 로고
    • Indel and carryforward correction (ICC): A new analysis approach for processing 454 pyrosequencing data
    • Deng, W. et al. Indel and Carryforward Correction (ICC): a new analysis approach for processing 454 pyrosequencing data. Bioinformatics 29, 2402-2409, doi:10.1093/bioinformatics/btt434 (2013).
    • (2013) Bioinformatics , vol.29 , pp. 2402-2409
    • Deng, W.1
  • 22
    • 84868109835 scopus 로고    scopus 로고
    • Wrestling with the repertoire: The promise and perils of next generation sequencing for antigen receptors
    • Baum, P. D., Venturi, V. & Price, D. A. Wrestling with the repertoire: The promise and perils of next generation sequencing for antigen receptors. Eur. J. Immunol. 42, 2834-2839, doi:10.1002/eji.201242999 (2012).
    • (2012) Eur. J. Immunol. , vol.42 , pp. 2834-2839
    • Baum, P.D.1    Venturi, V.2    Price, D.A.3
  • 23
    • 84868154295 scopus 로고    scopus 로고
    • Next generation sequencing for TCR repertoire profiling: Platform-specific features and correction algorithms
    • Bolotin, D. A. et al. Next generation sequencing for TCR repertoire profiling: Platform-specific features and correction algorithms. Eur. J. Immunol. 42, 3073-3083, doi:10.1002/eji.201242517 (2012).
    • (2012) Eur. J. Immunol. , vol.42 , pp. 3073-3083
    • Bolotin, D.A.1
  • 24
    • 84900860392 scopus 로고    scopus 로고
    • Using synthetic templates to design an unbiased multiplex PCR assay
    • Carlson, C. S. et al. Using synthetic templates to design an unbiased multiplex PCR assay. Nat. Commun. 4, 2680, doi:10.1038/ncomms3680 (2013).
    • (2013) Nat. Commun. , vol.4 , pp. 2680
    • Carlson, C.S.1
  • 25
    • 84899991983 scopus 로고    scopus 로고
    • Developmental pathway for potent V1V2-directed HIVneutralizing antibodies
    • Doria-Rose, N. A. et al. Developmental pathway for potent V1V2-directed HIVneutralizing antibodies. Nature 509, 55-62, doi:10.1038/nature13036 (2014).
    • (2014) Nature , vol.509 , pp. 55-62
    • Doria-Rose, N.A.1
  • 26
    • 84883187027 scopus 로고    scopus 로고
    • Broadly neutralizing antibodies and the search for an HIV-1 vaccine: The end of the beginning
    • Kwong, P. D., Mascola, J. R. & Nabel, G. J. Broadly neutralizing antibodies and the search for an HIV-1 vaccine: the end of the beginning. Nat. Rev. Immunol. 13, 693-701, doi:10.1038/nri3516 (2013).
    • (2013) Nat. Rev. Immunol. , vol.13 , pp. 693-701
    • Kwong, P.D.1    Mascola, J.R.2    Nabel, G.J.3
  • 27
    • 84878519611 scopus 로고    scopus 로고
    • Broadly neutralizing antibody PGT121 allosterically modulates CD4 binding via recognition of the HIV-1 gp120 V3 base and multiple surrounding glycans
    • Julien, J.-P. et al. Broadly Neutralizing Antibody PGT121 Allosterically Modulates CD4 Binding via Recognition of the HIV-1 gp120 V3 Base and Multiple Surrounding Glycans. PLoS Pathog. 9, e1003342, doi:10.1371/journal.ppat.1003342 (2013).
    • (2013) PLoS Pathog. , vol.9 , pp. e1003342
    • Julien, J.-P.1
  • 28
    • 84887626950 scopus 로고    scopus 로고
    • Therapeutic efficacy of potent neutralizing HIV-1-specific monoclonal antibodies in SHIV-infected rhesus monkeys
    • Barouch, D. H. et al. Therapeutic efficacy of potent neutralizing HIV-1-specific monoclonal antibodies in SHIV-infected rhesus monkeys. Nature 503, 224-228, doi:10.1038/nature12744 (2013).
    • (2013) Nature , vol.503 , pp. 224-228
    • Barouch, D.H.1
  • 29
    • 84877609579 scopus 로고    scopus 로고
    • Rational HIV immunogen design to target specific germline B cell receptors
    • Jardine, J. et al. Rational HIV Immunogen Design to Target Specific Germline B Cell Receptors. Science 340, 711-716, doi:10.1126/science.1234150 (2013).
    • (2013) Science , vol.340 , pp. 711-716
    • Jardine, J.1
  • 30
    • 84860759632 scopus 로고    scopus 로고
    • B-cell-lineage immunogen design in vaccine development with HIV-1 as a case study
    • Haynes, B. F., Kelsoe, G., Harrison, S. C. & Kepler, T. B. B-cell-lineage immunogen design in vaccine development with HIV-1 as a case study. Nat. Biotechnol. 30, 423-433, doi:10.1038/nbt.2197 (2012).
    • (2012) Nat. Biotechnol. , vol.30 , pp. 423-433
    • Haynes, B.F.1    Kelsoe, G.2    Harrison, S.C.3    Kepler, T.B.4
  • 31
    • 84883440456 scopus 로고    scopus 로고
    • Deep sequencing of the murine igh repertoire reveals complex regulation of nonrandom v gene rearrangement frequencies
    • Choi, N. M. et al. Deep Sequencing of the Murine Igh Repertoire Reveals Complex Regulation of Nonrandom V Gene Rearrangement Frequencies. J. Immunol. 191, 2393-2402, doi:10.4049/jimmunol.1301279 (2013).
    • (2013) J. Immunol. , vol.191 , pp. 2393-2402
    • Choi, N.M.1
  • 32
    • 80052925616 scopus 로고    scopus 로고
    • Sequence and structural convergence of broad and potent HIV antibodies that mimic CD4 binding
    • Scheid, J. F. et al. Sequence and Structural Convergence of Broad and Potent HIV Antibodies That Mimic CD4 Binding. Science 333, 1633-1637, doi:10.1126/science.1207227 (2011).
    • (2011) Science , vol.333 , pp. 1633-1637
    • Scheid, J.F.1
  • 33
    • 84876797103 scopus 로고    scopus 로고
    • Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus
    • Liao, H.-X. et al. Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus. Nature 496, 469-476, doi:10.1038/nature12053 (2013).
    • (2013) Nature , vol.496 , pp. 469-476
    • Liao, H.-X.1
  • 34
    • 84856398949 scopus 로고    scopus 로고
    • Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes
    • Shiroguchi, K., Jia, T. Z., Sims, P. A. & Xie, X. S. Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes. Proc. Natl. Acad. Sci. USA 109, 1347-1352, doi:10.1073/pnas.1118018109 (2012).
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109 , pp. 1347-1352
    • Shiroguchi, K.1    Jia, T.Z.2    Sims, P.A.3    Xie, X.S.4
  • 35
    • 84055200527 scopus 로고    scopus 로고
    • Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID
    • Jabara, C. B., Jones, C. D., Roach, J., Anderson, J. A. & Swanstrom, R. Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID. Proc. Natl. Acad. Sci. USA 108, 20166-20171, doi:10.1073/pnas.1110064108 (2011).
    • (2011) Proc. Natl. Acad. Sci. USA , vol.108 , pp. 20166-20171
    • Jabara, C.B.1    Jones, C.D.2    Roach, J.3    Anderson, J.A.4    Swanstrom, R.5
  • 36
    • 74549167783 scopus 로고    scopus 로고
    • Regulation of adaptive immunity by the innate immune system
    • Iwasaki, A. & Medzhitov, R. Regulation of Adaptive Immunity by the Innate Immune System. Science 327, 291-295, doi:10.1126/science.1183021 (2010).
    • (2010) Science , vol.327 , pp. 291-295
    • Iwasaki, A.1    Medzhitov, R.2
  • 37
    • 77954933984 scopus 로고    scopus 로고
    • The origins of vertebrate adaptive immunity
    • Litman, G. W., Rast, J. P. & Fugmann, S. D. The origins of vertebrate adaptive immunity. Nat. Rev. Immunol. 10, 543-553, doi:10.1038/nri2807 (2010).
    • (2010) Nat. Rev. Immunol. , vol.10 , pp. 543-553
    • Litman, G.W.1    Rast, J.P.2    Fugmann, S.D.3
  • 38
    • 84878356025 scopus 로고    scopus 로고
    • Accelerating next-generation vaccine development for global disease prevention
    • Koff, W. C. et al. Accelerating Next-Generation Vaccine Development for Global Disease Prevention. Science 340, 1232910, doi:10.1126/science.1232910 (2013).
    • (2013) Science , vol.340 , pp. 1232910
    • Koff, W.C.1
  • 39
    • 84867630116 scopus 로고    scopus 로고
    • A blueprint for HIV vaccine discovery
    • Burton, D. R. et al. A Blueprint for HIV Vaccine Discovery. Cell Host Microbe 12, 396-407, doi:10.1016/j.chom.2012.09.008 (2012).
    • (2012) Cell Host Microbe , vol.12 , pp. 396-407
    • Burton, D.R.1
  • 40
    • 77952311370 scopus 로고    scopus 로고
    • The role of antibodies in HIV vaccines
    • Mascola, J. R. & Montefiori, D. C. The Role of Antibodies in HIV Vaccines. Annu. Rev. Immunol. 28, 413-444, doi:10.1146/annurev-immunol-030409-101256 (2010).
    • (2010) Annu. Rev. Immunol. , vol.28 , pp. 413-444
    • Mascola, J.R.1    Montefiori, D.C.2
  • 41
    • 84883796903 scopus 로고    scopus 로고
    • Antibodies in HIV-1 vaccine development and therapy
    • Klein, F. et al. Antibodies in HIV-1 Vaccine Development and Therapy. Science 341, 1199-1204, doi:10.1126/science.1241144 (2013).
    • (2013) Science , vol.341 , pp. 1199-1204
    • Klein, F.1
  • 42
    • 84879109338 scopus 로고    scopus 로고
    • Convergent antibody signatures in human dengue
    • Parameswaran, P. et al. Convergent antibody signatures in human dengue. Cell Host Microbe 13, 691-700, doi:10.1016/j.chom.2013.05.008 (2013).
    • (2013) Cell Host Microbe , vol.13 , pp. 691-700
    • Parameswaran, P.1
  • 43
    • 67650453747 scopus 로고    scopus 로고
    • 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
    • Simek, M. D. 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. J. Virol. 83, 7337-7348, doi:10.1128/jvi.00110-09 (2009).
    • (2009) J. Virol. , vol.83 , pp. 7337-7348
    • Simek, M.D.1
  • 44
    • 23244434512 scopus 로고    scopus 로고
    • Human immunodeficiency virus type 1 env clones from acute and early subtype B infections for standardized assessments of vaccine-elicited neutralizing antibodies
    • Li, M. et al. Human immunodeficiency virus type 1 env clones from acute and early subtype B infections for standardized assessments of vaccine-elicited neutralizing antibodies. J. Virol. 79, 10108-10125, doi:10.1128/jvi.79.16.10108-10125.2005 (2005).
    • (2005) J. Virol. , vol.79 , pp. 10108-10125
    • Li, M.1
  • 45
    • 73949127978 scopus 로고    scopus 로고
    • Tiered categorization of a diverse panel of HIV-1 env pseudoviruses for assessment of neutralizing antibodies
    • Seaman, M. S. et al. Tiered Categorization of a Diverse Panel of HIV-1 Env Pseudoviruses for Assessment of Neutralizing Antibodies. J. Virol. 84, 1439-1452, doi:10.1128/jvi.02108-09 (2010).
    • (2010) J. Virol. , vol.84 , pp. 1439-1452
    • Seaman, M.S.1
  • 46
    • 70350320690 scopus 로고    scopus 로고
    • Mechanismof human immunodeficiency virus type 1 resistance to monoclonal antibody b12 that effectively targets the site of CD4 attachment
    • Wu, X. et al. Mechanismof Human Immunodeficiency Virus Type 1 Resistance to Monoclonal Antibody b12 That Effectively Targets the Site of CD4 Attachment. J. Virol. 83, 10892-10907, doi:10.1128/jvi.01142-09 (2009).
    • (2009) J. Virol. , vol.83 , pp. 10892-10907
    • Wu, X.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.