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Volumn 15, Issue 1, 2014, Pages

Quantitative assessment of the robustness of next-generation sequencing of antibody variable gene repertoires from immunized mice

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ANIMAL CELL; ANIMAL TISSUE; ANTIBODY LIBRARY; ANTIBODY SECRETING CELL; ANTIBODY SPECIFICITY; ARTICLE; CELL STIMULATION; COMPLEMENTARITY DETERMINING REGION; CORRELATION COEFFICIENT; FEMALE; MOUSE; NEXT GENERATION SEQUENCING; NONHUMAN; PRACTICE GUIDELINE; QUANTITATIVE ANALYSIS; REPRODUCIBILITY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ISOLATION; SPECIES RICHNESS; ANIMAL; BAGG ALBINO MOUSE; CELL CLONE; GENETICS; HIGH THROUGHPUT SEQUENCING; IMMUNIZATION; IMMUNOGLOBULIN VARIABLE REGION; PROCEDURES; VDJ RECOMBINATION;

EID: 84923870910     PISSN: None     EISSN: 14712172     Source Type: Journal    
DOI: 10.1186/s12865-014-0040-5     Document Type: Article
Times cited : (47)

References (89)
  • 2
    • 84859717525 scopus 로고    scopus 로고
    • Germinal center selection and the development of memory B and plasma cells
    • Shlomchik MJ, Weisel F: Germinal center selection and the development of memory B and plasma cells. Immunol Rev 2012, 247:52-63.
    • (2012) Immunol Rev , vol.247 , pp. 52-63
    • Shlomchik, M.J.1    Weisel, F.2
  • 3
    • 84871430515 scopus 로고    scopus 로고
    • The establishment of the plasma cell survival niche in the bone marrow
    • Chu VT, Berek C: The establishment of the plasma cell survival niche in the bone marrow. Immunol Rev 2013, 251:177-188.
    • (2013) Immunol Rev , vol.251 , pp. 177-188
    • Chu, V.T.1    Berek, C.2
  • 5
    • 33749018225 scopus 로고    scopus 로고
    • Competence and competition: the challenge of becoming a long-lived plasma cell
    • Radbruch A, Muehlinghaus G, Luger EO: Competence and competition: the challenge of becoming a long-lived plasma cell. Nat Rev Immunol 2006, 6:741-750.
    • (2006) Nat Rev Immunol , vol.6 , pp. 741-750
    • Radbruch, A.1    Muehlinghaus, G.2    Luger, E.O.3
  • 8
    • 0020534965 scopus 로고
    • Somatic generation of antibody diversity
    • Tonegawa S: Somatic generation of antibody diversity. Nature 1983, 302:575-581.
    • (1983) Nature , vol.302 , pp. 575-581
    • Tonegawa, S.1
  • 9
    • 0034268780 scopus 로고    scopus 로고
    • Class switch recombination and hypermutation require activation-induced cytidine deaminase (AID), a potential RNA editing enzyme
    • Muramatsu M, Kinoshita K, Fagarasan S, Yamada S, Shinkai Y, Honjo T: Class switch recombination and hypermutation require activation-induced cytidine deaminase (AID), a potential RNA editing enzyme. Cell 2000, 102:553-563.
    • (2000) Cell , vol.102 , pp. 553-563
    • Muramatsu, M.1    Kinoshita, K.2    Fagarasan, S.3    Yamada, S.4    Shinkai, Y.5    Honjo, T.6
  • 10
    • 0033711628 scopus 로고    scopus 로고
    • Diversity in the CDR3 region of V(H) is sufficient for most antibody specificities
    • Xu JL, Davis MM: Diversity in the CDR3 region of V(H) is sufficient for most antibody specificities. Immunity 2000, 13:37-45.
    • (2000) Immunity , vol.13 , pp. 37-45
    • Xu, J.L.1    Davis, M.M.2
  • 11
    • 84861114055 scopus 로고    scopus 로고
    • Structural consensus among antibodies defines the antigen binding site
    • Kunik V, Peters B, Ofran Y: Structural consensus among antibodies defines the antigen binding site. PLoS Comput Biol 2012, 8:e1002388.
    • (2012) PLoS Comput Biol , vol.8 , pp. e1002388
    • Kunik, V.1    Peters, B.2    Ofran, Y.3
  • 12
    • 84885006229 scopus 로고    scopus 로고
    • The indistinguishability of epitopes from protein surface is explained by the distinct binding preferences of each of the six antigen-binding loops
    • Kunik V, Ofran Y: The indistinguishability of epitopes from protein surface is explained by the distinct binding preferences of each of the six antigen-binding loops. Protein Eng Des Sel 2013, 26:599-609.
    • (2013) Protein Eng Des Sel , vol.26 , pp. 599-609
    • Kunik, V.1    Ofran, Y.2
  • 13
    • 84882432416 scopus 로고    scopus 로고
    • Genetic measurement of memory B-cell recall using antibody repertoire sequencing
    • Vollmers C, Sit RV, Weinstein JA, Dekker CL, Quake SR: Genetic measurement of memory B-cell recall using antibody repertoire sequencing. Proc Natl Acad Sci 2013, 110:13463-13468.
    • (2013) Proc Natl Acad Sci , vol.110 , pp. 13463-13468
    • Vollmers, C.1    Sit, R.V.2    Weinstein, J.A.3    Dekker, C.L.4    Quake, S.R.5
  • 14
    • 84887433048 scopus 로고    scopus 로고
    • Network properties derived from deep sequencing of the human B-cell receptor repertoires delineates B-cell populations
    • Bashford-Rogers R, Palser A, Huntly B: Network properties derived from deep sequencing of the human B-cell receptor repertoires delineates B-cell populations. Genome Res 2013, 23:1874-1884.
    • (2013) Genome Res , vol.23 , pp. 1874-1884
    • Bashford-Rogers, R.1    Palser, A.2    Huntly, B.3
  • 15
    • 84885405356 scopus 로고    scopus 로고
    • The structural basis of antibody-antigen recognition
    • Sela-Culang I, Kunik V, Ofran Y: The structural basis of antibody-antigen recognition. Front Immunol 2013, 4:302.
    • (2013) Front Immunol , vol.4 , pp. 302
    • Sela-Culang, I.1    Kunik, V.2    Ofran, Y.3
  • 17
    • 84856185049 scopus 로고    scopus 로고
    • Rep-Seq: uncovering the immunological repertoire through next-generation sequencing
    • Benichou J, Ben-Hamo R, Louzoun Y, Efroni S: Rep-Seq: uncovering the immunological repertoire through next-generation sequencing. Immunology 2012, 135:183-191.
    • (2012) Immunology , vol.135 , pp. 183-191
    • Benichou, J.1    Ben-Hamo, R.2    Louzoun, Y.3    Efroni, S.4
  • 18
    • 79955711145 scopus 로고    scopus 로고
    • Systems immunology: complexity captured
    • Schubert C: Systems immunology: complexity captured. Nature 2011, 473:113-114.
    • (2011) Nature , vol.473 , pp. 113-114
    • Schubert, C.1
  • 19
    • 79960940363 scopus 로고    scopus 로고
    • Systems analysis of adaptive immunity by utilization of high-throughput technologies
    • Reddy ST, Georgiou G: Systems analysis of adaptive immunity by utilization of high-throughput technologies. Curr Opin Biotechnol 2011, 22:584-589.
    • (2011) Curr Opin Biotechnol , vol.22 , pp. 584-589
    • Reddy, S.T.1    Georgiou, G.2
  • 25
    • 77956551877 scopus 로고    scopus 로고
    • High-throughput immunoglobulin repertoire analysis distinguishes between human IgM memory and switched memory B-cell populations
    • Wu Y-C, Kipling D, Leong HS, Martin V, Ademokun AA, Dunn-Walters DK: High-throughput immunoglobulin repertoire analysis distinguishes between human IgM memory and switched memory B-cell populations. Blood 2010, 116:1070-1078.
    • (2010) Blood , vol.116 , pp. 1070-1078
    • Wu, Y.-C.1    Kipling, D.2    Leong, H.S.3    Martin, V.4    Ademokun, A.A.5    Dunn-Walters, D.K.6
  • 27
    • 84869438827 scopus 로고    scopus 로고
    • Proteomics-directed cloning of circulating antiviral human monoclonal antibodies
    • Sato S, Beausoleil SA, Popova L, Beaudet JG: Proteomics-directed cloning of circulating antiviral human monoclonal antibodies. Nature 2012, 30:1039-1043.
    • (2012) Nature , vol.30 , pp. 1039-1043
    • Sato, S.1    Beausoleil, S.A.2    Popova, L.3    Beaudet, J.G.4
  • 28
    • 84874092680 scopus 로고    scopus 로고
    • Lineage structure of the human antibody repertoire in response to influenza vaccination
    • Jiang N, He J, Weinstein JA: Lineage structure of the human antibody repertoire in response to influenza vaccination. Science 2013, 171:171ra19-171ra19.
    • (2013) Science , vol.171 , pp. 171ra19-171ra19
    • Jiang, N.1    He, J.2    Weinstein, J.A.3
  • 30
    • 84879511309 scopus 로고    scopus 로고
    • Correlation of gene expression and genome mutation in single B-cells
    • Weinstein JA, Zeng X, Chien Y-H, Quake SR: Correlation of gene expression and genome mutation in single B-cells. PLoS One 2013, 8:e67624.
    • (2013) PLoS One , vol.8 , pp. e67624
    • Weinstein, J.A.1    Zeng, X.2    Chien, Y.-H.3    Quake, S.R.4
  • 32
    • 0032870206 scopus 로고    scopus 로고
    • Functional diversity of natural IgM
    • Brissac C, Nobrega A, Carneiro J: Functional diversity of natural IgM. Int Immunol 1999, 11:1501-1507.
    • (1999) Int Immunol , vol.11 , pp. 1501-1507
    • Brissac, C.1    Nobrega, A.2    Carneiro, J.3
  • 34
    • 84892728434 scopus 로고    scopus 로고
    • Sequencing depth and coverage: key considerations in genomic analyses
    • Sims D, Sudbery I, Ilott NE, Heger A, Ponting CP: Sequencing depth and coverage: key considerations in genomic analyses. Nat Rev Genet 2014, 15:121-132.
    • (2014) Nat Rev Genet , vol.15 , pp. 121-132
    • Sims, D.1    Sudbery, I.2    Ilott, N.E.3    Heger, A.4    Ponting, C.P.5
  • 35
    • 84860756398 scopus 로고    scopus 로고
    • Performance comparison of benchtop high-throughput sequencing platforms
    • Loman NJ, Misra RV, Dallman TJ: Performance comparison of benchtop high-throughput sequencing platforms. Nature 2012,
    • (2012) Nature
    • Loman, N.J.1    Misra, R.V.2    Dallman, T.J.3
  • 37
    • 0017325828 scopus 로고
    • Immunoglobulin-containing cells in different lymphoid organs of the CBA mouse during its life-span
    • Haaijman JJ, Schuit HR, Hijmans W: Immunoglobulin-containing cells in different lymphoid organs of the CBA mouse during its life-span. Immunology 1977, 32:427-434.
    • (1977) Immunology , vol.32 , pp. 427-434
    • Haaijman, J.J.1    Schuit, H.R.2    Hijmans, W.3
  • 38
    • 0019373953 scopus 로고
    • The bone marrow: the major source of serum immunoglobulins, but still a neglected site of antibody formation
    • Benner R, Hijmans W, Haaijman JJ: The bone marrow: the major source of serum immunoglobulins, but still a neglected site of antibody formation. Clinical Exp Immunol 1981, 46:1-8.
    • (1981) Clinical Exp Immunol , vol.46 , pp. 1-8
    • Benner, R.1    Hijmans, W.2    Haaijman, J.J.3
  • 39
    • 0016155964 scopus 로고
    • Number and distribution of lymphocytes in man. A critical analysis
    • Trepel F: Number and distribution of lymphocytes in man. A critical analysis. Klin Wochenschr 1974, 52:511-515.
    • (1974) Klin Wochenschr , vol.52 , pp. 511-515
    • Trepel, F.1
  • 41
    • 84887433583 scopus 로고    scopus 로고
    • Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories
    • 't Hoen PAC, Friedländer MR, Almlöf J, Sammeth M, Pulyakhina I, Anvar SY, Laros JFJ, Buermans HPJ, Karlberg O, Brännvall M, van Ommen G-JB, Estivill X, Guigo R, Syvänen A-C, Gut IG, Dermitzakis ET, Antonorakis SE, Brazma A, Flicek P, Schreiber S, Rosenstiel P, Meitinger T, Strom TM, Lehrach H, Sudbrak R, Carracedo A, 't Hoen PAC, Pulyakhina I, Anvar SY, The GEUVADIS Consortium, et al: Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories. Nat Biotechnol 2013, 31:1015-1022.
    • (2013) Nat Biotechnol , vol.31 , pp. 1015-1022
  • 43
    • 84866996247 scopus 로고    scopus 로고
    • Antibody isolation from immunized animals: comparison of phage display and antibody discovery via V gene repertoire mining
    • Saggy I, Wine Y, Shefet-Carasso L, Nahary L, Georgiou G, Benhar I: Antibody isolation from immunized animals: comparison of phage display and antibody discovery via V gene repertoire mining. Protein Eng Des Sel 2012, 25:539-549.
    • (2012) Protein Eng Des Sel , vol.25 , pp. 539-549
    • Saggy, I.1    Wine, Y.2    Shefet-Carasso, L.3    Nahary, L.4    Georgiou, G.5    Benhar, I.6
  • 44
    • 33947316710 scopus 로고    scopus 로고
    • Methods for comparing the diversity of samples of the T cell receptor repertoire
    • Venturi V, Kedzierska K, Turner SJ, Doherty PC: Methods for comparing the diversity of samples of the T cell receptor repertoire. J Immunol Methods 2007, 312:182-195.
    • (2007) J Immunol Methods , vol.312 , pp. 182-195
    • Venturi, V.1    Kedzierska, K.2    Turner, S.J.3    Doherty, P.C.4
  • 45
    • 77649270288 scopus 로고    scopus 로고
    • Estimation of T-cell repertoire diversity and clonal size distribution by Poisson abundance models
    • Sepúlveda N, Paulino CD, Carneiro J: Estimation of T-cell repertoire diversity and clonal size distribution by Poisson abundance models. J Immunol Methods 2010, 353:124-137.
    • (2010) J Immunol Methods , vol.353 , pp. 124-137
    • Sepúlveda, N.1    Paulino, C.D.2    Carneiro, J.3
  • 46
    • 84887425111 scopus 로고    scopus 로고
    • Methods for diversity and overlap analysis in T-cell receptor populations
    • Rempala GA, Seweryn M: Methods for diversity and overlap analysis in T-cell receptor populations. J Math Biol 2012, 67:1339-1368.
    • (2012) J Math Biol , vol.67 , pp. 1339-1368
    • Rempala, G.A.1    Seweryn, M.2
  • 50
    • 84934443698 scopus 로고    scopus 로고
    • Using next-generation sequencing for discovery of high-frequency monoclonal antibodies in the variable gene repertoires from immunized mice
    • Haessler U, Reddy ST: Using next-generation sequencing for discovery of high-frequency monoclonal antibodies in the variable gene repertoires from immunized mice. Methods Mol Biol 2014, 1131:191-203.
    • (2014) Methods Mol Biol , vol.1131 , pp. 191-203
    • Haessler, U.1    Reddy, S.T.2
  • 51
    • 0031032155 scopus 로고    scopus 로고
    • Reliable cloning of functional antibody variable domains from hybridomas and spleen cell repertoires employing a reengineered phage display system
    • Krebber A, Bornhauser S, Burmester J, Honegger A, Willuda J, Bosshard HR, Plückthun A: Reliable cloning of functional antibody variable domains from hybridomas and spleen cell repertoires employing a reengineered phage display system. J Immunol Methods 1997, 201:35-55.
    • (1997) J Immunol Methods , vol.201 , pp. 35-55
    • Krebber, A.1    Bornhauser, S.2    Burmester, J.3    Honegger, A.4    Willuda, J.5    Bosshard, H.R.6    Plückthun, A.7
  • 55
    • 33646876613 scopus 로고    scopus 로고
    • Entropy and diversity
    • Jost L: Entropy and diversity. Oikos 2006, 113:363-375.
    • (2006) Oikos , vol.113 , pp. 363-375
    • Jost, L.1
  • 57
    • 35848969753 scopus 로고    scopus 로고
    • Duration of humoral immunity to common viral and vaccine antigens
    • Amanna IJ, Carlson NE, Slifka MK: Duration of humoral immunity to common viral and vaccine antigens. N Engl J Med 2007, 357:1903-1915.
    • (2007) N Engl J Med , vol.357 , pp. 1903-1915
    • Amanna, I.J.1    Carlson, N.E.2    Slifka, M.K.3
  • 58
  • 59
  • 60
    • 1842405362 scopus 로고    scopus 로고
    • Lifetime of plasma cells in the bone marrow
    • Manz RA, Thiel A, Radbruch A: Lifetime of plasma cells in the bone marrow. Nature 1997, 388:133-134.
    • (1997) Nature , vol.388 , pp. 133-134
    • Manz, R.A.1    Thiel, A.2    Radbruch, A.3
  • 61
    • 84884252950 scopus 로고    scopus 로고
    • Plasma cell homeostasis: the effects of chronic antigen stimulation and inflammation
    • Slocombe T, Brown S, Miles K, Gray M, Barr TA, Gray D: Plasma cell homeostasis: the effects of chronic antigen stimulation and inflammation. J Immunol Methods 2013, 191:3128-3138.
    • (2013) J Immunol Methods , vol.191 , pp. 3128-3138
    • Slocombe, T.1    Brown, S.2    Miles, K.3    Gray, M.4    Barr, T.A.5    Gray, D.6
  • 64
    • 77956413166 scopus 로고    scopus 로고
    • The relation between evenness and diversity
    • Jost L: The relation between evenness and diversity. Diversity 2010, 2:207-232.
    • (2010) Diversity , vol.2 , pp. 207-232
    • Jost, L.1
  • 66
    • 84865412764 scopus 로고    scopus 로고
    • Models and methods for analysis of lymphocyte repertoire generation, development, selection and evolution
    • Mehr R, Sternberg-Simon M, Michaeli M, Pickman Y: Models and methods for analysis of lymphocyte repertoire generation, development, selection and evolution. Immunol Lett 2012, 148:11-22.
    • (2012) Immunol Lett , vol.148 , pp. 11-22
    • Mehr, R.1    Sternberg-Simon, M.2    Michaeli, M.3    Pickman, Y.4
  • 70
    • 84888339051 scopus 로고    scopus 로고
    • A novel approach to tracking antigen-experienced CD4 T cells into functional compartments via tandem deep and shallow TCR clonotyping
    • Estorninho M, Gibson VB, Kronenberg-Versteeg D, Liu Y-F, Ni C, Cerosaletti K, Peakman M: A novel approach to tracking antigen-experienced CD4 T cells into functional compartments via tandem deep and shallow TCR clonotyping. J Immunol Methods 2013, 191:5430-5440.
    • (2013) J Immunol Methods , vol.191 , pp. 5430-5440
    • Estorninho, M.1    Gibson, V.B.2    Kronenberg-Versteeg, D.3    Liu, Y.-F.4    Ni, C.5    Cerosaletti, K.6    Peakman, M.7
  • 72
    • 84890565382 scopus 로고    scopus 로고
    • The role of replicates for error mitigation in next-generation sequencing
    • Robasky K, Lewis NE, Church GM: The role of replicates for error mitigation in next-generation sequencing. Nat Rev Genet 2014, 15:56-62.
    • (2014) Nat Rev Genet , vol.15 , pp. 56-62
    • Robasky, K.1    Lewis, N.E.2    Church, G.M.3
  • 74
    • 79959353421 scopus 로고    scopus 로고
    • Detection and quantification of rare mutations with massively parallel sequencing
    • Kinde I, Wu J, Papadopoulos N, Kinzler KW, Vogelstein B: Detection and quantification of rare mutations with massively parallel sequencing. Proc Natl Acad Sci 2011, 108:9530-9535.
    • (2011) Proc Natl Acad Sci , vol.108 , pp. 9530-9535
    • Kinde, I.1    Wu, J.2    Papadopoulos, N.3    Kinzler, K.W.4    Vogelstein, B.5
  • 75
    • 84055200527 scopus 로고    scopus 로고
    • Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID
    • Jabara CB, Jones CD, Roach J, Anderson JA, Swanstrom R: Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID. Proc Natl Acad Sci 2011, 108:20166-20171.
    • (2011) Proc Natl Acad Sci , vol.108 , pp. 20166-20171
    • Jabara, C.B.1    Jones, C.D.2    Roach, J.3    Anderson, J.A.4    Swanstrom, R.5
  • 80
    • 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, Ofek G, Yang Y, Zhang B, Louder MK, Lu G, McKee K, Pancera M, Skinner J, Zhang Z, Parks R, Eudailey J, Lloyd KE, Blinn J, Alam SM, Haynes BF, Simek M, Burton DR, Koff WC, Mullikin JC, Mascola JR, Shapiro L, Kwong PD, NISC Comparative Sequencing Program: Mining the antibodyome for HIV-1-neutralizing antibodies with next-generation sequencing and phylogenetic pairing of heavy/light chains. Proc Natl Acad Sci 2013, 110:6470-6475.
    • (2013) Proc Natl Acad Sci , vol.110 , pp. 6470-6475
  • 81
    • 84876797103 scopus 로고    scopus 로고
    • Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus
    • Liao HX, Lynch R, Zhou T, Gao F, Alam SM, Boyd SD: Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus. Nature 2013, 496:469-476.
    • (2013) Nature , vol.496 , pp. 469-476
    • Liao, H.X.1    Lynch, R.2    Zhou, T.3    Gao, F.4    Alam, S.M.5    Boyd, S.D.6
  • 84
    • 0005687347 scopus 로고
    • Diversity of planktonic foraminifera in deep-sea sediments
    • Berger WH, Parker FL: Diversity of planktonic foraminifera in deep-sea sediments. Science 1970, 168:1345-1347.
    • (1970) Science , vol.168 , pp. 1345-1347
    • Berger, W.H.1    Parker, F.L.2
  • 85
    • 84923866037 scopus 로고    scopus 로고
    • R Foundation for Statistical Computing: R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing
    • R Foundation for Statistical Computing: R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing; 2014.
    • (2014)
  • 87
    • 79251555660 scopus 로고    scopus 로고
    • VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R
    • Chen H, Boutros P: VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R. BMC Bioinform 2011, 12:35.
    • (2011) BMC Bioinform , vol.12 , pp. 35
    • Chen, H.1    Boutros, P.2
  • 88
    • 70349866687 scopus 로고    scopus 로고
    • ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data
    • Morgan M, Anders S, Lawrence M, Aboyoun P, Pagès H, Gentleman R: ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data. Bioinformatics 2009, 25:2607-2608.
    • (2009) Bioinformatics , vol.25 , pp. 2607-2608
    • Morgan, M.1    Anders, S.2    Lawrence, M.3    Aboyoun, P.4    Pagès, H.5    Gentleman, R.6


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