메뉴 건너뛰기




Volumn 32, Issue 13, 2016, Pages 1943-1951

RepgenHMM: A dynamic programming tool to infer the rules of immune receptor generation from sequence data

Author keywords

[No Author keywords available]

Indexed keywords

LYMPHOCYTE ANTIGEN RECEPTOR;

EID: 85007162628     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btw112     Document Type: Article
Times cited : (37)

References (44)
  • 2
    • 84868154295 scopus 로고    scopus 로고
    • Next generation sequencing for TCR repertoire profiling: Platform-specific features and correction algorithms
    • Bolotin,D.A. et al. (2012) Next generation sequencing for TCR repertoire profiling: platform-specific features and correction algorithms. Eur. J. Immunol., 42, 3073-3083.
    • (2012) Eur. J. Immunol. , vol.42 , pp. 3073-3083
    • Bolotin, D.A.1
  • 3
    • 84928898852 scopus 로고    scopus 로고
    • MiXCR: Software for comprehensive adaptive immunity profiling
    • Bolotin,D.A. et al. (2015) MiXCR: software for comprehensive adaptive immunity profiling. Nat. Methods, 12, 380-381.
    • (2015) Nat. Methods , vol.12 , pp. 380-381
    • Bolotin, D.A.1
  • 5
    • 48449094247 scopus 로고    scopus 로고
    • IMGT/V-QUEST: The highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis
    • Brochet,X. et al. (2008) IMGT/V-QUEST: The highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis. Nucleic Acids Res., 36, 503-508.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 503-508
    • Brochet, X.1
  • 6
    • 0034652015 scopus 로고    scopus 로고
    • The nucleotide-replacement spectrum under somatic hypermutation exhibits microsequence dependence that is strand-symmetric and distinct from that under germline mutation
    • Cowell,L.G. and Kepler,T.B. (2000) The nucleotide-replacement spectrum under somatic hypermutation exhibits microsequence dependence that is strand-symmetric and distinct from that under germline mutation. J. Immunol., 164, 1971-1976.
    • (2000) J. Immunol. , vol.164 , pp. 1971-1976
    • Cowell, L.G.1    Kepler, T.B.2
  • 7
    • 0032031498 scopus 로고    scopus 로고
    • Base-specific sequences that bias somatic hypermutation deduced by analysis of out-of-frame human IgVH genes
    • Dunn-Walters,D.K. et al. (1998) Base-specific sequences that bias somatic hypermutation deduced by analysis of out-of-frame human IgVH genes. J. Immunol. (Baltimore, MD.: 1950), 160, 2360-2364.
    • (1998) J. Immunol. (Baltimore, MD.: 1950) , vol.160 , pp. 2360-2364
    • Dunn-Walters, D.K.1
  • 9
    • 84937719428 scopus 로고    scopus 로고
    • Inferring processes underlying B-cell repertoire diversity
    • Elhanati,Y. et al. (2015) Inferring processes underlying B-cell repertoire diversity. Philos. Trans. R. Soc. Lond. Ser. B: Biol. Sci., 370, 20140243.
    • (2015) Philos. Trans. R. Soc. Lond. Ser. B: Biol. Sci. , vol.370 , pp. 20140243
    • Elhanati, Y.1
  • 10
    • 84937682989 scopus 로고    scopus 로고
    • Assigning and visualizing germline genes in antibody repertoires
    • Frost,S.D.W. et al. (2015) Assigning and visualizing germline genes in antibody repertoires. Philos. Trans. R. Soc. Lond. Ser. B: Biol. Sci., 370, 20140240.
    • (2015) Philos. Trans. R. Soc. Lond. Ser. B: Biol. Sci. , vol.370 , pp. 20140240
    • Frost, S.D.W.1
  • 11
    • 84923657453 scopus 로고    scopus 로고
    • Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin v gene segment alleles
    • Gadala-Maria,D. et al. (2015) Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles. Proc. Natl. Acad. Sci. U. S. A., 112, E862-E870.
    • (2015) Proc. Natl. Acad. Sci. U. S. A. , vol.112 , pp. E862-E870
    • Gadala-Maria, D.1
  • 12
    • 34547840205 scopus 로고    scopus 로고
    • IHMMune-align: Hidden Markov model-based alignment and identification of germline genes in rearranged immunoglobulin gene sequences
    • Gaeta,B.A. et al. (2007) iHMMune-align: hidden Markov model-based alignment and identification of germline genes in rearranged immunoglobulin gene sequences. Bioinformatics, 23, 1580-1587.
    • (2007) Bioinformatics , vol.23 , pp. 1580-1587
    • Gaeta, B.A.1
  • 14
    • 84893831480 scopus 로고    scopus 로고
    • The promise and challenge of high-throughput sequencing of the antibody repertoire
    • Georgiou,G. et al. (2014) The promise and challenge of high-throughput sequencing of the antibody repertoire. Nat. Biotechnol., 32, 158-168.
    • (2014) Nat. Biotechnol. , vol.32 , pp. 158-168
    • Georgiou, G.1
  • 15
    • 13444273444 scopus 로고    scopus 로고
    • IMGT/GENE-DB: A comprehensive database for human and mouse immunoglobulin and T cell receptor genes
    • Giudicelli,V. et al. (2005) IMGT/GENE-DB: A comprehensive database for human and mouse immunoglobulin and T cell receptor genes. Nucleic Acids Res., 33, D256-D261.
    • (2005) Nucleic Acids Res. , vol.33 , pp. D256-D261
    • Giudicelli, V.1
  • 16
    • 84927690488 scopus 로고    scopus 로고
    • Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair
    • Gouge,J. et al. (2015) Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair. EMBO J., 34, 1126-1142.
    • (2015) EMBO J. , vol.34 , pp. 1126-1142
    • Gouge, J.1
  • 17
    • 84871921179 scopus 로고    scopus 로고
    • NKT and MAIT invariant TCRa sequences can be produced efficiently by VJ gene recombination
    • Greenaway,H.Y. et al. (2013) NKT and MAIT invariant TCRa sequences can be produced efficiently by VJ gene recombination. Immunobiology, 218, 213-224.
    • (2013) Immunobiology , vol.218 , pp. 213-224
    • Greenaway, H.Y.1
  • 18
    • 33846475100 scopus 로고    scopus 로고
    • Role for rearranged variable gene segments in directing secondary T cell receptor alpha recombination
    • Hawwari,A. and Krangel,M.S. (2007) Role for rearranged variable gene segments in directing secondary T cell receptor alpha recombination. Proc. Natl. Acad. Sci. U. S. A., 104, 903-907.
    • (2007) Proc. Natl. Acad. Sci. U. S. A. , vol.104 , pp. 903-907
    • Hawwari, A.1    Krangel, M.S.2
  • 19
    • 0035865068 scopus 로고    scopus 로고
    • Ordered and coordinated rearrangement of the TCR locus: Role of secondary rearrangement in thymic selection
    • Huang,C.Y. and Kanagawa,O. (2001) Ordered and coordinated rearrangement of the TCR locus: role of secondary rearrangement in thymic selection. J. Immunol., 166, 2597-2601.
    • (2001) J. Immunol. , vol.166 , pp. 2597-2601
    • Huang, C.Y.1    Kanagawa, O.2
  • 20
    • 0842303307 scopus 로고    scopus 로고
    • Unraveling V(D)J recombination; Insights into gene regulation
    • Jung,D. and Alt,F.W. (2004) Unraveling V(D)J recombination; insights into gene regulation. Cell, 116, 299-311.
    • (2004) Cell , vol.116 , pp. 299-311
    • Jung, D.1    Alt, F.W.2
  • 21
    • 0030497923 scopus 로고    scopus 로고
    • Repertoires of antigen receptors in Tdt congenitally deficient mice
    • Komori,T. et al. (1996) Repertoires of antigen receptors in Tdt congenitally deficient mice. Int. Rev. Immunol., 13, 317-325.
    • (1996) Int. Rev. Immunol. , vol.13 , pp. 317-325
    • Komori, T.1
  • 23
    • 77951949737 scopus 로고    scopus 로고
    • SoDA2: A Hidden MarkovModel approach for identification of immunoglobulin rearrangements
    • Munshaw,S. and Kepler,T.B. (2010) SoDA2: A Hidden MarkovModel approach for identification of immunoglobulin rearrangements. Bioinformatics, 26, 867-872.
    • (2010) Bioinformatics , vol.26 , pp. 867-872
    • Munshaw, S.1    Kepler, T.B.2
  • 24
    • 84867095375 scopus 로고    scopus 로고
    • Statistical inference of the generation probability of T-cell receptors from sequence repertoires
    • Murugan,A. et al. (2012) Statistical inference of the generation probability of T-cell receptors from sequence repertoires. Proc. Natl. Acad. Sci. U. S. A., 109, 16161-16166.
    • (2012) Proc. Natl. Acad. Sci. U. S. A. , vol.109 , pp. 16161-16166
    • Murugan, A.1
  • 25
    • 33748744694 scopus 로고    scopus 로고
    • No evidence for the use of DIR, D-D fusions, chromosome 15 open reading frames or VHreplacement in the peripheral repertoire was found on application of an improved algorithm, JointML, to 6329 human immunoglobulin H rearrangements
    • Ohm-Laursen,L. et al. (2006) No evidence for the use of DIR, D-D fusions, chromosome 15 open reading frames or VHreplacement in the peripheral repertoire was found on application of an improved algorithm, JointML, to 6329 human immunoglobulin H rearrangements. Immunology, 119, 265-277.
    • (2006) Immunology , vol.119 , pp. 265-277
    • Ohm-Laursen, L.1
  • 26
    • 0035863918 scopus 로고    scopus 로고
    • The targeting of somatic hypermutation closely resembles that of meiotic mutation
    • Oprea,M. et al. (2001) The targeting of somatic hypermutation closely resembles that of meiotic mutation. J. Immunol., 166, 892-899.
    • (2001) J. Immunol. , vol.166 , pp. 892-899
    • Oprea, M.1
  • 27
    • 84925708269 scopus 로고    scopus 로고
    • VDJSeq-Solver: In silico V(D)J recombination detection tool
    • Paciello,G. et al. (2015) VDJSeq-Solver: in silico V(D)J recombination detection tool. Plos One, 10, e0118192.
    • (2015) Plos One , vol.10 , pp. e0118192
    • Paciello, G.1
  • 28
    • 84956797821 scopus 로고    scopus 로고
    • Consistency of VDJ rearrangement and substitution parameters enables accurate B cell receptor sequence annotation
    • Ralph,D.K. and Matsen,F. (2015) Consistency of VDJ rearrangement and substitution parameters enables accurate B cell receptor sequence annotation. PLoS computational biology, 12, e1004409.
    • (2015) PLoS Computational Biology , vol.12 , pp. e1004409
    • Ralph, D.K.1    Matsen, F.2
  • 29
    • 84885340198 scopus 로고    scopus 로고
    • Immunosequencing: Applications of immune repertoire deep sequencing
    • Robins,H. (2013) Immunosequencing: applications of immune repertoire deep sequencing. Curr. Opin. Immunol., 25, 646-652.
    • (2013) Curr. Opin. Immunol. , vol.25 , pp. 646-652
    • Robins, H.1
  • 30
    • 77950541195 scopus 로고    scopus 로고
    • Comprehensive assessment of T-cell receptor betachain diversity in alphabeta T cells
    • Robins,H.S. et al. (2009) Comprehensive assessment of T-cell receptor betachain diversity in alphabeta T cells. Blood, 114, 4099-4107.
    • (2009) Blood , vol.114 , pp. 4099-4107
    • Robins, H.S.1
  • 31
    • 84929612667 scopus 로고    scopus 로고
    • HTJoinSolver: Human immunoglobulin VDJ partitioning using approximate dynamic programming constrained by conserved motifs
    • Russ,D.E. et al. (2015) HTJoinSolver: Human immunoglobulin VDJ partitioning using approximate dynamic programming constrained by conserved motifs. BMC Bioinf., 16, 1-11.
    • (2015) BMC Bioinf. , vol.16 , pp. 1-11
    • Russ, D.E.1
  • 32
    • 79953164038 scopus 로고    scopus 로고
    • Recombination centres and the orchestration of V(D)J recombination
    • Schatz,D.G. and Ji,Y. (2011) Recombination centres and the orchestration of V(D)J recombination. Nat. Rev. Immunol., 11, 251-263.
    • (2011) Nat. Rev. Immunol. , vol.11 , pp. 251-263
    • Schatz, D.G.1    Ji, Y.2
  • 33
    • 80355122714 scopus 로고    scopus 로고
    • V(D)J recombination: Mechanisms of initiation
    • Schatz,D.G. and Swanson,P.C. (2011) V(D)J recombination: mechanisms of initiation. Annu. Rev. Genet., 45, 167-202.
    • (2011) Annu. Rev. Genet. , vol.45 , pp. 167-202
    • Schatz, D.G.1    Swanson, P.C.2
  • 34
    • 84892163383 scopus 로고    scopus 로고
    • Huge overlap of individual TCR beta repertoires
    • Shugay,M. et al. (2013) Huge overlap of individual TCR beta repertoires. Front. Immunol., 4, 466.
    • (2013) Front. Immunol. , vol.4 , pp. 466
    • Shugay, M.1
  • 35
    • 84901857468 scopus 로고    scopus 로고
    • Towards error-free profiling of immune repertoires
    • Shugay,M. et al. (2014) Towards error-free profiling of immune repertoires. Nat. Methods, 11, 653-655.
    • (2014) Nat. Methods , vol.11 , pp. 653-655
    • Shugay, M.1
  • 36
    • 2442717677 scopus 로고    scopus 로고
    • Characterization of the human Ig heavy chain antigen binding complementarity determining region 3 using a newly developed software algorithm, JOINSOLVER
    • Souto-Carneiro,M.M. et al. (2004) Characterization of the human Ig heavy chain antigen binding complementarity determining region 3 using a newly developed software algorithm, JOINSOLVER. J. Immunol. (Baltimore, MD.: 1950), 172, 6790-6802.
    • (2004) J. Immunol. (Baltimore, MD.: 1950) , vol.172 , pp. 6790-6802
    • Souto-Carneiro, M.M.1
  • 37
    • 26844567958 scopus 로고    scopus 로고
    • Hypermutation at A-T base pairs: The a nucleotide replacement spectrum is affected by adjacent nucleotides and there is no reverse complementarity of sequences flanking mutated A and T nucleotides
    • Spencer,J. and Dunn-Walters,D.K. (2005) Hypermutation at A-T base pairs: The a nucleotide replacement spectrum is affected by adjacent nucleotides and there is no reverse complementarity of sequences flanking mutated A and T nucleotides. J. Immunol., 175, 5170-5177.
    • (2005) J. Immunol. , vol.175 , pp. 5170-5177
    • Spencer, J.1    Dunn-Walters, D.K.2
  • 38
    • 84874671063 scopus 로고    scopus 로고
    • Decombinator: A tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine
    • Thomas,N. et al. (2013) Decombinator: A tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine. Bioinformatics (Oxford, England), 29, 542-550.
    • (2013) Bioinformatics (Oxford, England) , vol.29 , pp. 542-550
    • Thomas, N.1
  • 39
    • 79955022207 scopus 로고    scopus 로고
    • A mechanism for TCR sharing between T cell subsets and individuals revealed by pyrosequencing
    • Venturi,V. et al. (2011) A mechanism for TCR sharing between T cell subsets and individuals revealed by pyrosequencing. J. Immunol. (Baltimore, MD.: 1950), 186, 4285-4294.
    • (2011) J. Immunol. (Baltimore, MD.: 1950) , vol.186 , pp. 4285-4294
    • Venturi, V.1
  • 40
    • 32544437698 scopus 로고    scopus 로고
    • SoDA: Implementation of a 3D alignment algorithm for inference of antigen receptor recombinations
    • Volpe,J.M. et al. (2006) SoDA: implementation of a 3D alignment algorithm for inference of antigen receptor recombinations. Bioinformatics (Oxford, England), 22, 438-444.
    • (2006) Bioinformatics (Oxford, England) , vol.22 , pp. 438-444
    • Volpe, J.M.1
  • 41
    • 57649176319 scopus 로고    scopus 로고
    • Ab-origin: An enhanced tool to identify the sourcing gene segments in germline for rearranged antibodies
    • Wang,X. et al. (2008) Ab-origin: an enhanced tool to identify the sourcing gene segments in germline for rearranged antibodies. BMC Bioinf., 9, S20.
    • (2008) BMC Bioinf. , vol.9 , pp. S20
    • Wang, X.1
  • 42
    • 33748511226 scopus 로고    scopus 로고
    • A model for TCR gene segment use
    • Warmflash,A. and Dinner,A.R. (2006) A model for TCR gene segment use. J. Immunol., 177, 3857-3864.
    • (2006) J. Immunol. , vol.177 , pp. 3857-3864
    • Warmflash, A.1    Dinner, A.R.2
  • 43
    • 85060747534 scopus 로고    scopus 로고
    • IgBLAST: An immunoglobulin variable domain sequence analysis tool
    • Ye,J. et al. (2013) IgBLAST: an immunoglobulin variable domain sequence analysis tool. Nucleic Acids Res., 41, 1-7.
    • (2013) Nucleic Acids Res. , vol.41 , pp. 1-7
    • Ye, J.1
  • 44
    • 84899102474 scopus 로고    scopus 로고
    • Distinctive properties of identical twins' TCR repertoires revealed by high-throughput sequencing
    • Zvyagin,I.V. et al. (2014) Distinctive properties of identical twins' TCR repertoires revealed by high-throughput sequencing. Proc. Natl. Acad. Sci. U. S. A., 111, 5980-5985.
    • (2014) Proc. Natl. Acad. Sci. U. S. A. , vol.111 , pp. 5980-5985
    • Zvyagin, I.V.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.