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Volumn 10, Issue 3, 2015, Pages

VDJSeq-Solver: In silico V(D)J recombination detection tool

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; CLONAL VARIATION; COMPUTER PROGRAM; CONTROLLED STUDY; DNA POLYMORPHISM; GENE LOCUS; GENE MAPPING; GENE REARRANGEMENT; HIGH THROUGHPUT SEQUENCING; LARGE CELL LYMPHOMA; LYMPHOCYTE SUBPOPULATION; MANTLE CELL LYMPHOMA; METHODOLOGY; MOLECULAR CLONING; NEXT GENERATION SEQUENCING; POLYMERASE CHAIN REACTION; RNA EXTRACTION; RNA SEQUENCE; SEQUENCE ALIGNMENT; TUMOR CELL; VDJ RECOMBINATION; CELL CLONE; COMPUTER SIMULATION; GENETICS; HUMAN; IMMUNOGLOBULIN GENE; LYMPHOMA, LARGE B-CELL, DIFFUSE; LYMPHOMA, MANTLE-CELL; PROCEDURES; SEQUENCE ANALYSIS; SOFTWARE;

EID: 84925708269     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0118192     Document Type: Article
Times cited : (12)

References (72)
  • 1
    • 33646181086 scopus 로고    scopus 로고
    • Mechanism and control of V(D) J recombination at the immunoglobulin heavy chain locus
    • PMID: 16551259
    • Jung D, Giallourakis C, Mostoslavsky R, Alt FW. Mechanism and control of V(D)J recombination at the immunoglobulin heavy chain locus. Annu Rev Immunol. 2006; 24: 541-570. doi: 10.1146/annurev.immunol.23.021704.115830 PMID: 16551259
    • (2006) Annu Rev Immunol , vol.24 , pp. 541-570
    • Jung, D.1    Giallourakis, C.2    Mostoslavsky, R.3    Alt, F.W.4
  • 2
    • 84859383686 scopus 로고    scopus 로고
    • Chromatin topology and the regulation of antigen receptor assembly
    • PMID: 22224771
    • Bossen C, Mansson R, Murre C. Chromatin topology and the regulation of antigen receptor assembly. Annu Rev Immunol. 2012; 30: 337-356. doi: 10.1146/annurev-immunol-020711-075003 PMID: 22224771
    • (2012) Annu Rev Immunol , vol.30 , pp. 337-356
    • Bossen, C.1    Mansson, R.2    Murre, C.3
  • 3
    • 0842303307 scopus 로고    scopus 로고
    • Unraveling V(D) J recombination; Insights into gene regulation
    • Jung D, Alt FW. Unraveling V(D)J recombination; insights into gene regulation. Cell. 2004; 116: 299-311. doi: 10.1016/S0092-8674(04)00039-X PMID: 14744439
    • (2004) Cell , vol.116 , pp. 299-311
    • Jung, D.1    Alt, F.W.2
  • 4
    • 0036240127 scopus 로고    scopus 로고
    • The mechanism and regulation of chromosomal V(D)
    • PMID: 11983152
    • Bassing CH, Swat W, Alt FW. The mechanism and regulation of chromosomal V(D)J recombination. Cell. 2002; 109: S45-S55. doi: 10.1016/S0092-8674(02)00675-X PMID: 11983152
    • (2002) J Recombination. Cell , vol.109 , pp. S45-S55
    • Bassing, C.H.1    Swat, W.2    Alt, F.W.3
  • 5
    • 0041646843 scopus 로고
    • Joining of immunoglobulin heavy chain gene segments: Implications from a chromosome with evidence of three D-JH fusions
    • Alt FW, Baltimore D. Joining of immunoglobulin heavy chain gene segments: implications from a chromosome with evidence of three D-JH fusions. Proceedings of the National Academy of Sciences. 1982; 79: 4118-4122. doi: 10.1073/pnas.79.13.4118
    • (1982) Proceedings of the National Academy of Sciences , vol.79 , pp. 4118-4122
    • Alt, F.W.1    Baltimore, D.2
  • 8
    • 16844381831 scopus 로고    scopus 로고
    • Mechanisms of B-cell lymphoma pathogenesis
    • PMID: 15803153
    • Kuppers R. Mechanisms of B-cell lymphoma pathogenesis. Nat Rev Cancer. 2005; 5: 251-262. doi: 10.1038/nrc1589 PMID: 15803153
    • (2005) Nat Rev Cancer , vol.5 , pp. 251-262
    • Kuppers, R.1
  • 9
    • 0026646742 scopus 로고
    • Expression of immunoglobulin heavy chain variable gene (VH) in B-chronic lymphocytic leukemia (B-CLL) and B-prolymphocytic leukemia (B-PLL) cell lines. "restricted" usage of VH3 family
    • PMID: 1318012
    • Bertin PA, MArti GE. Expression of immunoglobulin heavy chain variable gene (VH) in B-chronic lymphocytic leukemia (B-CLL) and B-prolymphocytic leukemia (B-PLL) cell lines. "Restricted" usage of VH3 family. Ann N Y Acad Sci. 1992; 651: 464-466. doi: 10.1111/j.1749-6632.1992.tb24646.x PMID: 1318012
    • (1992) Ann N y Acad Sci , vol.651 , pp. 464-466
    • Bertin, P.A.1    Marti, G.E.2
  • 10
    • 0000634555 scopus 로고
    • Developmentally restricted immunoglobulin heavy chain variable region gene expressed at high frequency in chronic lymphocytic leukemia
    • Kipps TJ, Tomhave E, Pratt LF, Duffy S, Chen PP, Carson DA, et al. Developmentally restricted immunoglobulin heavy chain variable region gene expressed at high frequency in chronic lymphocytic leukemia. Proc Natl Acad Sci USA. 1982; 86: 5913-5917. doi: 10.1073/pnas.86.15.5913
    • (1982) Proc Natl Acad Sci USA , vol.86 , pp. 5913-5917
    • Kipps, T.J.1    Tomhave, E.2    Pratt, L.F.3    Duffy, S.4    Chen, P.P.5    Carson, D.A.6
  • 11
    • 0027360335 scopus 로고
    • V gene usage by seven hybrids derived from CD5 + B-cell chronic lymphocytic leukemia and displaying autoantibody activity
    • PMID: 7693035
    • Pritsch O, Magnac C, Dumas G, Egile C, Dighiero G. V gene usage by seven hybrids derived from CD5 + B-cell chronic lymphocytic leukemia and displaying autoantibody activity. Blood. 1993; 82: 3103-3112. PMID: 7693035
    • (1993) Blood , vol.82 , pp. 3103-3112
    • Pritsch, O.1    Magnac, C.2    Dumas, G.3    Egile, C.4    Dighiero, G.5
  • 12
    • 0029665035 scopus 로고
    • Restricted immunoglobulin VH region repertoire in chronic lymphocytic leukemia patients with autoimmune hemolytic anemia
    • PMID: 8611714
    • Efremov DG, Ivanovski M, Siljanovski N, Pozzato G, Cevreska L, Fais F, et al. Restricted immunoglobulin VH region repertoire in chronic lymphocytic leukemia patients with autoimmune hemolytic anemia. Blood. 19961, 87: 3869-3876. PMID: 8611714
    • (1961) Blood. , vol.87 , pp. 3869-3876
    • Efremov, D.G.1    Ivanovski, M.2    Siljanovski, N.3    Pozzato, G.4    Cevreska, L.5    Fais, F.6
  • 13
    • 0030639650 scopus 로고    scopus 로고
    • Ig VH1 genes expressed in B-cell chronic lymphocytic leukemia exhibit distinctive molecular features
    • PMID: 8977195
    • Johnson TA, Rassenti LZ, Kipps TJ. Ig VH1 genes expressed in B-cell chronic lymphocytic leukemia exhibit distinctive molecular features. J Immunol. 1997; 158: 235-246. PMID: 8977195
    • (1997) J Immunol , vol.158 , pp. 235-246
    • Johnson, T.A.1    Rassenti, L.Z.2    Kipps, T.J.3
  • 14
    • 0030905707 scopus 로고    scopus 로고
    • Differential rates of somatic hypermutation in V(H) genes among subsets of chronic lymphocytic leukemia defined by chromosomal abnormalities
    • PMID: 9166858
    • Oscier DG, Thompsett A, Zhu D, Stevenson FK. Differential rates of somatic hypermutation in V(H) genes among subsets of chronic lymphocytic leukemia defined by chromosomal abnormalities. Blood. 1997; 89: 4153-4160. PMID: 9166858
    • (1997) Blood , vol.89 , pp. 4153-4160
    • Oscier, D.G.1    Thompsett, A.2    Zhu, D.3    Stevenson, F.K.4
  • 15
    • 0032532668 scopus 로고    scopus 로고
    • Chronic lymphocytic leukemia Bcells express restricted sets of mutated and unmutated antigen receptors
    • PMID: 9788964
    • Fais F, Ghiotto F, Hashimoto S, Sellars B, Valetto A, Allen SL, et al. Chronic lymphocytic leukemia Bcells express restricted sets of mutated and unmutated antigen receptors. J Clin Invest. 1998; 102: 1515-1525. doi: 10.1172/JCI3009 PMID: 9788964
    • (1998) J Clin Invest , vol.102 , pp. 1515-1525
    • Fais, F.1    Ghiotto, F.2    Hashimoto, S.3    Sellars, B.4    Valetto, A.5    Allen, S.L.6
  • 16
    • 0032817836 scopus 로고    scopus 로고
    • Clonal evolution as judged by immunoglobulin heavy chain gene rearrangements in relapsing precursor-B acute lymphoblastic leukemia
    • Rosenquist R, Thunberg U, Li AH, Forestier E, Lnnerholm G, Lindh J, et al. Clonal evolution as judged by immunoglobulin heavy chain gene rearrangements in relapsing precursor-B acute lymphoblastic leukemia. J Clin Invest. 1999; 63: 171-179.
    • (1999) J Clin Invest , vol.63 , pp. 171-179
    • Rosenquist, R.1    Thunberg, U.2    Li, A.H.3    Forestier, E.4    Lnnerholm, G.5    Lindh, J.6
  • 17
    • 33947644251 scopus 로고    scopus 로고
    • Similarities and differences between the light and heavy chain Ig variable region gene repertoires in chronic lymphocytic leukemia
    • PMID: 17380195
    • Ghiotto F, Faedis F, Albesiano E, Sison C, Valetto A, Gaidano G, et al. Similarities and differences between the light and heavy chain Ig variable region gene repertoires in chronic lymphocytic leukemia. Mol Med. 2006; 12: 300-308. doi: 10.2119/2006-00080.Ghiotto PMID: 17380195
    • (2006) Mol Med , vol.12 , pp. 300-308
    • Ghiotto, F.1    Faedis, F.2    Albesiano, E.3    Sison, C.4    Valetto, A.5    Gaidano, G.6
  • 18
    • 79953317492 scopus 로고    scopus 로고
    • The B-cell antigen receptor in atypical chronic lymphocytic leukemia with t(14;19)(q32;q13) demonstrates remarkable stereotypy
    • PMID: 20715110
    • Schweighofer CD, Huh YO, Luthra R, Sargent RL, Ketterling RP, Knudson RA, et al. The B-cell antigen receptor in atypical chronic lymphocytic leukemia with t(14;19)(q32;q13) demonstrates remarkable stereotypy. Int J Cancer. 2011; 128: 2759-2764. doi: 10.1002/ijc.25605 PMID: 20715110
    • (2011) Int J Cancer , vol.128 , pp. 2759-2764
    • Schweighofer, C.D.1    Huh, Y.O.2    Luthra, R.3    Sargent, R.L.4    Ketterling, R.P.5    Knudson, R.A.6
  • 19
    • 0033567968 scopus 로고    scopus 로고
    • Ig v gene mutation status and CD38 expression as novel prognostic indicators in chronic lymphocytic leukemia
    • PMID: 10477712
    • Damle RN, Wasil T, Fais F, Ghiotto F, Valetto A, Allen SL, et al. Ig V gene mutation status and CD38 expression as novel prognostic indicators in chronic lymphocytic leukemia. Blood. 1999; 94: 1840-1847. PMID: 10477712
    • (1999) Blood , vol.94 , pp. 1840-1847
    • Damle, R.N.1    Wasil, T.2    Fais, F.3    Ghiotto, F.4    Valetto, A.5    Allen, S.L.6
  • 20
    • 0033567907 scopus 로고    scopus 로고
    • Unmutated Ig V(H) genes are associated with a more aggressive form of chronic lymphocytic leukemia
    • PMID: 10477713
    • Hamblin TJ, Davis Z, Gardiner A, Oscier DG, Stevenson FK. Unmutated Ig V(H) genes are associated with a more aggressive form of chronic lymphocytic leukemia. Blood. 1999; 94: 1848-1854. PMID: 10477713
    • (1999) Blood , vol.94 , pp. 1848-1854
    • Hamblin, T.J.1    Davis, Z.2    Gardiner, A.3    Oscier, D.G.4    Stevenson, F.K.5
  • 21
    • 79953685152 scopus 로고    scopus 로고
    • The impact of next-generation sequencing on genomics
    • Zhang J, Chiodini R, Badr A, Zhang G. The impact of next-generation sequencing on genomics. J of Genet Genomics. 2011; 38: 95-109. doi: 10.1016/j.jgg.2011.02.003
    • (2011) J of Genet Genomics , vol.38 , pp. 95-109
    • Zhang, J.1    Chiodini, R.2    Badr, A.3    Zhang, G.4
  • 22
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: A revolutionary tool for transcriptomics
    • Zhong W, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics 2009; 10: 57-63. doi: 10.1038/nrg2484
    • (2009) Nature Reviews Genetics , vol.10 , pp. 57-63
    • Zhong, W.1    Gerstein, M.2    Snyder, M.3
  • 23
    • 3242876679 scopus 로고    scopus 로고
    • IMGT/V-QUEST, an integrated software program for immunoglobulin and T cell receptor V-J and V-D-J rearrangement analysis
    • PMID: 15215425
    • Giudicelli V, Chaume D, Lefranc MP. IMGT/V-QUEST, an integrated software program for immunoglobulin and T cell receptor V-J and V-D-J rearrangement analysis. Nucleic Acids Research. 2004; 32: W435-W440. doi: 10.1093/nar/gkh412 PMID: 15215425
    • (2004) Nucleic Acids Research , vol.32 , pp. W435-W440
    • Giudicelli, V.1    Chaume, D.2    Lefranc, M.P.3
  • 24
    • 34547840205 scopus 로고    scopus 로고
    • IHMMune-align: Hidden Markov model-based alignment and Bioinformatics of germline genes in rearranged immunoglobulin gene sequences
    • Gaeta BA, Malming HR, Jackson KJ, Bain ME, Wilson P, Collins AM. IHMMune-align: hidden Markov model-based alignment and Bioinformatics of germline genes in rearranged immunoglobulin gene sequences. Immunology. 2007; 23: 1580-1587.
    • (2007) Immunology , vol.23 , pp. 1580-1587
    • Gaeta, B.A.1    Malming, H.R.2    Jackson, K.J.3    Bain, M.E.4    Wilson, P.5    Collins, A.M.6
  • 25
    • 33748744694 scopus 로고    scopus 로고
    • No evidence for the use of DIR, D-D fusions, chromosome 15 open reading frames or VH replacement in the peripheral repertoire was found on application of an improved algorithm, JointML, to 6329 human immunoglobulin H rearrangements
    • Laursen O, Nielsen M, Larsen SR, Barington T. No evidence for the use of DIR, D-D fusions, chromosome 15 open reading frames or VH replacement in the peripheral repertoire was found on application of an improved algorithm, JointML, to 6329 human immunoglobulin H rearrangements. Immunology. 2006; 119: 265-277. doi: 10.1111/j.1365-2567.2006.02431.x
    • (2006) Immunology , vol.119 , pp. 265-277
    • Laursen, O.1    Nielsen, M.2    Larsen, S.R.3    Barington, T.4
  • 26
    • 84925714250 scopus 로고    scopus 로고
    • IMGT/V-QUEST: An algorithm for Immunoglobulin and T cell receptor sequence analysis. Actes des Journes Ouvertes Biologie Informatique et Mathematiques
    • Brochet X, Lefranc MP, Giudicelli V. IMGT/V-QUEST: an algorithm for Immunoglobulin and T cell receptor sequence analysis. Actes des Journes Ouvertes Biologie, Informatique et Mathematiques. JOBIM 2007. 2007: 329-330.
    • (2007) JOBIM , vol.2007 , pp. 329-330
    • Brochet, X.1    Lefranc, M.P.2    Giudicelli, V.3
  • 27
    • 79958045471 scopus 로고    scopus 로고
    • IMGT/V-QUEST: IMGT standardized analysis of the immunoglobulin (IG) and T cell receptor (TR) nucleotide sequences
    • pdb- prot5633, PMID: 21632778
    • Giudicelli V, Brochet X, Lefranc MP. IMGT/V-QUEST: IMGT standardized analysis of the immunoglobulin (IG) and T cell receptor (TR) nucleotide sequences. Cold Spring Harb Protoc. 2011; 6: pdb- prot5633. doi: 10.1101/pdb.prot5633 PMID: 21632778
    • (2011) Cold Spring Harb Protoc , vol.6
    • Giudicelli, V.1    Brochet, X.2    Lefranc, M.P.3
  • 28
    • 84867350002 scopus 로고    scopus 로고
    • IMGT()tools for the nucleotide analysis of immunoglobulin (IG) and T cell receptor (TR) V-( D)-J repertoires, polymorphisms, and IG mutations: IMGT/VQUEST and IMGT/HighV-QUEST for NGS
    • PMID: 22665256
    • Alamyar E, Duroux P, Lefranc MP, Giudicelli V. IMGT() tools for the nucleotide analysis of immunoglobulin (IG) and T cell receptor (TR) V-(D)-J repertoires, polymorphisms, and IG mutations: IMGT/VQUEST and IMGT/HighV-QUEST for NGS. Methods Mol Biol. 2012; 882: 569-604. doi: 10.1007/978-1-61779-842-9-32 PMID: 22665256
    • (2012) Methods Mol Biol , vol.882 , pp. 569-604
    • Alamyar, E.1    Duroux, P.2    Lefranc, M.P.3    Giudicelli, V.4
  • 29
    • 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-Carneriro MM, Longo NS, Russ DE, Sun HW, Lipsky PE. Characterization of the Human IG Heavy Chain Antigen Binding Complementarity Determining Region 3 Using a Newly Developed Software Algorithm, JOINSOLVER. The Journal of Immunology. 2004; 172: 6790-6802. doi: 10.4049/jimmunol.172.11.6790
    • (2004) The Journal of Immunology , vol.172 , pp. 6790-6802
    • Souto-Carneriro, M.M.1    Longo, N.S.2    Russ, D.E.3    Sun, H.W.4    Lipsky, P.E.5
  • 30
    • 9644277298 scopus 로고    scopus 로고
    • IMGT/JunctionAnalysis: The first tool for the analysis of the immunoglobulin and T-cell receptor complex V-J and V-D-J JUNCTIONs
    • Monod MY, Giudicelli V, Chaume D, Lefranc MP. IMGT/JunctionAnalysis: the first tool for the analysis of the immunoglobulin and T-cell receptor complex V-J and V-D-J JUNCTIONs. Bioinformatics. 2004; 20: i379-i385. doi: 10.1093/bioinformatics/bth945
    • (2004) Bioinformatics , vol.20 , pp. i379-i385
    • Monod, M.Y.1    Giudicelli, V.2    Chaume, D.3    Lefranc, M.P.4
  • 31
    • 79958026088 scopus 로고    scopus 로고
    • IMGT/junctionanalysis: IMGT standardized analysis of the V-J and V-D-J junctions of the rearranged immunoglobulins (IG) and T cell receptors (TR)
    • Giudicelli V, Lefranc MP. IMGT/junctionanalysis: IMGT standardized analysis of the V-J and V-D-J junctions of the rearranged immunoglobulins (IG) and T cell receptors (TR). Cold Spring Harb Protoc. 2011; 6: 716-725.
    • (2011) Cold Spring Harb Protoc , vol.6 , pp. 716-725
    • Giudicelli, V.1    Lefranc, M.P.2
  • 32
    • 32544437698 scopus 로고    scopus 로고
    • SoDA: Implementation of a 3D alignment algorithm for inference of antigen receptor recombinations
    • PMID: 16357034
    • Volpe JM, Cowell LG, Kepler TB. SoDA: implementation of a 3D alignment algorithm for inference of antigen receptor recombinations. Bioinformatics 2006; 22: 438-444. doi: 10.1093/bioinformatics/btk004 PMID: 16357034
    • (2006) Bioinformatics , vol.22 , pp. 438-444
    • Volpe, J.M.1    Cowell, L.G.2    Kepler, T.B.3
  • 33
    • 84862269218 scopus 로고    scopus 로고
    • Expressed antibody repertoires in human cord blood cells: 454 sequencing and IMGT/High V-QUEST analysis of germline gene usage, junctional diversity, and somatic mutations
    • PMID: 22200891
    • Prabakaran P, Chen W, Singarayan MG, Stewart CC, Streaker E, Feng Y, et al. Expressed antibody repertoires in human cord blood cells: 454 sequencing and IMGT/High V-QUEST analysis of germline gene usage, junctional diversity, and somatic mutations. Immunogenetics. 2011; 64: 337-350. doi: 10.1007/s00251-011-0595-8 PMID: 22200891
    • (2011) Immunogenetics , vol.64 , pp. 337-350
    • Prabakaran, P.1    Chen, W.2    Singarayan, M.G.3    Stewart, C.C.4    Streaker, E.5    Feng, Y.6
  • 34
    • 84857011935 scopus 로고    scopus 로고
    • Divergent human populations show extensive shared IGK rearrangements in peripheral blood B-cells
    • PMID: 21789596
    • Jackson KJL, Wang Y, Gaeta BA, Pomat W, Siba P, Rimmer J, et al. Divergent human populations show extensive shared IGK rearrangements in peripheral blood B-cells. Immunogenetics. 2012; 64: 3-14. doi: 10.1007/s00251-011-0559-z PMID: 21789596
    • (2012) Immunogenetics , vol.64 , pp. 3-14
    • Jackson, K.J.L.1    Wang, Y.2    Gaeta, B.A.3    Pomat, W.4    Siba, P.5    Rimmer, J.6
  • 35
    • 84867834056 scopus 로고    scopus 로고
    • 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
    • Alamyar E, Giudicelli V, Li S, Duroux P, Lefranc MP. 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 Research. 2012; 8: 26.
    • (2012) Immunome Research , vol.8 , pp. 26
    • Alamyar, E.1    Giudicelli, V.2    Li, S.3    Duroux, P.4    Lefranc, M.P.5
  • 36
    • 84884165599 scopus 로고    scopus 로고
    • IMGT/HighV QUEST paradigm for T-cell receptor IMGT clonotype diverity and next generation repertoire immunoprofiling
    • Li S, Lefranc MP, Miles JJ, Alamyar E, Giudicelli V, Duroux P, et al. IMGT/HighV QUEST paradigm for T-cell receptor IMGT clonotype diverity and next generation repertoire immunoprofiling. Nature Communications. 2013; 4: 1-13.
    • (2013) Nature Communications , vol.4 , pp. 1-13
    • Li, S.1    Lefranc, M.P.2    Miles, J.J.3    Alamyar, E.4    Giudicelli, V.5    Duroux, P.6
  • 37
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • PMID: 19261174
    • Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology. 2009; 10: R25. doi: 10.1186/gb-2009-10-3-r25 PMID: 19261174
    • (2009) Genome Biology , vol.10 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 38
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: Discovering splice junctions with RNA-Seq
    • PMID: 19289445
    • Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009; 25: 1105-1111. doi: 10.1093/bioinformatics/btp120 PMID: 19289445
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 39
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • PMID: 20110278
    • Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010; 26: 841-842. doi: 10.1093/bioinformatics/btq033 PMID: 20110278
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 41
    • 0036954986 scopus 로고    scopus 로고
    • Genetic diversity of the immunoglobulin heavy chain VK region
    • Li H, Cui X, Pramanik S, Chimge NO. Genetic diversity of the immunoglobulin heavy chain VK region. Immunology Review. 2002; 190: 53-68. doi: 10.1034/j.1600-065X.2002.19005.x
    • (2002) Immunology Review , vol.190 , pp. 53-68
    • Li, H.1    Cui, X.2    Pramanik, S.3    Chimge, N.O.4
  • 43
    • 78651486046 scopus 로고    scopus 로고
    • Identification of fusion genes in breast cancer by paired-end RNA-sequencing
    • PMID: 21247443
    • Edgren H, Murumagi A, Kangaspeska S, Nicorici D, Hongisto V, Kleivi K, et al. Identification of fusion genes in breast cancer by paired-end RNA-sequencing. Genome Biology. 2011; 12: R6. doi: 10.1186/gb-2011-12-1-r6 PMID: 21247443
    • (2011) Genome Biology , vol.12 , pp. R6
    • Edgren, H.1    Murumagi, A.2    Kangaspeska, S.3    Nicorici, D.4    Hongisto, V.5    Kleivi, K.6
  • 45
    • 0026911327 scopus 로고
    • A simplified method of detection of clonal rearrangements of the T-cell receptor-gamma chain gene
    • PMID: 1342963
    • McCarthy KP, Sloane JP, Kabarowski JH, Matutes E, Wiedemann LM. A simplified method of detection of clonal rearrangements of the T-cell receptor-gamma chain gene. Diagn Mol Pathol. 1992; 1: 173-179. doi: 10.1097/00019606-199209000-00003 PMID: 1342963
    • (1992) Diagn Mol Pathol , vol.1 , pp. 173-179
    • McCarthy, K.P.1    Sloane, J.P.2    Kabarowski, J.H.3    Matutes, E.4    Wiedemann, L.M.5
  • 46
    • 0027753103 scopus 로고
    • Detection of clonal B-cell populations in paraffin-embedded tissues by polymerase chain reaction
    • Kppers R, Zhao M, Rajewsky K, Hansmann ML. Detection of clonal B-cell populations in paraffin-embedded tissues by polymerase chain reaction. Am J Pathol. 1993; 143: 230-239.
    • (1993) Am J Pathol , vol.143 , pp. 230-239
    • Kppers, R.1    Zhao, M.2    Rajewsky, K.3    Hansmann, M.L.4
  • 47
    • 0028910571 scopus 로고
    • Routine application of polymerase chain reaction in the diagnosis of monoclonality of B-cell lymphoid proliferations
    • PMID: 7735551
    • Achille A, Scarpa A, Montresor M, Scardoni M, Zamboni G, Chilosi M, et al. Routine application of polymerase chain reaction in the diagnosis of monoclonality of B-cell lymphoid proliferations. Diagn Mol Pathol. 1995; 4: 14-24. doi: 10.1097/00019606-199503000-00005 PMID: 7735551
    • (1995) Diagn Mol Pathol , vol.4 , pp. 14-24
    • Achille, A.1    Scarpa, A.2    Montresor, M.3    Scardoni, M.4    Zamboni, G.5    Chilosi, M.6
  • 48
    • 0025767278 scopus 로고
    • An improved method for detection of B-lymphoid clonality by polymerase chain reaction
    • PMID: 1909411
    • Deane M, McCarthy KP, Wiedemann LM, Norton JD. An improved method for detection of B-lymphoid clonality by polymerase chain reaction. Leukemia. 1991; 5: 726-730. PMID: 1909411
    • (1991) Leukemia , vol.5 , pp. 726-730
    • Deane, M.1    McCarthy, K.P.2    Wiedemann, L.M.3    Norton, J.D.4
  • 49
    • 9144265458 scopus 로고    scopus 로고
    • Design and standardization of PCR primers and protocols for detection of clonal immunoglobulin and T-cell receptor gene recombinations in suspect lymphoproliferations: Report of the BIOMED-2 Concerted Action BMH4-CT98-3936. Leukemia
    • Van Dongen JJM, Langerak AW, Brggemann M, Evans PAS, Hummel M, Lavender FL, et al. Design and standardization of PCR primers and protocols for detection of clonal immunoglobulin and T-cell receptor gene recombinations in suspect lymphoproliferations: report of the BIOMED-2 Concerted Action BMH4-CT98-3936. Leukemia: Official journal of the Leukemia Society of America, Leukemia Research Fund. 2003; 17: 2257-2317. doi: 10.1038/sj.leu.2403202
    • (2003) Official Journal of the Leukemia Society of America, Leukemia Research Fund , vol.17 , pp. 2257-2317
    • Van Dongen, J.J.M.1    Langerak, A.W.2    Brggemann, M.3    Evans, P.A.S.4    Hummel, M.5    Lavender, F.L.6
  • 50
    • 0027752682 scopus 로고
    • Detection of immunoglobulin heavy-chain gene rearrangements by Southern blot analysis: Recommendations for optimal results
    • PMID: 7902888
    • Beishuizen A, Verhoeven MA, Mol EJ, Breit TM, Wolvers-Tettero IL, Van Dongen JJ. Detection of immunoglobulin heavy-chain gene rearrangements by Southern blot analysis: recommendations for optimal results. Leukemia. 1993; 7: 2045-2053. PMID: 7902888
    • (1993) Leukemia , vol.7 , pp. 2045-2053
    • Beishuizen, A.1    Verhoeven, M.A.2    Mol, E.J.3    Breit, T.M.4    Wolvers-Tettero, I.L.5    Van Dongen, J.J.6
  • 51
    • 0027489873 scopus 로고
    • Southern blot patterns, frequencies, and junctional diversity of T-cell receptor-delta gene rearrangements in acute lymphoblastic leukemia
    • PMID: 8219197
    • Breit TM, Wolvers-Tettero IL, Beishuizen A, Verhoeven MA, VanWering ER, Van Dongen JJ. Southern blot patterns, frequencies, and junctional diversity of T-cell receptor-delta gene rearrangements in acute lymphoblastic leukemia. Blood. 1993; 82: 3063-3074. PMID: 8219197
    • (1993) Blood , vol.82 , pp. 3063-3074
    • Breit, T.M.1    Wolvers-Tettero, I.L.2    Beishuizen, A.3    Verhoeven, M.A.4    Vanwering, E.R.5    Van Dongen, J.J.6
  • 52
    • 33846492425 scopus 로고    scopus 로고
    • Polymerase chain reaction- based clonality testing in tissue samples with reactive lymphoproliferations: Usefulness and pitfalls. A report of the BIOMED-2 Concerted Action BMH4-CT98-3936
    • PMID: 17170729
    • Langerak AW, Molina TJ, Lavender FL, Pearson D, Flohr T, Sambade C, et al. Polymerase chain reaction- based clonality testing in tissue samples with reactive lymphoproliferations: usefulness and pitfalls. A report of the BIOMED-2 Concerted Action BMH4-CT98-3936. Leukemia. 2006; 21: 222-229. doi: 10.1038/sj.leu.2404482 PMID: 17170729
    • (2006) Leukemia , vol.21 , pp. 222-229
    • Langerak, A.W.1    Molina, T.J.2    Lavender, F.L.3    Pearson, D.4    Flohr, T.5    Sambade, C.6
  • 53
    • 33846528976 scopus 로고    scopus 로고
    • Improved reliability of lymphoma diagnostics via PCR-based clonality testing: Report of the BIOMED-2 Concerted Action BHM4-CT98-3936
    • PMID: 17170732
    • Van Krieken JHJM, Langerak AW, Macintyre EA, Kneba M, Hodges E, Sanz RG, et al. Improved reliability of lymphoma diagnostics via PCR-based clonality testing: report of the BIOMED-2 Concerted Action BHM4-CT98-3936. Leukemia. 2006; 21: 201-206. doi: 10.1038/sj.leu.2404467 PMID: 17170732
    • (2006) Leukemia , vol.21 , pp. 201-206
    • Van Krieken, J.H.J.M.1    Langerak, A.W.2    Macintyre, E.A.3    Kneba, M.4    Hodges, E.5    Sanz, R.G.6
  • 54
    • 77956906544 scopus 로고    scopus 로고
    • Pitfalls in TCR gene clonality testing: Teaching cases
    • PMID: 19669208
    • Groenen PJ, Langerak AW, van Dongen JJ, van Krieken JH. Pitfalls in TCR gene clonality testing: teaching cases. J Hematop. 2008; 1: 97-109. doi: 10.1007/s12308-008-0013-9 PMID: 19669208
    • (2008) J Hematop , vol.1 , pp. 97-109
    • Groenen, P.J.1    Langerak, A.W.2    Van Dongen, J.J.3    Van Krieken, J.H.4
  • 56
    • 11144356992 scopus 로고    scopus 로고
    • Remarkably similar antigen receptors among a subset of patients with chronic lymphocytic leukemia
    • PMID: 15057307
    • Ghiotto F, Fais F, Valetto A, Albesiano E, Hashimoto S, Dono MR, et al. Remarkably similar antigen receptors among a subset of patients with chronic lymphocytic leukemia. J Clin Invest. 2004; 113: 1008-1016. doi: 10.1172/JCI19399 PMID: 15057307
    • (2004) J Clin Invest , vol.113 , pp. 1008-1016
    • Ghiotto, F.1    Fais, F.2    Valetto, A.3    Albesiano, E.4    Hashimoto, S.5    Dono, M.R.6
  • 57
    • 4344704897 scopus 로고    scopus 로고
    • Multiple distinct sets of stereotyped antigen receptors indicate a role for antigen in promoting chronic lymphocytic leukemia
    • PMID: 15314077
    • Messmer BT, Albesiano E, Efremov DG, Ghiotto F, Allen SL, Kolitz J, et al. Multiple distinct sets of stereotyped antigen receptors indicate a role for antigen in promoting chronic lymphocytic leukemia. J Exp Med. 2004; 200: 519-525. doi: 10.1084/jem.20040544 PMID: 15314077
    • (2004) J Exp Med , vol.200 , pp. 519-525
    • Messmer, B.T.1    Albesiano, E.2    Efremov, D.G.3    Ghiotto, F.4    Allen, S.L.5    Kolitz, J.6
  • 58
    • 7244232709 scopus 로고    scopus 로고
    • Subsets with restricted immunoglobulin gene rearrangement features indicate a role for antigen selection in the development of chronic lymphocytic leukemia
    • PMID: 15217826
    • Tobin G, Thunberg U, Karlsson K, Murray F, Laurell A, Willander K, et al. Subsets with restricted immunoglobulin gene rearrangement features indicate a role for antigen selection in the development of chronic lymphocytic leukemia. Blood. 2004; 104: 2879-2885. doi: 10.1182/blood-2004-01-0132 PMID: 15217826
    • (2004) Blood , vol.104 , pp. 2879-2885
    • Tobin, G.1    Thunberg, U.2    Karlsson, K.3    Murray, F.4    Laurell, A.5    Willander, K.6
  • 59
    • 10744230550 scopus 로고    scopus 로고
    • Chronic lymphocytic leukemias utilizing the VH3-21 gene display highly restricted Vlambda2-14 gene use and homologous CDR3s: Implicating recognition of a common antigen epitope
    • PMID: 12586612
    • Tobin G, Thunberg U, Johnson A, Eriksson I, Sderberg O, Karlsson K, et al. Chronic lymphocytic leukemias utilizing the VH3-21 gene display highly restricted Vlambda2-14 gene use and homologous CDR3s: implicating recognition of a common antigen epitope. Blood. 2003; 101: 4952-4957. doi: 10.1182/blood-2002-11-3485 PMID: 12586612
    • (2003) Blood , vol.101 , pp. 4952-4957
    • Tobin, G.1    Thunberg, U.2    Johnson, A.3    Eriksson, I.4    Sderberg, O.5    Karlsson, K.6
  • 60
    • 84859256604 scopus 로고    scopus 로고
    • Inhibiting B-cell receptor signaling pathways in chronic lymphocytic leukemia
    • PMID: 22105489
    • Burger JA. Inhibiting B-cell receptor signaling pathways in chronic lymphocytic leukemia. Curr Hematol Malig Rep. 2012; 7: 26-33. doi: 10.1007/s11899-011-0104-z PMID: 22105489
    • (2012) Curr Hematol Malig Rep , vol.7 , pp. 26-33
    • Burger, J.A.1
  • 61
    • 4944244255 scopus 로고    scopus 로고
    • Chronic lymphocytic leukemia B-cells of more than 1 per cent of patients express virtually identical immunoglobulins
    • PMID: 15217828
    • Widhopf GF, Rassenti LZ, Toy TL, Gribben JG, Wierda WG, Kipps TJ. Chronic lymphocytic leukemia B-cells of more than 1 per cent of patients express virtually identical immunoglobulins. Blood. 2004; 104: 2499-2504. doi: 10.1182/blood-2004-03-0818 PMID: 15217828
    • (2004) Blood , vol.104 , pp. 2499-2504
    • Widhopf, G.F.1    Rassenti, L.Z.2    Toy, T.L.3    Gribben, J.G.4    Wierda, W.G.5    Kipps, T.J.6
  • 62
    • 38949111420 scopus 로고    scopus 로고
    • Impact of immune thrombocytopenia on the clinical course of chronic lymphocytic leukemia
    • PMID: 17986663
    • Visco C, Ruggeri M, Evangelista ML, Stasi R, Zanotti R, Giaretta I, et al. Impact of immune thrombocytopenia on the clinical course of chronic lymphocytic leukemia. Blood. 2008; 111: 1110-1116. doi: 10.1182/blood-2007-09-111492 PMID: 17986663
    • (2008) Blood , vol.111 , pp. 1110-1116
    • Visco, C.1    Ruggeri, M.2    Evangelista, M.L.3    Stasi, R.4    Zanotti, R.5    Giaretta, I.6
  • 63
    • 77954948781 scopus 로고    scopus 로고
    • ZAP-70 expression is associated with increased risk of autoimmune cytopenias in CLL patients
    • PMID: 20575031
    • Zanotti R, Frattini F, Ghia P, Visco C, Zam A, Perbellini O, et al. ZAP-70 expression is associated with increased risk of autoimmune cytopenias in CLL patients. Am J Hematol. 2010; 85: 494-498. doi: 10.1002/ajh.21737 PMID: 20575031
    • (2010) Am J Hematol , vol.85 , pp. 494-498
    • Zanotti, R.1    Frattini, F.2    Ghia, P.3    Visco, C.4    Zam, A.5    Perbellini, O.6
  • 64
    • 82555165949 scopus 로고    scopus 로고
    • The microenvironment in mantle cell lymphoma: Cellular and molecular pathways and emerging targeted therapies
    • PMID: 21945516
    • Burger JA, Ford RJ. The microenvironment in mantle cell lymphoma: cellular and molecular pathways and emerging targeted therapies. Semin Cancer Biol. 2011; 21: 308-312. doi: 10.1016/j.semcancer.2011.09.006 PMID: 21945516
    • (2011) Semin Cancer Biol , vol.21 , pp. 308-312
    • Burger, J.A.1    Ford, R.J.2
  • 65
    • 33644851486 scopus 로고    scopus 로고
    • Genomic and expression profiling identifies the B-cell associated tyrosine kinase Syk as a possible therapeutic target in mantle cell lymphoma
    • PMID: 16409295
    • Rinaldi A, Kwee I, Taborelli M, Largo C, Uccella S, Martin V, et al. Genomic and expression profiling identifies the B-cell associated tyrosine kinase Syk as a possible therapeutic target in mantle cell lymphoma. British Journal of Haematology. 2006; 132: 303-316. doi: 10.1111/j.1365-2141.2005.05883.x PMID: 16409295
    • (2006) British Journal of Haematology , vol.132 , pp. 303-316
    • Rinaldi, A.1    Kwee, I.2    Taborelli, M.3    Largo, C.4    Uccella, S.5    Martin, V.6
  • 66
    • 80052929598 scopus 로고    scopus 로고
    • Is there a role for antigen selection in mantle cell lymphoma? Immunogenetic support from a series of 807 cases
    • PMID: 21791422
    • Hadzidimitriou A, Agathangelidis A, Darzentas N, Murray F, Delfau-Larue MH, Pedersen LB, et al. Is there a role for antigen selection in mantle cell lymphoma? Immunogenetic support from a series of 807 cases. Blood. 2011; 118: 3088-3095. doi: 10.1182/blood-2011-03-343434 PMID: 21791422
    • (2011) Blood , vol.118 , pp. 3088-3095
    • Hadzidimitriou, A.1    Agathangelidis, A.2    Darzentas, N.3    Murray, F.4    Delfau-Larue, M.H.5    Pedersen, L.B.6
  • 67
    • 79960917689 scopus 로고    scopus 로고
    • Phospho-proteomic analysis of mantle cell lymphoma cells suggests a pro-survival role of B-cell receptor signaling
    • Pighi C, Gu TL, Dalai I, Barbi S, Parolini C, Bertolaso A, et al. Phospho-proteomic analysis of mantle cell lymphoma cells suggests a pro-survival role of B-cell receptor signaling. Cell Oncol. 2011; 34: 151-153. doi: 10.1007/s13402-011-0019-7
    • (2011) Cell Oncol , vol.34 , pp. 151-153
    • Pighi, C.1    Gu, T.L.2    Dalai, I.3    Barbi, S.4    Parolini, C.5    Bertolaso, A.6
  • 68
    • 41349110211 scopus 로고    scopus 로고
    • SYK-dependent tonic B-cell receptor signaling is a rational treatment target in diffuse large B-cell lymphoma
    • PMID: 18006696
    • Chen L, Monti S, Juszczynski P, Daley J, Chen W, Witzig TE, et al. SYK-dependent tonic B-cell receptor signaling is a rational treatment target in diffuse large B-cell lymphoma. Blood. 2008; 111: 2230-2237. doi: 10.1182/blood-2007-07-100115 PMID: 18006696
    • (2008) Blood , vol.111 , pp. 2230-2237
    • Chen, L.1    Monti, S.2    Juszczynski, P.3    Daley, J.4    Chen, W.5    Witzig, T.E.6
  • 69
    • 77956551877 scopus 로고    scopus 로고
    • High-throughput immunoglobulin repertoire analysis distinguishes between human IgM memory and switched memory B-cell populations
    • PMID: 20457872
    • Wu YC, Peeling 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. doi: 10.1182/blood-2010-03-275859 PMID: 20457872
    • (2010) Blood , vol.116 , pp. 1070-1078
    • Wu, Y.C.1    Peeling, D.2    Leong, H.S.3    Martin, V.4    Ademokun, A.A.5    Dunn-Walters, D.K.6
  • 70
    • 84860494449 scopus 로고    scopus 로고
    • Antibody repertoires in humanized NOD-scid-IL2Rnull mice and human B cells reveals human-like diversification and tolerance checkpoints in the mouse
    • PMID: 22558161
    • Ippolito GC, Hoi KH, Reddy ST, Carroll SM, Ge X, Rogosch T, et al. Antibody repertoires in humanized NOD-scid-IL2Rnull mice and human B cells reveals human-like diversification and tolerance checkpoints in the mouse. PLoS One. 2012; 7: e35497. doi: 10.1371/journal.pone.0035497 PMID: 22558161
    • (2012) PLoS One , vol.7 , pp. e35497
    • Ippolito, G.C.1    Hoi, K.H.2    Reddy, S.T.3    Carroll, S.M.4    Ge, X.5    Rogosch, T.6
  • 71
    • 77954601328 scopus 로고    scopus 로고
    • Measurement and clinical monitoring of human lymphocyte clonality by massively parallel VDJ pyrosequencing
    • Boyd SD, Marshall EL, Merker JD, Maniar JM, Zhang LN, Sahaf B, et al. Measurement and clinical monitoring of human lymphocyte clonality by massively parallel VDJ pyrosequencing. Sci Transl Med. 2009; 1: 12ra23. doi: 10.1126/scitranslmed.3000540
    • (2009) Sci Transl Med , vol.1 , pp. 12ra23
    • Boyd, S.D.1    Marshall, E.L.2    Merker, J.D.3    Maniar, J.M.4    Zhang, L.N.5    Sahaf, B.6
  • 72
    • 84925791057 scopus 로고    scopus 로고
    • Accessed 2015 Gen 23
    • The HPC Polito Project. Available: http://www.hpc.polito.it. Accessed 2015 Gen 23.
    • The HPC Polito Project


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