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Volumn 42, Issue 16, 2014, Pages

Impact of next-generation sequencing error on analysis of barcoded plasmid libraries of known complexity and sequence

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; AMPLICON; ARTICLE; BIOINFORMATICS; CALCULATION; DNA BASE COMPOSITION; MOLECULAR LIBRARY; NEXT GENERATION SEQUENCING; PLASMID; POLYMERASE CHAIN REACTION; RELIABILITY; REPRODUCIBILITY; SEQUENCE ANALYSIS; STOCHASTIC MODEL; SYSTEMATIC ERROR; ARTIFACT; DNA SEQUENCE; GENE LIBRARY; HIGH THROUGHPUT SEQUENCING; PROCEDURES;

EID: 84921354094     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku607     Document Type: Article
Times cited : (29)

References (62)
  • 7
    • 80052050274 scopus 로고    scopus 로고
    • Hematopoietic stem cell gene therapy for adenosine deaminase-deficient severe combined immunodeficiency leads to long-term immunological recovery and metabolic correction
    • Gaspar, H.B., Cooray, S., Gilmour, K.C., Parsley, K.L., Zhang, F., Adams, S., Bjorkegren, E., Bayford, J., Brown, L., Davies, E.G. et al. (2011) Hematopoietic stem cell gene therapy for adenosine deaminase-deficient severe combined immunodeficiency leads to long-term immunological recovery and metabolic correction. Sci. Transl. Med., 3, 97ra80.
    • (2011) Sci. Transl. Med. , vol.3 , pp. 97ra80
    • Gaspar, H.B.1    Cooray, S.2    Gilmour, K.C.3    Parsley, K.L.4    Zhang, F.5    Adams, S.6    Bjorkegren, E.7    Bayford, J.8    Brown, L.9    Davies, E.G.10
  • 8
    • 33645734405 scopus 로고    scopus 로고
    • Correction of X-linked chronic granulomatous disease by gene therapy, augmented by insertional activation of MDS1-EVI1, PRDM16 or SETBP1
    • Ott, M.G., Schmidt, M., Schwarzwaelder, K., Stein, S., Siler, U., Koehl, U., Glimm, H., Kühlcke, K., Schilz, A., Kunkel, H. et al. (2006) Correction of X-linked chronic granulomatous disease by gene therapy, augmented by insertional activation of MDS1-EVI1, PRDM16 or SETBP1. Nat. Med., 12, 401-409.
    • (2006) Nat. Med. , vol.12 , pp. 401-409
    • Ott, M.G.1    Schmidt, M.2    Schwarzwaelder, K.3    Stein, S.4    Siler, U.5    Koehl, U.6    Glimm, H.7    Kühlcke, K.8    Schilz, A.9    Kunkel, H.10
  • 13
    • 80051775476 scopus 로고    scopus 로고
    • T cells with chimeric antigen receptors have potent antitumor effects and can establish memory in patients with advanced leukemia
    • Kalos, M., Levine, B.L., Porter, D.L., Katz, S., Grupp, S.a., Bagg, A. and June, C.H. (2011) T cells with chimeric antigen receptors have potent antitumor effects and can establish memory in patients with advanced leukemia. Sci. Transl. Med., 3, 95ra73.
    • (2011) Sci. Transl. Med. , vol.3 , pp. 95ra73
    • Kalos, M.1    Levine, B.L.2    Porter, D.L.3    Katz, S.4    Grupp, S.A.5    Bagg, A.6    June, C.H.7
  • 15
    • 77953955389 scopus 로고    scopus 로고
    • Dynamics of gene-modified progenitor cells analyzed by tracking retroviral integration sites in a human SCID-X1 gene therapy trial
    • Wang, G.P., Berry, C.C., Malani, N., Leboulch, P., Fischer, A., Hacein-Bey-Abina, S., Cavazzana-Calvo, M. and Bushman, F.D. (2010) Dynamics of gene-modified progenitor cells analyzed by tracking retroviral integration sites in a human SCID-X1 gene therapy trial. Blood, 115, 4356-4366.
    • (2010) Blood , vol.115 , pp. 4356-4366
    • Wang, G.P.1    Berry, C.C.2    Malani, N.3    Leboulch, P.4    Fischer, A.5    Hacein-Bey-Abina, S.6    Cavazzana-Calvo, M.7    Bushman, F.D.8
  • 19
    • 76249131912 scopus 로고    scopus 로고
    • Genomic instability and myelodysplasia with monosomy 7 consequent to EVI1 activation after gene therapy for chronic granulomatous disease
    • Stein, S., Ott, M.G., Schultze-Strasser, S., Jauch, A., Burwinkel, B., Kinner, A., Schmidt, M., Krämer, A., Schwäble, J., Glimm, H. et al. (2010) Genomic instability and myelodysplasia with monosomy 7 consequent to EVI1 activation after gene therapy for chronic granulomatous disease. Nat. Med., 16, 198-204.
    • (2010) Nat. Med. , vol.16 , pp. 198-204
    • Stein, S.1    Ott, M.G.2    Schultze-Strasser, S.3    Jauch, A.4    Burwinkel, B.5    Kinner, A.6    Schmidt, M.7    Krämer, A.8    Schwäble, J.9    Glimm, H.10
  • 21
    • 53249105450 scopus 로고    scopus 로고
    • Flanking-sequence exponential anchored-polymerase chain reaction amplification: A sensitive and highly specific method for detecting retroviral integrant-host-junction sequences
    • Pule, M.A., Rousseau, A., Vera, J., Heslop, H.E., Brenner, M.K. and Vanin, E.F. (2008) Flanking-sequence exponential anchored-polymerase chain reaction amplification: a sensitive and highly specific method for detecting retroviral integrant-host-junction sequences. Cytotherapy, 10, 526-539.
    • (2008) Cytotherapy , vol.10 , pp. 526-539
    • Pule, M.A.1    Rousseau, A.2    Vera, J.3    Heslop, H.E.4    Brenner, M.K.5    Vanin, E.F.6
  • 24
    • 84872820248 scopus 로고    scopus 로고
    • High efficiency restriction enzyme-free linear amplification-mediated polymerase chain reaction approach for tracking lentiviral integration sites does not abrogate retrieval bias
    • Wu, C., Jares, A., Winkler, T., Xie, J., Metais, J.-Y. and Dunbar, C.E. (2013) High efficiency restriction enzyme-free linear amplification-mediated polymerase chain reaction approach for tracking lentiviral integration sites does not abrogate retrieval bias. Hum. Gene Ther., 24, 38-47.
    • (2013) Hum. Gene Ther. , vol.24 , pp. 38-47
    • Wu, C.1    Jares, A.2    Winkler, T.3    Xie, J.4    Metais, J.-Y.5    Dunbar, C.E.6
  • 26
    • 84873560054 scopus 로고    scopus 로고
    • Comparison of sequencing platforms for single nucleotide variant calls in a human sample
    • Ratan, A., Miller, W., Guillory, J., Stinson, J., Seshagiri, S. and Schuster, S.C. (2013) Comparison of sequencing platforms for single nucleotide variant calls in a human sample. PLoS One, 8, e55089.
    • (2013) PLoS One , vol.8 , pp. e55089
    • Ratan, A.1    Miller, W.2    Guillory, J.3    Stinson, J.4    Seshagiri, S.5    Schuster, S.C.6
  • 27
    • 79956066785 scopus 로고    scopus 로고
    • Comparison of sequence reads obtained from three next-generation sequencing platforms
    • Suzuki, S., Ono, N., Furusawa, C., Ying, B.-W. and Yomo, T. (2011) Comparison of sequence reads obtained from three next-generation sequencing platforms. PLoS One, 6, e19534.
    • (2011) PLoS One , vol.6 , pp. e19534
    • Suzuki, S.1    Ono, N.2    Furusawa, C.3    Ying, B.-W.4    Yomo, T.5
  • 28
    • 77958575588 scopus 로고    scopus 로고
    • Ultra high throughput sequencing in human DNA variation detection: A comparative study on the NDUFA3-PRPF31 region
    • Benaglio, P. and Rivolta, C. (2010) Ultra high throughput sequencing in human DNA variation detection: a comparative study on the NDUFA3-PRPF31 region. PLoS One, 5, e13071.
    • (2010) PLoS One , vol.5 , pp. e13071
    • Benaglio, P.1    Rivolta, C.2
  • 31
    • 84888212251 scopus 로고    scopus 로고
    • Analysis of the clonal growth and differentiation dynamics of primitive barcoded human cord blood cells in NSG mice
    • Cheung, A.M.S., Nguyen, L. V, Carles, A., Beer, P., Miller, P.H., Knapp, D.J.H.F., Dhillon, K., Hirst, M. and Eaves, C.J. (2013) Analysis of the clonal growth and differentiation dynamics of primitive barcoded human cord blood cells in NSG mice. Blood, 122, 3129-3137.
    • (2013) Blood , vol.122 , pp. 3129-3137
    • Cheung, A.M.S.1    Nguyen, L.V.2    Carles, A.3    Beer, P.4    Miller, P.H.5    Knapp, D.J.H.F.6    Dhillon, K.7    Hirst, M.8    Eaves, C.J.9
  • 32
    • 84886924368 scopus 로고    scopus 로고
    • Heterogeneity of young and aged murine hematopoietic stem cells revealed by quantitative clonal analysis using cellular barcoding
    • Verovskaya, E., Broekhuis, M.J.C., Zwart, E., Ritsema, M., van Os, R., de Haan, G. and Bystrykh, L. V (2013) Heterogeneity of young and aged murine hematopoietic stem cells revealed by quantitative clonal analysis using cellular barcoding. Blood, 122, 523-532.
    • (2013) Blood , vol.122 , pp. 523-532
    • Verovskaya, E.1    Broekhuis, M.J.C.2    Zwart, E.3    Ritsema, M.4    Van Os, R.5    De Haan, G.6    Bystrykh, L.V.7
  • 34
    • 84887892419 scopus 로고    scopus 로고
    • Arrayed lentiviral barcoding for quantification analysis of hematopoietic dynamics
    • Grosselin, J., Sii-Felice, K., Payen, E., Chretien, S., Roux, D.T.-L. and Leboulch, P. (2013) Arrayed lentiviral barcoding for quantification analysis of hematopoietic dynamics. Stem Cells, 31, 2162-2171.
    • (2013) Stem Cells , vol.31 , pp. 2162-2171
    • Grosselin, J.1    Sii-Felice, K.2    Payen, E.3    Chretien, S.4    Roux, D.T.-L.5    Leboulch, P.6
  • 35
    • 80054719497 scopus 로고    scopus 로고
    • Tracking single hematopoietic stem cells in vivo using high-throughput sequencing in conjunction with viral genetic barcoding
    • Lu, R., Neff, N.F., Quake, S.R. and Weissman, I.L. (2011) Tracking single hematopoietic stem cells in vivo using high-throughput sequencing in conjunction with viral genetic barcoding. Nat. Biotechnol., 29, 928-933.
    • (2011) Nat. Biotechnol. , vol.29 , pp. 928-933
    • Lu, R.1    Neff, N.F.2    Quake, S.R.3    Weissman, I.L.4
  • 37
    • 77952009127 scopus 로고    scopus 로고
    • Lymphomagenesis in SCID-X1 mice following lentivirus-mediated phenotype correction independent of insertional mutagenesis and gammac overexpression
    • Ginn, S.L., Liao, S.H.Y., Dane, A.P., Hu, M., Hyman, J., Finnie, J.W., Zheng, M., Cavazzana-Calvo, M., Alexander, S.I., Thrasher, A.J. et al. (2010) Lymphomagenesis in SCID-X1 mice following lentivirus-mediated phenotype correction independent of insertional mutagenesis and gammac overexpression. Mol. Ther., 18, 965-976.
    • (2010) Mol. Ther. , vol.18 , pp. 965-976
    • Ginn, S.L.1    Liao, S.H.Y.2    Dane, A.P.3    Hu, M.4    Hyman, J.5    Finnie, J.W.6    Zheng, M.7    Cavazzana-Calvo, M.8    Alexander, S.I.9    Thrasher, A.J.10
  • 38
    • 0034040751 scopus 로고    scopus 로고
    • Gene transfer by lentiviral vectors is limited by nuclear translocation and rescued by HIV-1 pol sequences
    • Follenzi, A., Ailles, L.E., Bakovic, S., Geuna, M. and Naldini, L. (2000) Gene transfer by lentiviral vectors is limited by nuclear translocation and rescued by HIV-1 pol sequences. Nat. Genet., 25, 217-222.
    • (2000) Nat. Genet. , vol.25 , pp. 217-222
    • Follenzi, A.1    Ailles, L.E.2    Bakovic, S.3    Geuna, M.4    Naldini, L.5
  • 39
    • 84934438960 scopus 로고    scopus 로고
    • UNAFold: Software for nucleic acid folding and hybridization
    • Markham, N.R. and Zuker, M. (2008) UNAFold: software for nucleic acid folding and hybridization. Methods Mol. Biol., 453, 3-31.
    • (2008) Methods Mol. Biol. , vol.453 , pp. 3-31
    • Markham, N.R.1    Zuker, M.2
  • 40
    • 0002051540 scopus 로고    scopus 로고
    • BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT
    • Hall, T. (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser., 41, 95-98.
    • (1999) Nucleic Acids Symp. Ser. , vol.41 , pp. 95-98
    • Hall, T.1
  • 41
    • 0002167717 scopus 로고
    • Demonstration of the Expand PCR System's greater fidelity and higher yields with a lacI-based PCR fidelity assay
    • Frey, B. and Suppmann, B. (1995) Demonstration of the Expand PCR System's greater fidelity and higher yields with a lacI-based PCR fidelity assay. Biochemica, 2, 34-35.
    • (1995) Biochemica , vol.2 , pp. 34-35
    • Frey, B.1    Suppmann, B.2
  • 42
    • 84903646201 scopus 로고    scopus 로고
    • Deep sequencing of evolving pathogen populations: Applications, errors, and bioinformatic solutions
    • McElroy, K., Thomas, T. and Luciani, F. (2014) Deep sequencing of evolving pathogen populations: applications, errors, and bioinformatic solutions. Microb. Inform. Exp., 4, 1.
    • (2014) Microb. Inform. Exp. , vol.4 , pp. 1
    • McElroy, K.1    Thomas, T.2    Luciani, F.3
  • 44
    • 84893810443 scopus 로고    scopus 로고
    • Error analysis of deep sequencing of phage libraries: Peptides censored in sequencing
    • Matochko, W.L. and Derda, R. (2013) Error analysis of deep sequencing of phage libraries: peptides censored in sequencing. Comput. Math. Methods Med., 2013, 491612.
    • (2013) Comput. Math. Methods Med. , vol.2013 , pp. 491612
    • Matochko, W.L.1    Derda, R.2
  • 45
    • 67650074197 scopus 로고    scopus 로고
    • Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing
    • Qu, W., Hashimoto, S.-I. and Morishita, S. (2009) Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing. Genome Res., 19, 1309-1315.
    • (2009) Genome Res. , vol.19 , pp. 1309-1315
    • Qu, W.1    Hashimoto, S.-I.2    Morishita, S.3
  • 46
    • 78649901946 scopus 로고    scopus 로고
    • Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies
    • Zagordi, O., Klein, R., Däumer, M. and Beerenwinkel, N. (2010) Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies. Nucleic Acids Res., 38, 7400-7409.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 7400-7409
    • Zagordi, O.1    Klein, R.2    Däumer, M.3    Beerenwinkel, N.4
  • 48
    • 84870027011 scopus 로고    scopus 로고
    • Ultrafast clustering algorithms for metagenomic sequence analysis
    • Li, W., Fu, L., Niu, B., Wu, S. and Wooley, J. (2012) Ultrafast clustering algorithms for metagenomic sequence analysis. Brief. Bioinform., 13, 656-668.
    • (2012) Brief. Bioinform. , vol.13 , pp. 656-668
    • Li, W.1    Fu, L.2    Niu, B.3    Wu, S.4    Wooley, J.5
  • 49
    • 84874964797 scopus 로고    scopus 로고
    • Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data
    • Beerenwinkel, N., Günthard, H.F., Roth, V. and Metzner, K.J. (2012) Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data. Front. Microbiol., 3, 329.
    • (2012) Front. Microbiol. , vol.3 , pp. 329
    • Beerenwinkel, N.1    Günthard, H.F.2    Roth, V.3    Metzner, K.J.4
  • 50
    • 80455126001 scopus 로고    scopus 로고
    • Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems
    • Minoche, A.E., Dohm, J.C. and Himmelbauer, H. (2011) Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems. Genome Biol., 12, R112.
    • (2011) Genome Biol. , vol.12 , pp. R112
    • Minoche, A.E.1    Dohm, J.C.2    Himmelbauer, H.3
  • 51
    • 79751526431 scopus 로고    scopus 로고
    • Identification of errors introduced during high throughput sequencing of the T cell receptor repertoire
    • Nguyen, P., Ma, J., Pei, D., Obert, C., Cheng, C. and Geiger, T.L. (2011) Identification of errors introduced during high throughput sequencing of the T cell receptor repertoire. BMC Genomics, 12, 106.
    • (2011) BMC Genomics , vol.12 , pp. 106
    • Nguyen, P.1    Ma, J.2    Pei, D.3    Obert, C.4    Cheng, C.5    Geiger, T.L.6
  • 54
    • 70350023532 scopus 로고    scopus 로고
    • Improved base calling for the Illumina Genome Analyzer using machine learning strategies
    • Kircher, M., Stenzel, U. and Kelso, J. (2009) Improved base calling for the Illumina Genome Analyzer using machine learning strategies. Genome Biol., 10, R83.
    • (2009) Genome Biol. , vol.10 , pp. R83
    • Kircher, M.1    Stenzel, U.2    Kelso, J.3
  • 55
    • 52649157765 scopus 로고    scopus 로고
    • Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
    • Dohm, J.C., Lottaz, C., Borodina, T. and Himmelbauer, H. (2008) Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res., 36, e105.
    • (2008) Nucleic Acids Res. , vol.36 , pp. e105
    • Dohm, J.C.1    Lottaz, C.2    Borodina, T.3    Himmelbauer, H.4
  • 57
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead, B., Trapnell, C., Pop, M. and Salzberg, S.L. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
    • (2009) Genome Biol. , vol.10 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 61
    • 84862961025 scopus 로고    scopus 로고
    • High-throughput VDJ sequencing for quantification of minimal residual disease in chronic lymphocytic leukemia and immune reconstitution assessment
    • Logan, A.C., Gao, H., Wang, C., Sahaf, B., Jones, C.D., Marshall, E.L., Buño, I., Armstrong, R., Fire, A.Z., Weinberg, K.I. et al. (2011) High-throughput VDJ sequencing for quantification of minimal residual disease in chronic lymphocytic leukemia and immune reconstitution assessment. Proc. Natl Acad. Sci. U.S.A., 108, 21194-21199.
    • (2011) Proc. Natl Acad. Sci. U.S.A. , vol.108 , pp. 21194-21199
    • Logan, A.C.1    Gao, H.2    Wang, C.3    Sahaf, B.4    Jones, C.D.5    Marshall, E.L.6    Buño, I.7    Armstrong, R.8    Fire, A.Z.9    Weinberg, K.I.10


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