메뉴 건너뛰기




Volumn 1, Issue 5, 2011, Pages 413-418

Ultra-deep sequencing for the analysis of viral populations

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; HAPLOTYPE; NONHUMAN; POLYMERASE CHAIN REACTION; POPULATION STRUCTURE; PRIORITY JOURNAL; STATISTICAL ANALYSIS; VIRAL GENETICS; VIRUS MUTATION;

EID: 81755185962     PISSN: 18796257     EISSN: 18796265     Source Type: Journal    
DOI: 10.1016/j.coviro.2011.07.008     Document Type: Review
Times cited : (135)

References (44)
  • 1
    • 0015133749 scopus 로고
    • Selforganization of matter and the evolution of biological macromolecules
    • M. Eigen Selforganization of matter and the evolution of biological macromolecules Naturwissenschaften 58 1971 465 523
    • (1971) Naturwissenschaften , vol.58 , pp. 465-523
    • Eigen, M.1
  • 2
    • 0030747157 scopus 로고    scopus 로고
    • RNA virus mutations and fitness for survival
    • E. Domingo, and J.J. Holland RNA virus mutations and fitness for survival Annu Rev Microbiol 51 1997 151 178
    • (1997) Annu Rev Microbiol , vol.51 , pp. 151-178
    • Domingo, E.1    Holland, J.J.2
  • 5
    • 31144465690 scopus 로고    scopus 로고
    • Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population
    • M. Vignuzzi, J.K. Stone, J.J. Arnold, C.E. Cameron, and R. Andino Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population Nature 439 2006 344 348
    • (2006) Nature , vol.439 , pp. 344-348
    • Vignuzzi, M.1    Stone, J.K.2    Arnold, J.J.3    Cameron, C.E.4    Andino, R.5
  • 8
    • 48749086685 scopus 로고    scopus 로고
    • Minority HIV-1 drug resistance mutations are present in antiretroviral treatment-naïve populations and associate with reduced treatment efficacy
    • J.A. Johnson, J.-F. Li, X. Wei, J. Lipscomb, D. Irlbeck, C. Craig, A. Smith, D.E. Bennett, M. Monsour, and P. Sandstrom Minority HIV-1 drug resistance mutations are present in antiretroviral treatment-naïve populations and associate with reduced treatment efficacy PLoS Med 5 2008 e158
    • (2008) PLoS Med , vol.5 , pp. 158
    • Johnson, J.A.1    Li, J.-F.2    Wei, X.3    Lipscomb, J.4    Irlbeck, D.5    Craig, C.6    Smith, A.7    Bennett, D.E.8    Monsour, M.9    Sandstrom, P.10
  • 10
    • 52949096084 scopus 로고    scopus 로고
    • Next-generation DNA sequencing methods
    • E.R. Mardis Next-generation DNA sequencing methods Annu Rev Genomics Hum Genet 9 2008 387 402
    • (2008) Annu Rev Genomics Hum Genet , vol.9 , pp. 387-402
    • Mardis, E.R.1
  • 12
    • 34547643929 scopus 로고    scopus 로고
    • Characterization of mutation spectra with ultra-deep pyrosequencing: Application to HIV-1 drug resistance
    • C. Wang, Y. Mitsuya, B. Gharizadeh, M. Ronaghi, and R.W. Shafer Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance Genome Res 17 2007 1195 1201
    • (2007) Genome Res , vol.17 , pp. 1195-1201
    • Wang, C.1    Mitsuya, Y.2    Gharizadeh, B.3    Ronaghi, M.4    Shafer, R.W.5
  • 14
    • 67650682133 scopus 로고    scopus 로고
    • Low-abundance HIV drug-resistant viral variants in treatment-experienced persons correlate with historical antiretroviral use
    • T. Le, J. Chiarella, B.B. Simen, B. Hanczaruk, M. Egholm, M.L. Landry, K. Dieckhaus, M.I. Rosen, and M.J. Kozal Low-abundance HIV drug-resistant viral variants in treatment-experienced persons correlate with historical antiretroviral use PLoS ONE 4 2009 e6079
    • (2009) PLoS ONE , vol.4 , pp. 6079
    • Le, T.1    Chiarella, J.2    Simen, B.B.3    Hanczaruk, B.4    Egholm, M.5    Landry, M.L.6    Dieckhaus, K.7    Rosen, M.I.8    Kozal, M.J.9
  • 17
    • 78651260993 scopus 로고    scopus 로고
    • In-depth analysis of G-to-A hypermutation rate in HIV-1 env DNA induced by endogenous APOBEC3 proteins using massively parallel sequencing
    • S.A. Knoepfel, F.D. Giallonardo, M. Däumer, A. Thielen, and K.J. Metzner In-depth analysis of G-to-A hypermutation rate in HIV-1 env DNA induced by endogenous APOBEC3 proteins using massively parallel sequencing J Virol Methods 171 2011 329 338
    • (2011) J Virol Methods , vol.171 , pp. 329-338
    • Knoepfel, S.A.1    Giallonardo, F.D.2    Däumer, M.3    Thielen, A.4    Metzner, K.J.5
  • 18
    • 79851502517 scopus 로고    scopus 로고
    • Deep sequencing to infer HIV-1 co-receptor usage: Application to three clinical trials of maraviroc in treatment-experienced patients
    • L.C. Swenson, T. Mo, W.W.Y. Dong, X. Zhong, C.K. Woods, M.A. Jensen, A. Thielen, D. Chapman, M. Lewis, and I. James Deep sequencing to infer HIV-1 co-receptor usage: application to three clinical trials of maraviroc in treatment-experienced patients J Infect Dis 203 2011 237 245
    • (2011) J Infect Dis , vol.203 , pp. 237-245
    • Swenson, L.C.1    Mo, T.2    Dong, W.W.Y.3    Zhong, X.4    Woods, C.K.5    Jensen, M.A.6    Thielen, A.7    Chapman, D.8    Lewis, M.9    James, I.10
  • 19
  • 20
    • 78649469126 scopus 로고    scopus 로고
    • Structure of HIV-1 quasi-species as early indicator for switches of co-receptor tropism
    • J.N. Dybowski, D. Heider, and D. Hoffmann Structure of HIV-1 quasi-species as early indicator for switches of co-receptor tropism AIDS Res Ther 7 2010 41
    • (2010) AIDS Res Ther , vol.7 , pp. 41
    • Dybowski, J.N.1    Heider, D.2    Hoffmann, D.3
  • 21
    • 77952709675 scopus 로고    scopus 로고
    • Hepatitis C virus transmission bottlenecks analyzed by deep sequencing
    • G.P. Wang, S.A. Sherrill-Mix, K.-M. Chang, C. Quince, and F.D. Bushman Hepatitis C virus transmission bottlenecks analyzed by deep sequencing J Virol 84 2010 6218 6228
    • (2010) J Virol , vol.84 , pp. 6218-6228
    • Wang, G.P.1    Sherrill-Mix, S.A.2    Chang, K.-M.3    Quince, C.4    Bushman, F.D.5
  • 23
    • 59649083962 scopus 로고    scopus 로고
    • Use of massively parallel ultradeep pyrosequencing to characterize the genetic diversity of hepatitis B virus in drug-resistant and drug-naive patients and to detect minor variants in reverse transcriptase and hepatitis B S antigen
    • M. Solmone, D. Vincenti, M.C.F. Prosperi, A. Bruselles, G. Ippolito, and M.R. Capobianchi Use of massively parallel ultradeep pyrosequencing to characterize the genetic diversity of hepatitis B virus in drug-resistant and drug-naive patients and to detect minor variants in reverse transcriptase and hepatitis B S antigen J Virol 83 2009 1718 1726
    • (2009) J Virol , vol.83 , pp. 1718-1726
    • Solmone, M.1    Vincenti, D.2    Prosperi, M.C.F.3    Bruselles, A.4    Ippolito, G.5    Capobianchi, M.R.6
  • 24
    • 65649130002 scopus 로고    scopus 로고
    • Ultra-deep pyrosequencing of hepatitis B virus quasispecies from nucleoside and nucleotide reverse-transcriptase inhibitor (NRTI)-treated patients and NRTI-naive patients
    • S. Margeridon-Thermet, N.S. Shulman, A. Ahmed, R. Shahriar, T. Liu, C. Wang, S.P. Holmes, F. Babrzadeh, B. Gharizadeh, and B. Hanczaruk Ultra-deep pyrosequencing of hepatitis B virus quasispecies from nucleoside and nucleotide reverse-transcriptase inhibitor (NRTI)-treated patients and NRTI-naive patients J Infect Dis 199 2009 1275 1285
    • (2009) J Infect Dis , vol.199 , pp. 1275-1285
    • Margeridon-Thermet, S.1    Shulman, N.S.2    Ahmed, A.3    Shahriar, R.4    Liu, T.5    Wang, C.6    Holmes, S.P.7    Babrzadeh, F.8    Gharizadeh, B.9    Hanczaruk, B.10
  • 27
    • 79551712478 scopus 로고    scopus 로고
    • Beyond the consensus: Dissecting within-host viral population diversity of foot-and-mouth disease virus by using next-generation genome sequencing
    • C.F. Wright, M.J. Morelli, G. Thébaud, N.J. Knowles, P. Herzyk, D.J. Paton, D.T. Haydon, and D.P. King Beyond the consensus: dissecting within-host viral population diversity of foot-and-mouth disease virus by using next-generation genome sequencing J Virol 85 2011 2266 2275
    • (2011) J Virol , vol.85 , pp. 2266-2275
    • Wright, C.F.1    Morelli, M.J.2    Thébaud, G.3    Knowles, N.J.4    Herzyk, P.5    Paton, D.J.6    Haydon, D.T.7    King, D.P.8
  • 28
    • 79958069377 scopus 로고    scopus 로고
    • Extensive genome-wide variability of human cytomegalovirus in congenitally infected infants
    • N. Renzette, B. Bhattacharjee, J.D. Jensen, L. Gibson, and T.F. Kowalik Extensive genome-wide variability of human cytomegalovirus in congenitally infected infants PLoS Pathog 7 2011 e1001344
    • (2011) PLoS Pathog , vol.7 , pp. 1001344
    • Renzette, N.1    Bhattacharjee, B.2    Jensen, J.D.3    Gibson, L.4    Kowalik, T.F.5
  • 30
    • 73349110099 scopus 로고    scopus 로고
    • Wrinkles in the rare biosphere: Pyrosequencing errors can lead to artificial inflation of diversity estimates
    • V. Kunin, A. Engelbrektson, H. Ochman, and P. Hugenholtz Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates Environ Microbiol 12 2010 118 123
    • (2010) Environ Microbiol , vol.12 , pp. 118-123
    • Kunin, V.1    Engelbrektson, A.2    Ochman, H.3    Hugenholtz, P.4
  • 32
    • 78649901946 scopus 로고    scopus 로고
    • Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies
    • O. Zagordi, R. Klein, M. Däumer, and N. Beerenwinkel Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies Nucleic Acids Res 38 2010 7400 7409
    • (2010) Nucleic Acids Res , vol.38 , pp. 7400-7409
    • Zagordi, O.1    Klein, R.2    Däumer, M.3    Beerenwinkel, N.4
  • 34
    • 77956304094 scopus 로고    scopus 로고
    • Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions
    • J. Reeder, and R. Knight Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions Nat Methods 7 2010 668 669
    • (2010) Nat Methods , vol.7 , pp. 668-669
    • Reeder, J.1    Knight, R.2
  • 35
    • 34948842866 scopus 로고    scopus 로고
    • Accuracy and quality of massively parallel DNA pyrosequencing
    • S. Huse, J. Huber, H. Morrison, M. Sogin, and D. Welch Accuracy and quality of massively parallel DNA pyrosequencing Genome Biol 8 2007 R143
    • (2007) Genome Biol , vol.8 , pp. 143
    • Huse, S.1    Huber, J.2    Morrison, H.3    Sogin, M.4    Welch, D.5
  • 38
    • 77950840976 scopus 로고    scopus 로고
    • Deep sequencing of a genetically heterogeneous sample: Local haplotype reconstruction and read error correction
    • O. Zagordi, L. Geyrhofer, V. Roth, and N. Beerenwinkel Deep sequencing of a genetically heterogeneous sample: local haplotype reconstruction and read error correction J Comput Biol 17 2010 417 428
    • (2010) J Comput Biol , vol.17 , pp. 417-428
    • Zagordi, O.1    Geyrhofer, L.2    Roth, V.3    Beerenwinkel, N.4
  • 39
    • 79955125679 scopus 로고    scopus 로고
    • ShoRAH: Estimating the genetic diversity of a mixed sample from next-generation sequencing data
    • O. Zagordi, A. Bhattacharya, N. Eriksson, and N. Beerenwinkel ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data BMC Bioinformatics 12 2011 119
    • (2011) BMC Bioinformatics , vol.12 , pp. 119
    • Zagordi, O.1    Bhattacharya, A.2    Eriksson, N.3    Beerenwinkel, N.4
  • 40
    • 40549123712 scopus 로고    scopus 로고
    • Population sequencing using short reads: HIV as a case study
    • R.B. Altman, A.K. Dunker, L. Hunter, T. Murray, T.E. Klein, World Scientific
    • V. Jojic, T. Hertz, and N. Jojic Population sequencing using short reads: HIV as a case study R.B. Altman, A.K. Dunker, L. Hunter, T. Murray, T.E. Klein, Pacific Symposium on Biocomputing 2008 World Scientific 114 125
    • (2008) Pacific Symposium on Biocomputing , pp. 114-125
    • Jojic, V.1    Hertz, T.2    Jojic, N.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.