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Volumn 6, Issue 7, 2011, Pages

Performance of Ultra-Deep pyrosequencing in analysis of HIV-1 pol gene variation

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTICAL ERROR; ARTICLE; BASE PAIRING; BIOTECHNOLOGY; FREQUENCY ANALYSIS; GENE AMPLIFICATION; GENE SEQUENCE; GENETIC RECOMBINATION; GENETIC SCREENING; GENETIC VARIABILITY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; IN VITRO STUDY; MOLECULAR CLONING; NONHUMAN; POLYMERASE CHAIN REACTION; PYROSEQUENCING; REPRODUCIBILITY; STRUCTURAL GENE; ULTRA DEEP PYROSEQUENCING; DNA SEQUENCE; GENETICS; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE;

EID: 79960714085     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0022741     Document Type: Article
Times cited : (39)

References (24)
  • 1
    • 24044455869 scopus 로고    scopus 로고
    • Genome sequencing in microfabricated high-density picolitre reactors
    • Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
    • (2005) Nature , vol.437 , pp. 376-380
    • Margulies, M.1    Egholm, M.2    Altman, W.E.3    Attiya, S.4    Bader, J.S.5
  • 2
    • 75749105459 scopus 로고    scopus 로고
    • Ultradeep sequencing of a human ultraconserved region reveals somatic and constitutional genomic instability
    • De Grassi A, Segala C, Iannelli F, Volorio S, Bertario L, et al. (2010) Ultradeep sequencing of a human ultraconserved region reveals somatic and constitutional genomic instability. PLoS Biol 8: e1000275.
    • (2010) PLoS Biol , vol.8
    • de Grassi, A.1    Segala, C.2    Iannelli, F.3    Volorio, S.4    Bertario, L.5
  • 3
    • 44349191457 scopus 로고    scopus 로고
    • Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing
    • Campbell PJ, Stephens PJ, Pleasance ED, O'Meara S, Li H, et al. (2008) Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet 40: 722-729.
    • (2008) Nat Genet , vol.40 , pp. 722-729
    • Campbell, P.J.1    Stephens, P.J.2    Pleasance, E.D.3    O'Meara, S.4    Li, H.5
  • 4
    • 67650682133 scopus 로고    scopus 로고
    • Low-abundance HIV drug-resistant viral variants in treatment-experienced persons correlate with historical antiretroviral use
    • Le T, Chiarella J, Simen BB, Hanczaruk B, Egholm M, et al. (2009) Low-abundance HIV drug-resistant viral variants in treatment-experienced persons correlate with historical antiretroviral use. PLoS One 4: e6079.
    • (2009) PLoS One , vol.4
    • Le, T.1    Chiarella, J.2    Simen, B.B.3    Hanczaruk, B.4    Egholm, M.5
  • 5
    • 55249120981 scopus 로고    scopus 로고
    • Minority human immunodeficiency virus type 1 variants in antiretroviral-naive persons with reverse transcriptase codon 215 revertant mutations
    • Mitsuya Y, Varghese V, Wang C, Liu TF, Holmes SP, et al. (2008) Minority human immunodeficiency virus type 1 variants in antiretroviral-naive persons with reverse transcriptase codon 215 revertant mutations. J Virol 82: 10747-10755.
    • (2008) J Virol , vol.82 , pp. 10747-10755
    • Mitsuya, Y.1    Varghese, V.2    Wang, C.3    Liu, T.F.4    Holmes, S.P.5
  • 6
    • 61849172898 scopus 로고    scopus 로고
    • Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes
    • Simen BB, Simons JF, Hullsiek KH, Novak RM, Macarthur RD, et al. (2009) Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes. J Infect Dis 199: 693-701.
    • (2009) J Infect Dis , vol.199 , pp. 693-701
    • Simen, B.B.1    Simons, J.F.2    Hullsiek, K.H.3    Novak, R.M.4    Macarthur, R.D.5
  • 7
    • 34547643929 scopus 로고    scopus 로고
    • Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance
    • Wang C, Mitsuya Y, Gharizadeh B, Ronaghi M, Shafer RW, (2007) Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance. Genome Res 17: 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
  • 8
    • 70350534553 scopus 로고    scopus 로고
    • Minority variants associated with transmitted and acquired HIV-1 nonnucleoside reverse transcriptase inhibitor resistance: implications for the use of second-generation nonnucleoside reverse transcriptase inhibitors
    • Varghese V, Shahriar R, Rhee SY, Liu T, Simen BB, et al. (2009) Minority variants associated with transmitted and acquired HIV-1 nonnucleoside reverse transcriptase inhibitor resistance: implications for the use of second-generation nonnucleoside reverse transcriptase inhibitors. J Acquir Immune Defic Syndr 52: 309-315.
    • (2009) J Acquir Immune Defic Syndr , vol.52 , pp. 309-315
    • Varghese, V.1    Shahriar, R.2    Rhee, S.Y.3    Liu, T.4    Simen, B.B.5
  • 9
    • 77955402078 scopus 로고    scopus 로고
    • Dynamics of HIV-1 Quasispecies during Antiviral Treatment Dissected Using Ultra-Deep Pyrosequencing
    • Hedskog C, Mild M, Jernberg J, Sherwood E, Bratt G, et al. (2010) Dynamics of HIV-1 Quasispecies during Antiviral Treatment Dissected Using Ultra-Deep Pyrosequencing. PLoS One 5: e11345.
    • (2010) PLoS One , vol.5
    • Hedskog, C.1    Mild, M.2    Jernberg, J.3    Sherwood, E.4    Bratt, G.5
  • 10
    • 67651055421 scopus 로고    scopus 로고
    • Detection of low-frequency pretherapy chemokine (CXC motif) receptor 4 (CXCR4)-using HIV-1 with ultra-deep pyrosequencing
    • Archer J, Braverman MS, Taillon BE, Desany B, James I, et al. (2009) Detection of low-frequency pretherapy chemokine (CXC motif) receptor 4 (CXCR4)-using HIV-1 with ultra-deep pyrosequencing. AIDS 23: 1209-1218.
    • (2009) AIDS , vol.23 , pp. 1209-1218
    • Archer, J.1    Braverman, M.S.2    Taillon, B.E.3    Desany, B.4    James, I.5
  • 11
    • 63549147504 scopus 로고    scopus 로고
    • Massively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte sub-populations
    • Rozera G, Abbate I, Bruselles A, Vlassi C, D'Offizi G, et al. (2009) Massively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte sub-populations. Retrovirology 6: 15.
    • (2009) Retrovirology , vol.6 , pp. 15
    • Rozera, G.1    Abbate, I.2    Bruselles, A.3    Vlassi, C.4    D'Offizi, G.5
  • 12
    • 66249094578 scopus 로고    scopus 로고
    • Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo
    • Tsibris AM, Korber B, Arnaout R, Russ C, Lo CC, et al. (2009) Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo. PLoS One 4: e5683.
    • (2009) PLoS One , vol.4
    • Tsibris, A.M.1    Korber, B.2    Arnaout, R.3    Russ, C.4    Lo, C.C.5
  • 13
    • 77952299935 scopus 로고    scopus 로고
    • Phylogenetic Analysis of Population-Based and Deep Sequencing Data to Identify Coevolving Sites in the nef Gene of HIV-1
    • Poon AF, Swenson LC, Dong WW, Deng W, Kosakovsky Pond SL, et al. (2009) Phylogenetic Analysis of Population-Based and Deep Sequencing Data to Identify Coevolving Sites in the nef Gene of HIV-1. Mol Biol Evol.
    • (2009) Mol Biol Evol
    • Poon, A.F.1    Swenson, L.C.2    Dong, W.W.3    Deng, W.4    Kosakovsky Pond, S.L.5
  • 14
    • 0030999422 scopus 로고    scopus 로고
    • Subtype-specific problems with quantification of plasma HIV-1 RNA
    • Alaeus A, Lidman K, Sonnerborg A, Albert J, (1997) Subtype-specific problems with quantification of plasma HIV-1 RNA. AIDS 11: 859-865.
    • (1997) AIDS , vol.11 , pp. 859-865
    • Alaeus, A.1    Lidman, K.2    Sonnerborg, A.3    Albert, J.4
  • 15
    • 0344629203 scopus 로고    scopus 로고
    • Bias and artifacts in multitemplate polymerase chain reactions (PCR)
    • Kanagawa T, (2003) Bias and artifacts in multitemplate polymerase chain reactions (PCR). J Biosci Bioeng 96: 317-323.
    • (2003) J Biosci Bioeng , vol.96 , pp. 317-323
    • Kanagawa, T.1
  • 17
    • 41949124934 scopus 로고    scopus 로고
    • Deciphering human immunodeficiency virus type 1 transmission and early envelope diversification by single-genome amplification and sequencing
    • Salazar-Gonzalez JF, Bailes E, Pham KT, Salazar MG, Guffey MB, et al. (2008) Deciphering human immunodeficiency virus type 1 transmission and early envelope diversification by single-genome amplification and sequencing. J Virol 82: 3952-3970.
    • (2008) J Virol , vol.82 , pp. 3952-3970
    • Salazar-Gonzalez, J.F.1    Bailes, E.2    Pham, K.T.3    Salazar, M.G.4    Guffey, M.B.5
  • 18
    • 0032052803 scopus 로고    scopus 로고
    • Stimulation and suppression of PCR-mediated recombination
    • Judo MS, Wedel AB, Wilson C, (1998) Stimulation and suppression of PCR-mediated recombination. Nucleic Acids Res 26: 1819-1825.
    • (1998) Nucleic Acids Res , vol.26 , pp. 1819-1825
    • Judo, M.S.1    Wedel, A.B.2    Wilson, C.3
  • 19
    • 75549083380 scopus 로고    scopus 로고
    • Reducing the impact of PCR-mediated recombination in molecular evolution and environmental studies using a new-generation high-fidelity DNA polymerase
    • Lahr DJ, Katz LA, (2009) Reducing the impact of PCR-mediated recombination in molecular evolution and environmental studies using a new-generation high-fidelity DNA polymerase. Biotechniques 47: 857-866.
    • (2009) Biotechniques , vol.47 , pp. 857-866
    • Lahr, D.J.1    Katz, L.A.2
  • 20
    • 78649901946 scopus 로고    scopus 로고
    • Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies
    • Zagordi O, Klein R, Daumer M, 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    Daumer, M.3    Beerenwinkel, N.4
  • 21
    • 77952572526 scopus 로고    scopus 로고
    • Frequent CXCR4 tropism of HIV-1 subtype A and CRF02_AG during late-stage disease-indication of an evolving epidemic in West Africa
    • Esbjornsson J, Mansson F, Martinez-Arias W, Vincic E, Biague AJ, et al. (2010) Frequent CXCR4 tropism of HIV-1 subtype A and CRF02_AG during late-stage disease-indication of an evolving epidemic in West Africa. Retrovirology 7: 23.
    • (2010) Retrovirology , vol.7 , pp. 23
    • Esbjornsson, J.1    Mansson, F.2    Martinez-Arias, W.3    Vincic, E.4    Biague, A.J.5
  • 22
    • 84908219488 scopus 로고
    • Statistical methods for assessing agreement between two methods of clinical measurement
    • Bland JM, Altman DG, (1986) Statistical methods for assessing agreement between two methods of clinical measurement. Lancet 1: 307-310.
    • (1986) Lancet , vol.1 , pp. 307-310
    • Bland, J.M.1    Altman, D.G.2
  • 23
    • 79960717109 scopus 로고    scopus 로고
    • Detection of Minority Resistance during Early HIV-1 Infection: Natural Variation and Spurious Detection Rather than Transmission and Evolution of Multiple Viral Variants
    • Gianella S, Delport W, Pacold ME, Young JA, Choi JY, et al. (2011) Detection of Minority Resistance during Early HIV-1 Infection: Natural Variation and Spurious Detection Rather than Transmission and Evolution of Multiple Viral Variants. J Virol.
    • (2011) J Virol
    • Gianella, S.1    Delport, W.2    Pacold, M.E.3    Young, J.A.4    Choi, J.Y.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.