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Volumn 10, Issue 3, 2015, Pages

Challenges with using Primer IDs to improve accuracy of next generation sequencing

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; PRIMER DNA;

EID: 84929157239     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0119123     Document Type: Article
Times cited : (24)

References (22)
  • 1
    • 77955402078 scopus 로고    scopus 로고
    • Dynamics of HIV-1 quasispecies during antiviral treatment dissected using ultra-deep pyrosequencing
    • PMID: 20628644
    • Hedskog C, Mild M, Jernberg J, Sherwood E, Bratt G, Leitner T, et al. Dynamics of HIV-1 quasispecies during antiviral treatment dissected using ultra-deep pyrosequencing. PLoS One 2010, 5:e11345. doi: 10.1371/journal.pone.0011345 PMID: 20628644
    • (2010) PLoS One , vol.5 , pp. e11345
    • Hedskog, C.1    Mild, M.2    Jernberg, J.3    Sherwood, E.4    Bratt, G.5    Leitner, T.6
  • 2
    • 34547829263 scopus 로고    scopus 로고
    • DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations
    • PMID: 17576693
    • Hoffmann C, Minkah N, Leipzig J, Wang G, Arens MQ, Tebas P, et al. DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations. Nucleic Acids Res 2007, 35:e91. PMID: 17576693
    • (2007) Nucleic Acids Res , vol.35 , pp. e91
    • Hoffmann, C.1    Minkah, N.2    Leipzig, J.3    Wang, G.4    Arens, M.Q.5    Tebas, P.6
  • 4
    • 61849172898 scopus 로고    scopus 로고
    • Low-abundance drugresistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes
    • PMID: 19210162
    • Simen BB, Simons JF, Hullsiek KH, Novak RM, Macarthur RD, Baxter JD, et al. Low-abundance drugresistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes. J Infect Dis 2009, 199:693-701. doi: 10.1086/596736 PMID: 19210162
    • (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    Baxter, J.D.6
  • 5
    • 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
    • PMID: 19734799
    • Varghese V, Shahriar R, Rhee SY, Liu T, Simen BB, Egholm M, et al. 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 DeficSyndr 2009, 52:309-315. doi: 10.1097/QAI.0b013e3181bca669 PMID: 19734799
    • (2009) J Acquir Immune DeficSyndr , vol.52 , pp. 309-315
    • Varghese, V.1    Shahriar, R.2    Rhee, S.Y.3    Liu, T.4    Simen, B.B.5    Egholm, M.6
  • 6
    • 79959438245 scopus 로고    scopus 로고
    • Systematic exploration of error sources in pyrosequencingflowgram data
    • PMID: 21685085
    • Balzer S, Malde K, Jonassen I. Systematic exploration of error sources in pyrosequencingflowgram data. Bioinformatics 2011, 27:i304-309. doi: 10.1093/bioinformatics/btr251 PMID: 21685085
    • (2011) Bioinformatics , vol.27 , pp. i304-i309
    • Balzer, S.1    Malde, K.2    Jonassen, I.3
  • 7
    • 84880760001 scopus 로고    scopus 로고
    • PCR-induced transitions are the major source of error in cleaned ultra-deep pyrosequencing data
    • PMID: 23894647
    • Brodin J, Mild M, Hedskog C, Sherwood E, Leitner T, Andersson B, et al. PCR-induced transitions are the major source of error in cleaned ultra-deep pyrosequencing data. PLoS One 2013, 8:e70388. doi: 10.1371/journal.pone.0070388 PMID: 23894647
    • (2013) PLoS One , vol.8 , pp. e70388
    • Brodin, J.1    Mild, M.2    Hedskog, C.3    Sherwood, E.4    Leitner, T.5    Andersson, B.6
  • 8
    • 80054839029 scopus 로고    scopus 로고
    • A comparison of parallel pyrosequencing and sanger clone-based sequencing and its impact on the characterization of the genetic diversity of HIV-1
    • PMID: 22039546
    • Liang B, Luo M, Scott-Herridge J, Semeniuk C, Mendoza M, Capina R, et al. A comparison of parallel pyrosequencing and sanger clone-based sequencing and its impact on the characterization of the genetic diversity of HIV-1. PLoS One 2011, 6:e26745. doi: 10.1371/journal.pone.0026745 PMID: 22039546
    • (2011) PLoS One , vol.6 , pp. e26745
    • Liang, B.1    Luo, M.2    Scott-Herridge, J.3    Semeniuk, C.4    Mendoza, M.5    Capina, R.6
  • 9
    • 84875002547 scopus 로고    scopus 로고
    • Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of Low-frequency drug resistance mutations in HIV-1 DNA
    • Shao W, Boltz VF, Spindler JE, Kearney MF, Maldarelli F, Mellors JW, et al. Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of Low-frequency drug resistance mutations in HIV-1 DNA. Retrovirology 2013, 10:18.
    • (2013) Retrovirology , vol.10 , pp. 18
    • Shao, W.1    Boltz, V.F.2    Spindler, J.E.3    Kearney, M.F.4    Maldarelli, F.5    Mellors, J.W.6
  • 11
    • 78649901946 scopus 로고    scopus 로고
    • Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies
    • PMID: 20671025
    • Zagordi O, Klein R, Daumer M, Beerenwinkel N. Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies. Nucleic Acids Res 2010, 38:7400-7409. doi: 10.1093/nar/gkq655 PMID: 20671025
    • (2010) Nucleic Acids Res , vol.38 , pp. 7400-7409
    • Zagordi, O.1    Klein, R.2    Daumer, M.3    Beerenwinkel, N.4
  • 12
    • 84055200527 scopus 로고    scopus 로고
    • Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID
    • PMID: 22135472
    • Jabara CB, Jones CD, Roach J, Anderson JA, Swanstrom R. Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID. Proc Natl Acad Sci U S A 2011, 108:20166-20171. doi: 10.1073/pnas.1110064108 PMID: 22135472
    • (2011) Proc Natl Acad Sci U S A , vol.108 , pp. 20166-20171
    • Jabara, C.B.1    Jones, C.D.2    Roach, J.3    Anderson, J.A.4    Swanstrom, R.5
  • 14
    • 77449144323 scopus 로고    scopus 로고
    • Parallel, tag-directed assembly of locally derived short sequence reads
    • PMID: 20081835
    • Hiatt JB, Patwardhan RP, Turner EH, Lee C, Shendure J. Parallel, tag-directed assembly of locally derived short sequence reads. Nat Methods 2010, 7:119-122. doi: 10.1038/nmeth.1416 PMID: 20081835
    • (2010) Nat Methods , vol.7 , pp. 119-122
    • Hiatt, J.B.1    Patwardhan, R.P.2    Turner, E.H.3    Lee, C.4    Shendure, J.5
  • 15
    • 84856484968 scopus 로고    scopus 로고
    • Counting absolute numbers of molecules using unique molecular identifiers
    • PMID: 22101854
    • Kivioja T, Vaharautio A, Karlsson K, Bonke M, Enge M, Linnarsson S, et al. Counting absolute numbers of molecules using unique molecular identifiers. Nat Methods 2012, 9:72-74. doi: 10.1038/nmeth.1778 PMID: 22101854
    • (2012) Nat Methods , vol.9 , pp. 72-74
    • Kivioja, T.1    Vaharautio, A.2    Karlsson, K.3    Bonke, M.4    Enge, M.5    Linnarsson, S.6
  • 16
    • 84858680178 scopus 로고    scopus 로고
    • Low prevalence of transmitted drug resistance in patients newly diagnosed with HIV-1 infection in Sweden 2003-2010
    • PMID: 22448246
    • Karlsson A, Bjorkman P, Bratt G, Ekvall H, Gisslen M, Sonnerborg A, et al. Low prevalence of transmitted drug resistance in patients newly diagnosed with HIV-1 infection in Sweden 2003-2010. PLoS One 2012, 7:e33484. doi: 10.1371/journal.pone.0033484 PMID: 22448246
    • (2012) PLoS One , vol.7 , pp. e33484
    • Karlsson, A.1    Bjorkman, P.2    Bratt, G.3    Ekvall, H.4    Gisslen, M.5    Sonnerborg, A.6
  • 17
    • 0026011260 scopus 로고
    • Few infected CD4+T cells but a high proportion of replicationcompetent provirus copies in asymptomatic human immunodeficiency virus type 1 infection
    • PMID: 1672165
    • Brinchmann JE, Albert J, Vartdal F. Few infected CD4+T cells but a high proportion of replicationcompetent provirus copies in asymptomatic human immunodeficiency virus type 1 infection. J Virol 1991, 65:2019-2023. PMID: 1672165
    • (1991) J Virol , vol.65 , pp. 2019-2023
    • Brinchmann, J.E.1    Albert, J.2    Vartdal, F.3
  • 18
    • 84903950182 scopus 로고    scopus 로고
    • Theoretical and experimental assessment of degenerate primer tagging in ultra-deep applications of next-generation sequencing
    • PMID: 24810852
    • Liang RH, Mo T, Dong W, Lee GQ, Swenson LC, McCloskey RM, et al. Theoretical and experimental assessment of degenerate primer tagging in ultra-deep applications of next-generation sequencing. Nucleic Acids Res 2014, 42:e98. doi: 10.1093/nar/gku355 PMID: 24810852
    • (2014) Nucleic Acids Res , vol.42 , pp. e98
    • Liang, R.H.1    Mo, T.2    Dong, W.3    Lee, G.Q.4    Swenson, L.C.5    McCloskey, R.M.6
  • 19
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • PMID: 15034147
    • Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32:1792-1797. PMID: 15034147
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 20
    • 79960714085 scopus 로고    scopus 로고
    • Performance of ultra-deep pyrosequencing in analysis of HIV-1 pol gene variation
    • PMID: 21799940
    • Mild M, Hedskog C, Jernberg J, Albert J. Performance of ultra-deep pyrosequencing in analysis of HIV-1 pol gene variation. PLoS One 2011, 6:e22741. doi: 10.1371/journal.pone.0022741 PMID: 21799940
    • (2011) PLoS One , vol.6 , pp. e22741
    • Mild, M.1    Hedskog, C.2    Jernberg, J.3    Albert, J.4
  • 21
    • 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
    • PMID: 19955476
    • Poon AF, Swenson LC, Dong WW, Deng W, Kosakovsky Pond SL, Brumme ZL, et al. Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1. Mol Biol Evol 2010, 27:819-832. doi: 10.1093/molbev/msp289 PMID: 19955476
    • (2010) Mol Biol Evol , vol.27 , pp. 819-832
    • Poon, A.F.1    Swenson, L.C.2    Dong, W.W.3    Deng, W.4    Kosakovsky Pond, S.L.5    Brumme, Z.L.6
  • 22
    • 84856398949 scopus 로고    scopus 로고
    • Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes
    • PMID: 22232676
    • Shiroguchi K, Jia TZ, Sims PA, Xie XS. Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes. Proc Natl Acad Sci U S A 2012, 109:1347-1352. doi: 10.1073/pnas.1118018109 PMID: 22232676
    • (2012) Proc Natl Acad Sci U S A , vol.109 , pp. 1347-1352
    • Shiroguchi, K.1    Jia, T.Z.2    Sims, P.A.3    Xie, X.S.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.