메뉴 건너뛰기




Volumn 9, Issue 10, 2014, Pages

Diverse and widespread contamination evident in the unmapped depths of high throughput sequencing data

Author keywords

[No Author keywords available]

Indexed keywords

PLANT DNA; BACTERIAL DNA;

EID: 84908564504     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0110808     Document Type: Article
Times cited : (154)

References (43)
  • 1
    • 0028840845 scopus 로고
    • Evidence of contamination in PCR laboratory disposables
    • Schmidt T, Hummel S, Herrmann B (1995) Evidence of contamination in PCR laboratory disposables. Naturwissenschaften 82(9): 423-31.
    • (1995) Naturwissenschaften , vol.82 , Issue.9 , pp. 423-431
    • Schmidt, T.1    Hummel, S.2    Herrmann, B.3
  • 3
    • 4444367098 scopus 로고    scopus 로고
    • Detection of bacterial DNA in blood samples from febrile patients: Underestimated infection or emerging contamination?
    • Peters RP, Mohammadi T, Vandenbroucke Grauls CM, Danner SA, van Agtmael MA, et al. (2004) Detection of bacterial DNA in blood samples from febrile patients: underestimated infection or emerging contamination? FEMS Immunol Med Microbiol 42(2): 249-53.
    • (2004) FEMS Immunol Med Microbiol , vol.42 , Issue.2 , pp. 249-253
    • Peters, R.P.1    Mohammadi, T.2    Vandenbroucke Grauls, C.M.3    Danner, S.A.4    Van Agtmael, M.A.5
  • 4
    • 33947253504 scopus 로고    scopus 로고
    • Residual DNA in thermostable DNA polymerases - A cause of irritation in diagnostic PCR and microarray assays
    • Ehricht R, Hotzel H, Sachse K, Slickers P (2007) Residual DNA in thermostable DNA polymerases - a cause of irritation in diagnostic PCR and microarray assays. Biologicals 35(2): 145-7.
    • (2007) Biologicals , vol.35 , Issue.2 , pp. 145-147
    • Ehricht, R.1    Hotzel, H.2    Sachse, K.3    Slickers, P.4
  • 6
    • 0028302306 scopus 로고
    • Identification and elimination of DNA sequences in Taq DNA polymerase
    • Hughes MS, Beck LA, Skuce RA (1994) Identification and elimination of DNA sequences in Taq DNA polymerase. J Clin Microbiol 32(8): 2007-8.
    • (1994) J Clin Microbiol , vol.32 , Issue.8 , pp. 2007-2008
    • Hughes, M.S.1    Beck, L.A.2    Skuce, R.A.3
  • 7
    • 80051836774 scopus 로고    scopus 로고
    • DNA extraction columns contaminated with murine sequences
    • Erlwein O, Robinson MJ, Dustan S, Weber J, Kaye S, et al. (2011) DNA extraction columns contaminated with murine sequences. PLoS One 6(8): e23484.
    • (2011) PLoS One , vol.6 , Issue.8 , pp. e23484
    • Erlwein, O.1    Robinson, M.J.2    Dustan, S.3    Weber, J.4    Kaye, S.5
  • 8
    • 0026052444 scopus 로고
    • Polymerase chain reaction: Trenches to benches
    • Persing DH (1991) Polymerase chain reaction: trenches to benches. J Clin Microbiol 29(7): 1281-5.
    • (1991) J Clin Microbiol , vol.29 , Issue.7 , pp. 1281-1285
    • Persing, D.H.1
  • 9
    • 77958605242 scopus 로고    scopus 로고
    • An efficient multistrategy DNA decontamination procedure of PCR reagents for hypersensitive PCR applications
    • Champlot S, Berthelot C, Pruvost M, Bennett EA, Grange T, et al. (2010) An efficient multistrategy DNA decontamination procedure of PCR reagents for hypersensitive PCR applications. PLoS One 5(9).
    • (2010) PLoS One , vol.5 , Issue.9
    • Champlot, S.1    Berthelot, C.2    Pruvost, M.3    Bennett, E.A.4    Grange, T.5
  • 10
    • 0034710344 scopus 로고    scopus 로고
    • An investigation of the rigor of interpretation rules for STRs derived from less than 100 pg of DNA
    • Gill P, Whitaker J, Flaxman C, Brown N, Buckleton J (2000) An investigation of the rigor of interpretation rules for STRs derived from less than 100 pg of DNA. Forensic Sci Int 112(1): 17-40.
    • (2000) Forensic Sci Int , vol.112 , Issue.1 , pp. 17-40
    • Gill, P.1    Whitaker, J.2    Flaxman, C.3    Brown, N.4    Buckleton, J.5
  • 12
    • 79951881661 scopus 로고    scopus 로고
    • Abundant human DNA contamination identified in non-primate genome databases
    • Longo MS, O'Neill MJ, O'Neill RJ (2011) Abundant human DNA contamination identified in non-primate genome databases. PLoS One 6(2): e16410.
    • (2011) PLoS One , vol.6 , Issue.2 , pp. e16410
    • Longo, M.S.1    O'neill, M.J.2    O'neill, R.J.3
  • 13
    • 0027286178 scopus 로고
    • Contamination of DNA database sequence entries with Escherichia coli insertion sequences
    • Binns M (1993) Contamination of DNA database sequence entries with Escherichia coli insertion sequences. Nucleic Acids Res 21(3): 779.
    • (1993) Nucleic Acids Res , vol.21 , Issue.3 , pp. 779
    • Binns, M.1
  • 14
    • 79952390994 scopus 로고    scopus 로고
    • Fast identification and removal of sequence contamination from genomic and metagenomic datasets
    • Schmieder R, Edwards R (2011) Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS One 6(3): e17288.
    • (2011) PLoS One , vol.6 , Issue.3 , pp. e17288
    • Schmieder, R.1    Edwards, R.2
  • 15
    • 0347297279 scopus 로고    scopus 로고
    • Evidence for a prokaryotic insertion-sequence contamination in eukaryotic sequences registered in different databases
    • Astua-Monge G, Lyznik A, Jones V, Mackenzie SA, Vallejos CE (2002) Evidence for a prokaryotic insertion-sequence contamination in eukaryotic sequences registered in different databases. Theor Appl Genet 104(1): 48-53.
    • (2002) Theor Appl Genet , vol.104 , Issue.1 , pp. 48-53
    • Astua-Monge, G.1    Lyznik, A.2    Jones, V.3    Mackenzie, S.A.4    Vallejos, C.E.5
  • 16
    • 84874420514 scopus 로고    scopus 로고
    • A microbial metagenome (Leucobacter sp.) in caenorhabditis whole genome sequences
    • Percudani R (2013) A Microbial Metagenome (Leucobacter sp.) in Caenorhabditis Whole Genome Sequences. Bioinform Biol Insights 7: 55-72.
    • (2013) Bioinform Biol Insights , vol.7 , pp. 55-72
    • Percudani, R.1
  • 17
    • 84901447173 scopus 로고    scopus 로고
    • Mining of public sequencing databases supports a non-dietary origin for putative foreign miRNAs: Underestimated effects of contamination in NGS
    • Tosar JP, Rovira C, Naya H, Cayota A (2014) Mining of public sequencing databases supports a non-dietary origin for putative foreign miRNAs: underestimated effects of contamination in NGS. RNA 20: 754-7.
    • (2014) RNA , vol.20 , pp. 754-757
    • Tosar, J.P.1    Rovira, C.2    Naya, H.3    Cayota, A.4
  • 18
    • 84908597338 scopus 로고    scopus 로고
    • Preparation of high-quality next-generation sequencing libraries from picogram quantities of target DNA
    • Parkinson NJ, Maslau S, Ferneyhough B, Zhang G, Gregory L, et al. (2012) Preparation of high-quality next-generation sequencing libraries from picogram quantities of target DNA. Genome Res 20: 754-7.
    • (2012) Genome Res , vol.20 , pp. 754-757
    • Parkinson, N.J.1    Maslau, S.2    Ferneyhough, B.3    Zhang, G.4    Gregory, L.5
  • 19
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memoryefficient alignment of short DNA sequences to the human genome
    • Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memoryefficient alignment of short DNA sequences to the human genome. Genome Biol 10(3): R25.
    • (2009) Genome Biol , vol.10 , Issue.3 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 20
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • International Human Genome Sequencing Consortium
    • International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409(6822): 860-921.
    • (2001) Nature , vol.409 , Issue.6822 , pp. 860-921
  • 21
    • 84881621602 scopus 로고    scopus 로고
    • Glm2: Fitting generalized linear models with convergence problems
    • Marschner IC (2011) glm2: fitting generalized linear models with convergence problems. The R journal 3(2): 12-5.
    • (2011) The R Journal , vol.3 , Issue.2 , pp. 12-15
    • Marschner, I.C.1
  • 23
    • 79953766940 scopus 로고    scopus 로고
    • Tumour evolution inferred by single-cell sequencing
    • Navin N, Kendall J, Troge J, Andrews P, Rodgers L, et al. (2011) Tumour evolution inferred by single-cell sequencing. Nature 472(7341): 90-4.
    • (2011) Nature , vol.472 , Issue.7341 , pp. 90-94
    • Navin, N.1    Kendall, J.2    Troge, J.3    Andrews, P.4    Rodgers, L.5
  • 24
    • 84869096434 scopus 로고    scopus 로고
    • DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution
    • Falconer E, Hills M, Naumann U, Poon SS, Chavez EA, et al. (2012) DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution. Nat Methods 9(11): 1107-12.
    • (2012) Nat Methods , vol.9 , Issue.11 , pp. 1107-1112
    • Falconer, E.1    Hills, M.2    Naumann, U.3    Poon, S.S.4    Chavez, E.A.5
  • 25
    • 79959403670 scopus 로고    scopus 로고
    • Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq
    • Islam S, Kjällquist U, Moliner A, Zajac P, Fan JB, et al. (2011) Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res 21(7): 1160-7.
    • (2011) Genome Res , vol.21 , Issue.7 , pp. 1160-1167
    • Islam, S.1    Kjällquist, U.2    Moliner, A.3    Zajac, P.4    Fan, J.B.5
  • 26
    • 84871447495 scopus 로고    scopus 로고
    • Probing meiotic recombination and aneuploidy of single sperm cells by whole-genome sequencing
    • Lu S, Zong C, Fan W, Yang M, Li J, et al. (2012) Probing meiotic recombination and aneuploidy of single sperm cells by whole-genome sequencing. Science 338(6114): 1627-30.
    • (2012) Science , vol.338 , Issue.6114 , pp. 1627-1630
    • Lu, S.1    Zong, C.2    Fan, W.3    Yang, M.4    Li, J.5
  • 27
    • 1542563409 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the mouse genome
    • Mouse genome sequencing consortium
    • Mouse genome sequencing consortium (2002) Initial sequencing and analysis of the mouse genome. Nature 420(6915): 520-62.
    • (2002) Nature , vol.420 , Issue.6915 , pp. 520-562
  • 28
  • 29
    • 0030801002 scopus 로고    scopus 로고
    • Gapped Blast and psi-Blast: A new generation of protein database search programs
    • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped Blast and psi-Blast: A new generation of protein database search programs. Nucleic Acids Res 25: 3389-402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3    Zhang, J.4    Zhang, Z.5
  • 30
    • 53849133826 scopus 로고    scopus 로고
    • Statistical assignment of DNA sequences using Bayesian phylogenetics
    • Munch K, Boomsma W, Huelsenbeck JP, Willerslev E, Nielsen R (2008) Statistical assignment of DNA sequences using Bayesian phylogenetics. Syst Biol 57(5): 750-7.
    • (2008) Syst Biol , vol.57 , Issue.5 , pp. 750-757
    • Munch, K.1    Boomsma, W.2    Huelsenbeck, J.P.3    Willerslev, E.4    Nielsen, R.5
  • 31
    • 84908587095 scopus 로고    scopus 로고
    • Accessed 2014 August 17
    • OBITool Development Team. Available: http://www.grenoble.prabi.fr/trac/ OBITools. Accessed 2014 August 17.
    • OBITool Development Team1
  • 32
  • 33
    • 84855295457 scopus 로고    scopus 로고
    • Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform
    • Kircher M, Sawyer S, Meyer M (2012) Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Rsch 40(1): e3.
    • (2012) Nucleic Acids Rsch , vol.40 , Issue.1 , pp. e3
    • Kircher, M.1    Sawyer, S.2    Meyer, M.3
  • 34
    • 84881505548 scopus 로고    scopus 로고
    • Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression
    • Combs PA, Eisen MB (2013) Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression. PLoS One 8(8): e71820.
    • (2013) PLoS One , vol.8 , Issue.8 , pp. e71820
    • Combs, P.A.1    Eisen, M.B.2
  • 35
    • 0031873791 scopus 로고    scopus 로고
    • Optimized procedure for DNA isolation from fresh and cryopreserved clotted human blood useful in clinical molecular testing
    • Salazar LA, Hirata MH, Cavalli SA, Machado MO, Hirata RD (1998) Optimized procedure for DNA isolation from fresh and cryopreserved clotted human blood useful in clinical molecular testing. Clin Chem 44(8): 1748-50.
    • (1998) Clin Chem , vol.44 , Issue.8 , pp. 1748-1750
    • Salazar, L.A.1    Hirata, M.H.2    Cavalli, S.A.3    Machado, M.O.4    Hirata, R.D.5
  • 36
    • 52249104714 scopus 로고    scopus 로고
    • Deoxyribonuclease activity and circulating DNA concentration in blood plasma of patients with prostate tumors
    • Cherepanova AV, Tamkovich SN, Bryzgunova OE, Vlassov VV, Laktionov PP (2008) Deoxyribonuclease activity and circulating DNA concentration in blood plasma of patients with prostate tumors. Ann N Y Acad Sci 1137: 218-21.
    • (2008) Ann N y Acad Sci , vol.1137 , pp. 218-221
    • Cherepanova, A.V.1    Tamkovich, S.N.2    Bryzgunova, O.E.3    Vlassov, V.V.4    Laktionov, P.P.5
  • 37
    • 39049154328 scopus 로고    scopus 로고
    • Skin microbiota: A source of disease or defence?
    • Cogen AL, Nizet V, Gallo RL (2009) Skin microbiota: a source of disease or defence? Br J Dermatology 158(3): 442-55.
    • (2009) Br J Dermatology , vol.158 , Issue.3 , pp. 442-455
    • Cogen, A.L.1    Nizet, V.2    Gallo, R.L.3
  • 38
    • 77953486683 scopus 로고    scopus 로고
    • Molecular analysis of Malassezia microflora on the skin of the patients with atopic dermatitis
    • Yim SM, Kim JY, Ko JH, Lee YW, Choe YB, et al. (2010) Molecular analysis of Malassezia microflora on the skin of the patients with atopic dermatitis. Ann Dermatol 22(1): 41-7.
    • (2010) Ann Dermatol , vol.22 , Issue.1 , pp. 41-47
    • Yim, S.M.1    Kim, J.Y.2    Ko, J.H.3    Lee, Y.W.4    Choe, Y.B.5
  • 39
    • 0016053069 scopus 로고
    • Predominant gram-positive bacteria in human feces: Numbers, variety, and persistence
    • Gossling J, Slack JM (1974) Predominant Gram-Positive Bacteria in Human Feces: Numbers, Variety, and Persistence. Infection and Immunity 9(4): 719-29.
    • (1974) Infection and Immunity , vol.9 , Issue.4 , pp. 719-729
    • Gossling, J.1    Slack, J.M.2
  • 40
    • 84875028824 scopus 로고    scopus 로고
    • Plant and fungal diversity in gut microbiota as revealed by molecular and culture investigations
    • Gouba N, Raoult D, Drancourt M (2013) Plant and fungal diversity in gut microbiota as revealed by molecular and culture investigations. PLOS ONE 8(3): e59474.
    • (2013) PLOS ONE , vol.8 , Issue.3 , pp. e59474
    • Gouba, N.1    Raoult, D.2    Drancourt, M.3
  • 41
    • 84855502918 scopus 로고    scopus 로고
    • Exogenous plant MIR168a specifically targets mammalian LDLRAP1: Evidence of cross-kingdom regulation by microRNA
    • Zhang L, Hou D, Chen X, Li D, Zhu L, et al. (2012) Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA. Cell Res 22(1): 107-26.
    • (2012) Cell Res , vol.22 , Issue.1 , pp. 107-126
    • Zhang, L.1    Hou, D.2    Chen, X.3    Li, D.4    Zhu, L.5
  • 42
    • 84879745242 scopus 로고    scopus 로고
    • Subglacial Lake Vostok (Antarctica) accretion ice contains a diverse set of sequences from aquatic, marine and sediment-inhabiting bacteria and eukarya
    • Shtarkman YM, Koçer ZA, Edgar R, Veerapaneni RS, D'Elia T, et al. (2013) Subglacial Lake Vostok (Antarctica) accretion ice contains a diverse set of sequences from aquatic, marine and sediment-inhabiting bacteria and eukarya. PLoS One 8(7): e67221.
    • (2013) PLoS One , vol.8 , Issue.7 , pp. e67221
    • Shtarkman, Y.M.1    Koçer, Z.A.2    Edgar, R.3    Veerapaneni, R.S.4    D'elia, T.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.