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Volumn 10, Issue 5, 2015, Pages

Deconstructing the polymerase chain reaction: Understanding and correcting bias associated with primer degeneracies and primer-template mismatches

Author keywords

[No Author keywords available]

Indexed keywords

DNA POLYMERASE; EXONUCLEASE; GENOMIC DNA; PRIMER DNA;

EID: 84930672461     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0128122     Document Type: Article
Times cited : (155)

References (35)
  • 2
    • 84863981120 scopus 로고    scopus 로고
    • Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
    • PMID: 22402401
    • Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, et al. (2012) Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. The ISME journal 6: 1621-1624. doi: 10.1038/ismej.2012.8 PMID: 22402401
    • (2012) The ISME Journal , vol.6 , pp. 1621-1624
    • Caporaso, J.G.1    Lauber, C.L.2    Walters, W.A.3    Berg-Lyons, D.4    Huntley, J.5
  • 4
    • 0027460328 scopus 로고
    • Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA
    • PMID: 7683183
    • Muyzer G, De Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Applied and Environmental Microbiology 59: 695-700. PMID: 7683183
    • (1993) Applied and Environmental Microbiology , vol.59 , pp. 695-700
    • Muyzer, G.1    De Waal, E.C.2    Uitterlinden, A.G.3
  • 5
    • 0031937375 scopus 로고    scopus 로고
    • Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA
    • PMID: 9464425
    • Marchesi JR, Sato T, Weightman AJ, Martin TA, Fry JC, et al. (1998) Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Applied and Environmental Microbiology 64: 795-799. PMID: 9464425
    • (1998) Applied and Environmental Microbiology , vol.64 , pp. 795-799
    • Marchesi, J.R.1    Sato, T.2    Weightman, A.J.3    Martin, T.A.4    Fry, J.C.5
  • 6
    • 34247098019 scopus 로고    scopus 로고
    • Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis
    • PMID: 17343679
    • Sipos R, Székely AJ, Palatinszky M, Révész S, Márialigeti K, et al. (2007) Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis. FEMS Microbiology Ecology 60: 341-350. PMID: 17343679
    • (2007) FEMS Microbiology Ecology , vol.60 , pp. 341-350
    • Sipos, R.1    Székely, A.J.2    Palatinszky, M.3    Révész, S.4    Márialigeti, K.5
  • 7
    • 29144445330 scopus 로고    scopus 로고
    • PCR-induced sequence artifacts and bias: Insights from comparison of two 16S rRNA clone libraries constructed from the same sample
    • PMID: 16332901
    • Acinas SG, Sarma-Rupavtarm R, Klepac-Ceraj V, Polz MF (2005) PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. Applied and Environmental Microbiology 71: 8966-8969. PMID: 16332901
    • (2005) Applied and Environmental Microbiology , vol.71 , pp. 8966-8969
    • Acinas, S.G.1    Sarma-Rupavtarm, R.2    Klepac-Ceraj, V.3    Polz, M.F.4
  • 8
    • 0031711754 scopus 로고    scopus 로고
    • Bias in template-to-product ratios in multitemplate PCR
    • PMID: 9758791
    • Polz MF, Cavanaugh CM (1998) Bias in template-to-product ratios in multitemplate PCR. Applied and Environmental Microbiology 64: 3724-3730. PMID: 9758791
    • (1998) Applied and Environmental Microbiology , vol.64 , pp. 3724-3730
    • Polz, M.F.1    Cavanaugh, C.M.2
  • 9
    • 0035432220 scopus 로고    scopus 로고
    • Optimization of annealing temperature to reduce bias caused by a primer mismatch in multitemplate PCR
    • PMID: 11472961
    • Ishii K, Fukui M (2001) Optimization of annealing temperature to reduce bias caused by a primer mismatch in multitemplate PCR. Applied and Environmental Microbiology 67: 3753-3755. PMID: 11472961
    • (2001) Applied and Environmental Microbiology , vol.67 , pp. 3753-3755
    • Ishii, K.1    Fukui, M.2
  • 10
    • 0031149569 scopus 로고    scopus 로고
    • Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries
    • PMID: 9161015
    • Chandler D, Fredrickson J, Brockman F (1997) Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries. Molecular Ecology 6: 475-482. PMID: 9161015
    • (1997) Molecular Ecology , vol.6 , pp. 475-482
    • Chandler, D.1    Fredrickson, J.2    Brockman, F.3
  • 11
    • 0030067991 scopus 로고    scopus 로고
    • Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR
    • PMID: 8593063
    • Suzuki MT, Giovannoni SJ (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Applied and Environmental Microbiology 62: 625-630. PMID: 8593063
    • (1996) Applied and Environmental Microbiology , vol.62 , pp. 625-630
    • Suzuki, M.T.1    Giovannoni, S.J.2
  • 12
    • 0345195995 scopus 로고    scopus 로고
    • Determination of microbial diversity in environmental samples: Pitfalls of PCR-based rRNA analysis
    • PMID: 9451814
    • V Wintzingerode F, Göbel UB, Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS microbiology reviews 21: 213-229. PMID: 9451814
    • (1997) FEMS Microbiology Reviews , vol.21 , pp. 213-229
    • V Wintzingerode, F.1    Göbel, U.B.2    Stackebrandt, E.3
  • 13
    • 42349100152 scopus 로고    scopus 로고
    • Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes
    • PMID: 18296538
    • Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA, et al. (2008) Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Applied and environmental microbiology 74: 2461-2470. doi: 10.1128/AEM.02272-07 PMID: 18296538
    • (2008) Applied and Environmental Microbiology , vol.74 , pp. 2461-2470
    • Frank, J.A.1    Reich, C.I.2    Sharma, S.3    Weisbaum, J.S.4    Wilson, B.A.5
  • 14
    • 84866065801 scopus 로고    scopus 로고
    • Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing
    • PMID: 22970184
    • Lee CK, Herbold CW, Polson SW, Wommack KE, Williamson SJ, et al. (2012) Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing. PLoS One 7: e44224. doi: 10.1371/journal.pone.0044224 PMID: 22970184
    • (2012) PLoS One , vol.7
    • Lee, C.K.1    Herbold, C.W.2    Polson, S.W.3    Wommack, K.E.4    Williamson, S.J.5
  • 15
    • 84868094960 scopus 로고    scopus 로고
    • Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance
    • PMID: 23133348
    • Kembel SW, Wu M, Eisen JA, Green JL (2012) Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance. PLoS computational biology 8: e1002743. doi: 10.1371/journal.pcbi.1002743 PMID: 23133348
    • (2012) PLoS Computational Biology , vol.8
    • Kembel, S.W.1    Wu, M.2    Eisen, J.A.3    Green, J.L.4
  • 16
    • 84860370749 scopus 로고    scopus 로고
    • Coverage evaluation of universal bacterial primers using the metagenomic datasets
    • PMID: 22554309
    • Mao D-P, Zhou Q, Chen C-Y, Quan Z-X (2012) Coverage evaluation of universal bacterial primers using the metagenomic datasets. BMC microbiology 12: 66. PMID: 22554309
    • (2012) BMC Microbiology , vol.12 , pp. 66
    • Mao, D.-P.1    Zhou, Q.2    Chen, C.-Y.3    Quan, Z.-X.4
  • 18
    • 77952285625 scopus 로고    scopus 로고
    • Denitrifying bacteria from the terrestrial subsurface exposed to mixed waste contamination
    • PMID: 20305024
    • Green SJ, Prakash O, Gihring TM, Akob DM, Jasrotia P, et al. (2010) Denitrifying bacteria from the terrestrial subsurface exposed to mixed waste contamination. Appl Environ Microbiol 76: 3244-3254. doi: 10.1128/AEM.03069-09 PMID: 20305024
    • (2010) Appl Environ Microbiol , vol.76 , pp. 3244-3254
    • Green, S.J.1    Prakash, O.2    Gihring, T.M.3    Akob, D.M.4    Jasrotia, P.5
  • 19
    • 84866335245 scopus 로고    scopus 로고
    • Genome sequences for six rhodanobacter strains, isolated from soils and the terrestrial subsurface, with variable denitrification capabilities
    • PMID: 22843592
    • Kostka JE, Green SJ, Rishishwar L, Prakash O, Katz LS, et al. (2012) Genome sequences for six rhodanobacter strains, isolated from soils and the terrestrial subsurface, with variable denitrification capabilities. J Bacteriol 194: 4461-4462. doi: 10.1128/JB.00871-12 PMID: 22843592
    • (2012) J Bacteriol , vol.194 , pp. 4461-4462
    • Kostka, J.E.1    Green, S.J.2    Rishishwar, L.3    Prakash, O.4    Katz, L.S.5
  • 20
    • 84855194204 scopus 로고    scopus 로고
    • Targeted amplicon sequencing (TAS): A scalable next-gen approach to multilocus, multitaxa phylogenetics
    • PMID: 22002916
    • Bybee SM, Bracken-Grissom H, Haynes BD, Hermansen RA, Byers RL, et al. (2011) Targeted amplicon sequencing (TAS): a scalable next-gen approach to multilocus, multitaxa phylogenetics. Genome biology and evolution 3: 1312-1323. doi: 10.1093/gbe/evr106 PMID: 22002916
    • (2011) Genome Biology and Evolution , vol.3 , pp. 1312-1323
    • Bybee, S.M.1    Bracken-Grissom, H.2    Haynes, B.D.3    Hermansen, R.A.4    Byers, R.L.5
  • 22
    • 84873578476 scopus 로고    scopus 로고
    • High throughput HLA genotyping using 454 sequencing and the Fluidigm Access Array system for simplified amplicon library preparation
    • PMID: 23398507
    • Moonsamy P, Williams T, Bonella P, Holcomb C, Höglund B, et al. (2013) High throughput HLA genotyping using 454 sequencing and the Fluidigm Access Array system for simplified amplicon library preparation. Tissue antigens 81: 141-149. doi: 10.1111/tan.12071 PMID: 23398507
    • (2013) Tissue Antigens , vol.81 , pp. 141-149
    • Moonsamy, P.1    Williams, T.2    Bonella, P.3    Holcomb, C.4    Höglund, B.5
  • 23
    • 0029036729 scopus 로고
    • 3-Nitropyrrole and 5-nitroindole as universal bases in primers for DNA sequencing and PCR
    • PMID: 7630712
    • Loakes D, Brown DM, Linde S, Hill F (1995) 3-Nitropyrrole and 5-nitroindole as universal bases in primers for DNA sequencing and PCR. Nucleic acids research 23: 2361-2366. PMID: 7630712
    • (1995) Nucleic Acids Research , vol.23 , pp. 2361-2366
    • Loakes, D.1    Brown, D.M.2    Linde, S.3    Hill, F.4
  • 24
    • 77952243141 scopus 로고    scopus 로고
    • QIIME allows analysis of high-throughput community sequencing data
    • PMID: 20383131
    • Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nature methods 7: 335-336. doi: 10.1038/nmeth.f.303 PMID: 20383131
    • (2010) Nature Methods , vol.7 , pp. 335-336
    • Caporaso, J.G.1    Kuczynski, J.2    Stombaugh, J.3    Bittinger, K.4    Bushman, F.D.5
  • 25
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • PMID: 20709691
    • Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461. doi: 10.1093/bioinformatics/btq461 PMID: 20709691
    • (2010) Bioinformatics , vol.26 , pp. 2460-2461
    • Edgar, R.C.1
  • 26
    • 84856563821 scopus 로고    scopus 로고
    • Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes
    • PMID: 21923700
    • Gihring TM, Green SJ, Schadt CW (2012) Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes. Environ Microbiol 14: 285-290. doi: 10.1111/j.1462-2920.2011.02550.x PMID: 21923700
    • (2012) Environ Microbiol , vol.14 , pp. 285-290
    • Gihring, T.M.1    Green, S.J.2    Schadt, C.W.3
  • 27
    • 84857122937 scopus 로고    scopus 로고
    • An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
    • PMID: 22134646
    • McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, et al. (2011) An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. The ISME journal 6: 610-618. doi: 10.1038/ismej.2011.139 PMID: 22134646
    • (2011) The ISME Journal , vol.6 , pp. 610-618
    • McDonald, D.1    Price, M.N.2    Goodrich, J.3    Nawrocki, E.P.4    DeSantis, T.Z.5
  • 28
    • 34548293679 scopus 로고    scopus 로고
    • Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
    • PMID: 17586664
    • Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology 73: 5261-5267. PMID: 17586664
    • (2007) Applied and Environmental Microbiology , vol.73 , pp. 5261-5267
    • Wang, Q.1    Garrity, G.M.2    Tiedje, J.M.3    Cole, J.R.4
  • 29
    • 84868270724 scopus 로고    scopus 로고
    • The Biological Observation Matrix (BIOM) format or: How I learned to stop worrying and love the ome-ome
    • PMID: 23587224
    • McDonald D, Clemente JC, Kuczynski J, Rideout JR, Stombaugh J, et al. (2012) The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. GigaScience 1: 7. doi: 10.1186/2047-217X-1-7 PMID: 23587224
    • (2012) GigaScience , vol.1 , pp. 7
    • McDonald, D.1    Clemente, J.C.2    Kuczynski, J.3    Rideout, J.R.4    Stombaugh, J.5
  • 30
    • 0027804103 scopus 로고
    • Non-parametric multivariate analyses of changes in community structure
    • Clarke KR (1993) Non-parametric multivariate analyses of changes in community structure. Australian journal of ecology 18: 117-143.
    • (1993) Australian Journal of Ecology , vol.18 , pp. 117-143
    • Clarke, K.R.1
  • 31
    • 67349235323 scopus 로고    scopus 로고
    • Quantitative effects of position and type of single mismatch on single base primer extension
    • PMID: 19285527
    • Wu J-H, Hong P-Y, Liu W-T (2009) Quantitative effects of position and type of single mismatch on single base primer extension. Journal of microbiological methods 77: 267-275. doi: 10.1016/j.mimet.2009.03.001 PMID: 19285527
    • (2009) Journal of Microbiological Methods , vol.77 , pp. 267-275
    • Wu, J.-H.1    Hong, P.-Y.2    Liu, W.-T.3
  • 32
    • 40549109538 scopus 로고    scopus 로고
    • Quantification of the detrimental effect of a single primer-template mismatch by real-time PCR using the 16S rRNA gene as an example
    • PMID: 18192413
    • Bru D, Martin-Laurent F, Philippot L (2008) Quantification of the detrimental effect of a single primer-template mismatch by real-time PCR using the 16S rRNA gene as an example. Applied and environmental microbiology 74: 1660-1663. doi: 10.1128/AEM.02403-07 PMID: 18192413
    • (2008) Applied and Environmental Microbiology , vol.74 , pp. 1660-1663
    • Bru, D.1    Martin-Laurent, F.2    Philippot, L.3
  • 33
    • 33846096244 scopus 로고    scopus 로고
    • Gene capture and random amplification for quantitative recovery of homologous genes
    • PMID: 17088045
    • Crosby LD, Criddle CS (2007) Gene capture and random amplification for quantitative recovery of homologous genes. Molecular and cellular probes 21: 140-147. PMID: 17088045
    • (2007) Molecular and Cellular Probes , vol.21 , pp. 140-147
    • Crosby, L.D.1    Criddle, C.S.2
  • 34
    • 58149179980 scopus 로고    scopus 로고
    • rrnDB: Documenting the number of rRNA and tRNA genes in bacteria and archaea
    • PMID: 18948294
    • Lee ZM-P, Bussema C, Schmidt TM (2009) rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea. Nucleic acids research 37: D489-D493. doi: 10.1093/nar/gkn689 PMID: 18948294
    • (2009) Nucleic Acids Research , vol.37 , pp. D489-D493
    • Lee, Z.M.-P.1    Bussema, C.2    Schmidt, T.M.3
  • 35
    • 79957556739 scopus 로고    scopus 로고
    • An efficient strategy for broad-range detection of low abundance bacteria without DNA decontamination of PCR reagents
    • PMID: 21637859
    • Chang S-S, Hsu H-L, Cheng J-C, Tseng C-P (2011) An efficient strategy for broad-range detection of low abundance bacteria without DNA decontamination of PCR reagents. PloS one 6: e20303. doi: 10.1371/journal.pone.0020303 PMID: 21637859
    • (2011) PloS One , vol.6
    • Chang, S.-S.1    Hsu, H.-L.2    Cheng, J.-C.3    Tseng, C.-P.4


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