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Volumn 7, Issue 10, 2012, Pages

FREQ-Seq: A Rapid, Cost-Effective, Sequencing-Based Method to Determine Allele Frequencies Directly from Mixed Populations

Author keywords

[No Author keywords available]

Indexed keywords

METHANOL; OLIGONUCLEOTIDE;

EID: 84868271227     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0047959     Document Type: Article
Times cited : (36)

References (41)
  • 3
    • 79955590028 scopus 로고    scopus 로고
    • Reciprocal sign epistasis between frequently experimentally evolved adaptive mutations causes a rugged fitness landscape
    • Kvitek DJ, Sherlock G, (2011) Reciprocal sign epistasis between frequently experimentally evolved adaptive mutations causes a rugged fitness landscape. PLoS Genet 7: e1002056.
    • (2011) PLoS Genet , vol.7
    • Kvitek, D.J.1    Sherlock, G.2
  • 4
    • 70350641005 scopus 로고    scopus 로고
    • Genome evolution and adaptation in a long-term experiment with Escherichia coli
    • Barrick JE, Yu DS, Yoon SH, Jeong H, Oh TK, et al. (2009) Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461: 1243-1247.
    • (2009) Nature , vol.461 , pp. 1243-1247
    • Barrick, J.E.1    Yu, D.S.2    Yoon, S.H.3    Jeong, H.4    Oh, T.K.5
  • 5
    • 75349114758 scopus 로고    scopus 로고
    • Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations
    • Conrad TM, Joyce AR, Applebee MK, Barrett CL, Xie B, et al. (2009) Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations. Genome Biol 10: R118.
    • (2009) Genome Biol , vol.10
    • Conrad, T.M.1    Joyce, A.R.2    Applebee, M.K.3    Barrett, C.L.4    Xie, B.5
  • 6
    • 77957746208 scopus 로고    scopus 로고
    • Genome-wide mutational diversity in an evolving population of Escherichia coli
    • Barrick JE, Lenski RE, (2009) Genome-wide mutational diversity in an evolving population of Escherichia coli. Cold Spring Harb Symp Quant Biol 74: 119-129.
    • (2009) Cold Spring Harb Symp Quant Biol , vol.74 , pp. 119-129
    • Barrick, J.E.1    Lenski, R.E.2
  • 8
    • 79952793415 scopus 로고    scopus 로고
    • Second-order selection for evolvability in a large Escherichia coli population
    • Woods RJ, Barrick JE, Cooper TF, Shrestha U, Kauth MR, et al. (2011) Second-order selection for evolvability in a large Escherichia coli population. Science 331: 1433-1436.
    • (2011) Science , vol.331 , pp. 1433-1436
    • Woods, R.J.1    Barrick, J.E.2    Cooper, T.F.3    Shrestha, U.4    Kauth, M.R.5
  • 9
    • 77955670221 scopus 로고    scopus 로고
    • Evolutionary fates within a microbial population highlight an essential role for protein folding during natural selection
    • Pena MI, Davlieva M, Bennett MR, Olson JS, Shamoo Y, (2010) Evolutionary fates within a microbial population highlight an essential role for protein folding during natural selection. Mol Syst Biol 6: 387.
    • (2010) Mol Syst Biol , vol.6 , pp. 387
    • Pena, M.I.1    Davlieva, M.2    Bennett, M.R.3    Olson, J.S.4    Shamoo, Y.5
  • 10
    • 0036590151 scopus 로고    scopus 로고
    • Universal, robust, highly quantitative SNP allele frequency measurement in DNA pools
    • Norton N, Williams NM, Williams HJ, Spurlock G, Kirov G, et al. (2002) Universal, robust, highly quantitative SNP allele frequency measurement in DNA pools. Hum Genet 110: 471-478.
    • (2002) Hum Genet , vol.110 , pp. 471-478
    • Norton, N.1    Williams, N.M.2    Williams, H.J.3    Spurlock, G.4    Kirov, G.5
  • 11
    • 41549155482 scopus 로고    scopus 로고
    • Quantitative Single-letter Sequencing: a method for simultaneously monitoring numerous known allelic variants in single DNA samples
    • Monsion B, Duborjal H, Blanc S, (2008) Quantitative Single-letter Sequencing: a method for simultaneously monitoring numerous known allelic variants in single DNA samples. BMC Genomics 9: 85.
    • (2008) BMC Genomics , vol.9 , pp. 85
    • Monsion, B.1    Duborjal, H.2    Blanc, S.3
  • 14
    • 0033786720 scopus 로고    scopus 로고
    • Long-term experimental evolution in Escherichia coli. IX. Characterization of insertion sequence-mediated mutations and rearrangements
    • Schneider D, Duperchy E, Coursange E, Lenski RE, Blot M, (2000) Long-term experimental evolution in Escherichia coli. IX. Characterization of insertion sequence-mediated mutations and rearrangements. Genetics 156: 477-488.
    • (2000) Genetics , vol.156 , pp. 477-488
    • Schneider, D.1    Duperchy, E.2    Coursange, E.3    Lenski, R.E.4    Blot, M.5
  • 15
    • 33644799347 scopus 로고    scopus 로고
    • Determination of allele frequency in pooled DNA: comparison of three PCR-based methods
    • Wilkening S, Hemminki K, Thirumaran RK, Bermejo JL, Bonn S, et al. (2005) Determination of allele frequency in pooled DNA: comparison of three PCR-based methods. Biotechniques 39: 853-858.
    • (2005) Biotechniques , vol.39 , pp. 853-858
    • Wilkening, S.1    Hemminki, K.2    Thirumaran, R.K.3    Bermejo, J.L.4    Bonn, S.5
  • 16
    • 58149166731 scopus 로고    scopus 로고
    • The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast
    • Gresham D, Desai MM, Tucker CM, Jenq HT, Pai DA, et al. (2008) The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast. PLoS Genet 4: e1000303.
    • (2008) PLoS Genet , vol.4
    • Gresham, D.1    Desai, M.M.2    Tucker, C.M.3    Jenq, H.T.4    Pai, D.A.5
  • 17
    • 77956328000 scopus 로고    scopus 로고
    • Bacterial charity work leads to population-wide resistance
    • Lee HH, Molla MN, Cantor CR, Collins JJ, (2010) Bacterial charity work leads to population-wide resistance. Nature 467: 82-85.
    • (2010) Nature , vol.467 , pp. 82-85
    • Lee, H.H.1    Molla, M.N.2    Cantor, C.R.3    Collins, J.J.4
  • 18
    • 0037404767 scopus 로고    scopus 로고
    • High-resolution SNP scan of chromosome 6p21 in pooled samples from patients with complex diseases
    • Herbon N, Werner M, Braig C, Gohlke H, Dutsch G, et al. (2003) High-resolution SNP scan of chromosome 6p21 in pooled samples from patients with complex diseases. Genomics 81: 510-518.
    • (2003) Genomics , vol.81 , pp. 510-518
    • Herbon, N.1    Werner, M.2    Braig, C.3    Gohlke, H.4    Dutsch, G.5
  • 19
    • 0036301060 scopus 로고    scopus 로고
    • Large-scale determination of SNP allele frequencies in DNA pools using MALDI-TOF mass spectrometry
    • Werner M, Sych M, Herbon N, Illig T, Konig IR, et al. (2002) Large-scale determination of SNP allele frequencies in DNA pools using MALDI-TOF mass spectrometry. Hum Mutat 20: 57-64.
    • (2002) Hum Mutat , vol.20 , pp. 57-64
    • Werner, M.1    Sych, M.2    Herbon, N.3    Illig, T.4    Konig, I.R.5
  • 20
    • 84861746437 scopus 로고    scopus 로고
    • Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA
    • Forshew T, Murtaza M, Parkinson C, Gale D, Tsui DW, et al. (2012) Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. Sci Transl Med 4: 136ra168.
    • (2012) Sci Transl Med , vol.4
    • Forshew, T.1    Murtaza, M.2    Parkinson, C.3    Gale, D.4    Tsui, D.W.5
  • 21
    • 79958842027 scopus 로고    scopus 로고
    • Quantitative and sensitive detection of rare mutations using droplet-based microfluidics
    • Pekin D, Skhiri Y, Baret J-C, Le Corre D, Mazutis L, et al. (2011) Quantitative and sensitive detection of rare mutations using droplet-based microfluidics. Lab on a Chip 11: 2156-2166.
    • (2011) Lab on a Chip , vol.11 , pp. 2156-2166
    • Pekin, D.1    Skhiri, Y.2    Baret, J.-C.3    Le Corre, D.4    Mazutis, L.5
  • 22
    • 0345097575 scopus 로고    scopus 로고
    • Formaldehyde-detoxifying role of the tetrahydromethanopterin-linked pathway in Methylobacterium extorquens AM1
    • Marx CJ, Chistoserdova L, Lidstrom ME, (2003) Formaldehyde-detoxifying role of the tetrahydromethanopterin-linked pathway in Methylobacterium extorquens AM1. J Bacteriol 185: 7160-7168.
    • (2003) J Bacteriol , vol.185 , pp. 7160-7168
    • Marx, C.J.1    Chistoserdova, L.2    Lidstrom, M.E.3
  • 23
    • 79957958115 scopus 로고    scopus 로고
    • Diminishing returns epistasis among beneficial mutations decelerates adaptation
    • Chou HH, Chiu HC, Delaney NF, Segre D, Marx CJ, (2011) Diminishing returns epistasis among beneficial mutations decelerates adaptation. Science 332: 1190-1192.
    • (2011) Science , vol.332 , pp. 1190-1192
    • Chou, H.H.1    Chiu, H.C.2    Delaney, N.F.3    Segre, D.4    Marx, C.J.5
  • 24
    • 70349690200 scopus 로고    scopus 로고
    • Fast growth increases the selective advantage of a mutation arising recurrently during evolution under metal limitation
    • Chou HH, Berthet J, Marx CJ, (2009) Fast growth increases the selective advantage of a mutation arising recurrently during evolution under metal limitation. PLoS Genet 5: e1000652.
    • (2009) PLoS Genet , vol.5
    • Chou, H.H.1    Berthet, J.2    Marx, C.J.3
  • 25
    • 84878305954 scopus 로고    scopus 로고
    • Clarity: An open source manager for laboratory automation
    • Delaney NF, Rojas Echenique JI, Marx CJ, (2012) Clarity: An open source manager for laboratory automation. J Lab Autom doi:10.1177/2211068212460237.
    • (2012) J Lab Autom
    • Delaney, N.F.1    Rojas Echenique, J.I.2    Marx, C.J.3
  • 28
    • 79551545281 scopus 로고    scopus 로고
    • Large scale loss of data in low-diversity illumina sequencing libraries can be recovered by deferred cluster calling
    • Krueger F, Andrews SR, Osborne CS, (2011) Large scale loss of data in low-diversity illumina sequencing libraries can be recovered by deferred cluster calling. PLoS One 6: e16607.
    • (2011) PLoS One , vol.6
    • Krueger, F.1    Andrews, S.R.2    Osborne, C.S.3
  • 29
    • 84861135633 scopus 로고    scopus 로고
    • Optimization of Gene Expression through Divergent Mutational Paths
    • Chou HH, Marx CJ, (2012) Optimization of Gene Expression through Divergent Mutational Paths. Cell Reports 1: 133-140.
    • (2012) Cell Reports , vol.1 , pp. 133-140
    • Chou, H.H.1    Marx, C.J.2
  • 30
    • 84863668598 scopus 로고    scopus 로고
    • Repeated, selection-driven genome reduction of accessory genes in experimental populations
    • Lee MC, Marx CJ, (2012) Repeated, selection-driven genome reduction of accessory genes in experimental populations. PLoS Genet 8: e1002651.
    • (2012) PLoS Genet , vol.8
    • Lee, M.C.1    Marx, C.J.2
  • 31
    • 56749107039 scopus 로고    scopus 로고
    • Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae
    • Kao KC, Sherlock G, (2008) Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae. Nat Genet 40: 1499-1504.
    • (2008) Nat Genet , vol.40 , pp. 1499-1504
    • Kao, K.C.1    Sherlock, G.2
  • 32
    • 55849152090 scopus 로고    scopus 로고
    • The effect of linkage on limits to artificial selection
    • Hill WG, Robertson A, (2007) The effect of linkage on limits to artificial selection. Genet Res 89: 311-336.
    • (2007) Genet Res , vol.89 , pp. 311-336
    • Hill, W.G.1    Robertson, A.2
  • 33
    • 61849168524 scopus 로고    scopus 로고
    • Clonal interference, multiple mutations and adaptation in large asexual populations
    • Fogle CA, Nagle JL, Desai MM, (2008) Clonal interference, multiple mutations and adaptation in large asexual populations. Genetics 180: 2163-2173.
    • (2008) Genetics , vol.180 , pp. 2163-2173
    • Fogle, C.A.1    Nagle, J.L.2    Desai, M.M.3
  • 34
    • 0033068946 scopus 로고    scopus 로고
    • The generation of multiple co-existing mal-regulatory mutations through polygenic evolution in glucose-limited populations of Escherichia coli
    • Notley-McRobb L, Ferenci T, (1999) The generation of multiple co-existing mal-regulatory mutations through polygenic evolution in glucose-limited populations of Escherichia coli. Environ Microbiol 1: 45-52.
    • (1999) Environ Microbiol , vol.1 , pp. 45-52
    • Notley-McRobb, L.1    Ferenci, T.2
  • 35
    • 2542583245 scopus 로고    scopus 로고
    • The fate of competing beneficial mutations in an asexual population
    • Gerrish PJ, Lenski RE, (1998) The fate of competing beneficial mutations in an asexual population. Genetica 102-103: 127-144.
    • (1998) Genetica , vol.102-103 , pp. 127-144
    • Gerrish, P.J.1    Lenski, R.E.2
  • 36
    • 0023376305 scopus 로고
    • Evolution of Escherichia coli during growth in a constant environment
    • Helling RB, Vargas CN, Adams J, (1987) Evolution of Escherichia coli during growth in a constant environment. Genetics 116: 349-358.
    • (1987) Genetics , vol.116 , pp. 349-358
    • Helling, R.B.1    Vargas, C.N.2    Adams, J.3
  • 37
    • 0018851543 scopus 로고
    • Regions of broad-host-range plasmid RK2 which are essential for replication and maintenance
    • Thomas CM, Meyer R, Helinski DR, (1980) Regions of broad-host-range plasmid RK2 which are essential for replication and maintenance. J Bacteriol 141: 213-222.
    • (1980) J Bacteriol , vol.141 , pp. 213-222
    • Thomas, C.M.1    Meyer, R.2    Helinski, D.R.3
  • 38
    • 70349674312 scopus 로고    scopus 로고
    • Asymmetric, bimodal trade-offs during adaptation of Methylobacterium to distinct growth substrates
    • Lee MC, Chou HH, Marx CJ, (2009) Asymmetric, bimodal trade-offs during adaptation of Methylobacterium to distinct growth substrates. Evolution 63: 2816-2830.
    • (2009) Evolution , vol.63 , pp. 2816-2830
    • Lee, M.C.1    Chou, H.H.2    Marx, C.J.3
  • 39
    • 0028365256 scopus 로고
    • Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial populations
    • Lenski RE, Travisano M, (1994) Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial populations. Proc Natl Acad Sci U S A 91: 6808-6814.
    • (1994) Proc Natl Acad Sci U S A , vol.91 , pp. 6808-6814
    • Lenski, R.E.1    Travisano, M.2
  • 40
    • 33847256353 scopus 로고    scopus 로고
    • The speed of evolution and maintenance of variation in asexual populations
    • Desai MM, Fisher DS, Murray AW, (2007) The speed of evolution and maintenance of variation in asexual populations. Curr Biol 17: 385-394.
    • (2007) Curr Biol , vol.17 , pp. 385-394
    • Desai, M.M.1    Fisher, D.S.2    Murray, A.W.3
  • 41
    • 0026279651 scopus 로고
    • Long-term experimental evolution in Escherichia coli. I. Adaptation and divergence during 2,000 generations
    • Lenski RE, Rose M R, Simpson, S C, Tadler, S C, (1991) Long-term experimental evolution in Escherichia coli. I. Adaptation and divergence during 2,000 generations. Am Nat 138: 1315-1341.
    • (1991) Am Nat , vol.138 , pp. 1315-1341
    • Lenski, R.E.1    Rose, M.R.2    Simpson, S.C.3    Tadler, S.C.4


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