메뉴 건너뛰기




Volumn 7, Issue , 2016, Pages

Droplet barcoding for massively parallel single-molecule deep sequencing

Author keywords

[No Author keywords available]

Indexed keywords

DNA; GENETIC ANALYSIS; HETEROGENEITY; MOLECULAR ANALYSIS; MUTATION; VIRUS;

EID: 84976609584     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms11784     Document Type: Article
Times cited : (82)

References (51)
  • 1
    • 72849144434 scopus 로고    scopus 로고
    • Sequencing technologies-The next generation
    • Metzker, M. L. Sequencing technologies-the next generation. Nat. Rev. Genet. 11, 31-46 (2010).
    • (2010) Nat. Rev. Genet. , vol.11 , pp. 31-46
    • Metzker, M.L.1
  • 2
    • 53649106195 scopus 로고    scopus 로고
    • Next-generation DNA sequencing
    • Shendure, J., Ji, H. Next-generation DNA sequencing. Nat. Biotechnol. 26, 1135-1145 (2008).
    • (2008) Nat. Biotechnol. , vol.26 , pp. 1135-1145
    • Shendure, J.1    Ji, H.2
  • 3
    • 75649124547 scopus 로고    scopus 로고
    • De novo assembly of human genomes with massively parallel short read sequencing
    • Li, R. et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265-272 (2010).
    • (2010) Genome Res. , vol.20 , pp. 265-272
    • Li, R.1
  • 4
    • 84874194145 scopus 로고    scopus 로고
    • Sequence assembly demystified
    • Nagarajan, N., Pop, M. Sequence assembly demystified. Nat. Rev. Genet. 14, 157-167 (2013).
    • (2013) Nat. Rev. Genet. , vol.14 , pp. 157-167
    • Nagarajan, N.1    Pop, M.2
  • 5
    • 84858386965 scopus 로고    scopus 로고
    • Unsupervised discovery of microbial population structure within metagenomes using nucleotide base composition
    • Saeed, I., Tang, S.-L., Halgamuge, S. K. Unsupervised discovery of microbial population structure within metagenomes using nucleotide base composition. Nucleic Acids Res. 40, e34 (2011).
    • (2011) Nucleic Acids Res. , vol.40 , pp. e34
    • Saeed, I.1    Tang, S.-L.2    Halgamuge, S.K.3
  • 7
    • 75749135218 scopus 로고    scopus 로고
    • Metagenomics: Facts and artifacts, and computational challenges
    • Wooley, J. C., Ye, Y. Metagenomics: facts and artifacts, and computational challenges. J. Comput. Sci. Technol. 25, 71-81 (2009).
    • (2009) J. Comput. Sci. Technol. , vol.25 , pp. 71-81
    • Wooley, J.C.1    Ye, Y.2
  • 8
    • 77954202495 scopus 로고    scopus 로고
    • A statistical method for the detection of variants from nextgeneration resequencing of DNA pools
    • Bansal, V. A statistical method for the detection of variants from nextgeneration resequencing of DNA pools. Bioinformatics 26, i318-i324 (2010).
    • (2010) Bioinformatics , vol.26 , pp. i318-i324
    • Bansal, V.1
  • 9
    • 79956314887 scopus 로고    scopus 로고
    • Genotype and SNP calling from next-generation sequencing data
    • Nielsen, R., Paul, J. S., Albrechtsen, A., Song, Y. S. Genotype and SNP calling from next-generation sequencing data. Nat. Rev. Genet. 12, 443-451 (2011).
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 443-451
    • Nielsen, R.1    Paul, J.S.2    Albrechtsen, A.3    Song, Y.S.4
  • 10
    • 84889677831 scopus 로고    scopus 로고
    • Mutational and fitness landscapes of an RNA virus revealed through population sequencing
    • Acevedo, A., Brodsky, L., Andino, R. Mutational and fitness landscapes of an RNA virus revealed through population sequencing. Nature 505, 686-690 (2014).
    • (2014) Nature , vol.505 , pp. 686-690
    • Acevedo, A.1    Brodsky, L.2    Andino, R.3
  • 11
    • 84863556835 scopus 로고    scopus 로고
    • Evolution and functional impact of rare coding variation from deep sequencing of human exomes
    • Tennessen, J. A. et al. Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science 337, 64-69 (2012).
    • (2012) Science , vol.337 , pp. 64-69
    • Tennessen, J.A.1
  • 12
    • 84856496549 scopus 로고    scopus 로고
    • Next generation sequencing and bioinformatic bottlenecks: The current state of metagenomic data analysis
    • Scholz, M. B., Lo, C.-C., Chain, P. S. Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. Curr. Opin. Biotechnol. 23, 9-15 (2012).
    • (2012) Curr. Opin. Biotechnol. , vol.23 , pp. 9-15
    • Scholz, M.B.1    Lo, C.-C.2    Chain, P.S.3
  • 13
    • 84880798154 scopus 로고    scopus 로고
    • Nonhybrid, finished microbial genome assemblies from longread SMRT sequencing data
    • Chin, C.-S. et al. Nonhybrid, finished microbial genome assemblies from longread SMRT sequencing data. Nat. Methods 10, 563-569 (2013).
    • (2013) Nat. Methods , vol.10 , pp. 563-569
    • Chin, C.-S.1
  • 14
    • 84905723571 scopus 로고    scopus 로고
    • Decoding long nanopore sequencing reads of natural DNA
    • Laszlo, A. H. et al. Decoding long nanopore sequencing reads of natural DNA. Nat. Biotechnol. 32, 829-833 (2014).
    • (2014) Nat. Biotechnol. , vol.32 , pp. 829-833
    • Laszlo, A.H.1
  • 15
  • 16
    • 79960226263 scopus 로고    scopus 로고
    • A method for counting PCR template molecules with application to next-generation sequencing
    • Casbon, J. A., Osborne, R. J., Brenner, S., Lichtenstein, C. P. A method for counting PCR template molecules with application to next-generation sequencing. Nucleic Acids Res. 39, e81 (2011).
    • (2011) Nucleic Acids Res. , vol.39 , pp. e81
    • Casbon, J.A.1    Osborne, R.J.2    Brenner, S.3    Lichtenstein, C.P.4
  • 17
    • 84875360897 scopus 로고    scopus 로고
    • Hierarchical molecular tagging to resolve long continuous sequences by massively parallel sequencing
    • Lundin, S. et al. Hierarchical molecular tagging to resolve long continuous sequences by massively parallel sequencing. Sci. Rep. 3, 1186 (2013).
    • (2013) Sci. Rep. , vol.3 , pp. 1186
    • Lundin, S.1
  • 18
    • 77449144323 scopus 로고    scopus 로고
    • Parallel tag-directed assembly of locally derived short sequence reads
    • Hiatt, J. B., Patwardhan, R. P., Turner, E. H., Lee, C., Shendure, J. Parallel, tag-directed assembly of locally derived short sequence reads. Nat. Methods 7, 119-122 (2010).
    • (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
  • 19
    • 84898654757 scopus 로고    scopus 로고
    • Whole-genome haplotyping using long reads and statistical methods
    • Kuleshov, V. et al. Whole-genome haplotyping using long reads and statistical methods. Nat. Biotechnol. 32, 261-266 (2014).
    • (2014) Nat. Biotechnol. , vol.32 , pp. 261-266
    • Kuleshov, V.1
  • 20
    • 84922537404 scopus 로고    scopus 로고
    • Haplotype-resolved whole-genome sequencing by contiguitypreserving transposition and combinatorial indexing
    • Amini, S. et al. Haplotype-resolved whole-genome sequencing by contiguitypreserving transposition and combinatorial indexing. Nat. Genet. 46, 1343-1349 (2014).
    • (2014) Nat. Genet. , vol.46 , pp. 1343-1349
    • Amini, S.1
  • 21
    • 84929684999 scopus 로고    scopus 로고
    • Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets
    • Macosko, E. Z. et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell 161, 1202-1214 (2015).
    • (2015) Cell , vol.161 , pp. 1202-1214
    • MacOsko, E.Z.1
  • 22
    • 84929684998 scopus 로고    scopus 로고
    • Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells
    • Klein, A. M. et al. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell 161, 1187-1201 (2015).
    • (2015) Cell , vol.161 , pp. 1187-1201
    • Klein, A.M.1
  • 23
    • 84930685084 scopus 로고    scopus 로고
    • High-throughput single-cell labeling (Hi-SCL) for RNA-seq using drop-based microfluidics
    • Rotem, A. et al. High-throughput single-cell labeling (Hi-SCL) for RNA-seq using drop-based microfluidics. PLoS ONE 10, e0116328 (2015).
    • (2015) PLoS ONE , vol.10 , pp. e0116328
    • Rotem, A.1
  • 24
    • 81255175501 scopus 로고    scopus 로고
    • High-throughput droplet digital PCR system for absolute quantitation of DNA copy number
    • Hindson, B. J. et al. High-throughput droplet digital PCR system for absolute quantitation of DNA copy number. Anal. Chem. 83, 8604-8610 (2011).
    • (2011) Anal. Chem. , vol.83 , pp. 8604-8610
    • Hindson, B.J.1
  • 25
    • 78649773164 scopus 로고    scopus 로고
    • Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition
    • Adey, A. et al. Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome Biol. 11, R119 (2010).
    • (2010) Genome Biol. , vol.11 , pp. R119
    • Adey, A.1
  • 26
    • 76449086930 scopus 로고    scopus 로고
    • Droplet merging in a straight microchannel using droplet size or viscosity difference
    • Jin, B.-J., Kim, Y. W., Lee, Y., Yoo, J. Y. Droplet merging in a straight microchannel using droplet size or viscosity difference. J. Micromech. Microeng. 20, 035003 (2010).
    • (2010) J. Micromech. Microeng. , vol.20 , pp. 035003
    • Jin, B.-J.1    Kim, Y.W.2    Lee, Y.3    Yoo, J.Y.4
  • 27
    • 79956361644 scopus 로고    scopus 로고
    • Faster multiple emulsification with drop splitting
    • Abate, A. R., Weitz, D. A. Faster multiple emulsification with drop splitting. Lab. Chip 11, 1911-1915 (2011).
    • (2011) Lab. Chip , vol.11 , pp. 1911-1915
    • Abate, A.R.1    Weitz, D.A.2
  • 28
    • 4544334667 scopus 로고    scopus 로고
    • Pinched flow fractionation: Continuous size separation of particles utilizing a laminar flow profile in a pinched microchannel
    • Yamada, M., Nakashima, M., Seki, M. Pinched flow fractionation: continuous size separation of particles utilizing a laminar flow profile in a pinched microchannel. Anal. Chem. 76, 5465-5471 (2004).
    • (2004) Anal. Chem. , vol.76 , pp. 5465-5471
    • Yamada, M.1    Nakashima, M.2    Seki, M.3
  • 29
    • 84867098660 scopus 로고    scopus 로고
    • Don't make a mista(g)ke: Is tag switching an overlooked source of error in amplicon pyrosequencing studies?
    • Carlsen, T. et al. Don't make a mista(g)ke: is tag switching an overlooked source of error in amplicon pyrosequencing studies? Fungal Ecol. 5, 747-749 (2012).
    • (2012) Fungal Ecol. , vol.5 , pp. 747-749
    • Carlsen, T.1
  • 30
    • 79951694175 scopus 로고    scopus 로고
    • Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
    • Aird, D. et al. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol. 12, R18 (2011).
    • (2011) Genome Biol. , vol.12 , pp. R18
    • Aird, D.1
  • 31
    • 77956838065 scopus 로고    scopus 로고
    • Advances in understanding cancer genomes through second-generation sequencing
    • Meyerson, M., Gabriel, S., Getz, G. Advances in understanding cancer genomes through second-generation sequencing. Nat. Rev. Genet. 11, 685-696 (2010).
    • (2010) Nat. Rev. Genet. , vol.11 , pp. 685-696
    • Meyerson, M.1    Gabriel, S.2    Getz, G.3
  • 32
    • 71749099456 scopus 로고    scopus 로고
    • Deep sequencing to reveal new variants in pooled DNA samples
    • Out, A. A. et al. Deep sequencing to reveal new variants in pooled DNA samples. Hum. Mutat. 30, 1703-1712 (2009).
    • (2009) Hum. Mutat. , vol.30 , pp. 1703-1712
    • Out, A.A.1
  • 33
    • 61849172898 scopus 로고    scopus 로고
    • Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes
    • Simen, B. B. et al. 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).
    • (2009) J. Infect. Dis. , vol.199 , pp. 693-701
    • Simen, B.B.1
  • 34
    • 84889659729 scopus 로고    scopus 로고
    • High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing
    • Lou, D. I. et al. High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing. Proc. Natl Acad. Sci. USA 110, 19872-19877 (2013).
    • (2013) Proc. Natl Acad. Sci. USA , vol.110 , pp. 19872-19877
    • Lou, D.I.1
  • 35
    • 0037167852 scopus 로고    scopus 로고
    • Detecting recent positive selection in the human genome from haplotype structure
    • Sabeti, P. C. et al. Detecting recent positive selection in the human genome from haplotype structure. Nature 419, 832-837 (2002).
    • (2002) Nature , vol.419 , pp. 832-837
    • Sabeti, P.C.1
  • 36
    • 84906220576 scopus 로고    scopus 로고
    • Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations
    • Giallonardo, F. D. et al. Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations. Nucleic Acids Res. 42, e115-e115 (2014).
    • (2014) Nucleic Acids Res. , vol.42 , pp. e115-e115
    • Giallonardo, F.D.1
  • 37
    • 84859178440 scopus 로고    scopus 로고
    • De novo genome assembly: What every biologist should know
    • Baker, M. De novo genome assembly: what every biologist should know. Nat. Methods 9, 333-337 (2012).
    • (2012) Nat. Methods , vol.9 , pp. 333-337
    • Baker, M.1
  • 38
    • 84942253473 scopus 로고    scopus 로고
    • Metassembler: Merging and optimizing de novo genome assemblies
    • Wences, A. H., Schatz, M. C. Metassembler: merging and optimizing de novo genome assemblies. Genome Biol. 16, 207 (2015).
    • (2015) Genome Biol. , vol.16 , pp. 207
    • Wences, A.H.1    Schatz, M.C.2
  • 39
    • 18344396798 scopus 로고    scopus 로고
    • Comprehensive human genome amplification using multiple displacement amplification
    • Dean, F. B. et al. Comprehensive human genome amplification using multiple displacement amplification. Proc. Natl Acad. Sci. USA 99, 5261-5266 (2002).
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 5261-5266
    • Dean, F.B.1
  • 41
    • 79955421607 scopus 로고    scopus 로고
    • Air-bubble-triggered drop formation in microfluidics
    • Abate, A. R., Weitz, D. A. Air-bubble-triggered drop formation in microfluidics. Lab. Chip 11, 1713 (2011).
    • (2011) Lab. Chip , vol.11 , pp. 1713
    • Abate, A.R.1    Weitz, D.A.2
  • 42
    • 33646536797 scopus 로고    scopus 로고
    • Synthesis of monodisperse bicolored janus particles with electrical anisotropy using a microfluidic co-flow system
    • Nisisako, T., Torii, T., Takahashi, T., Takizawa, Y. Synthesis of monodisperse bicolored janus particles with electrical anisotropy using a microfluidic co-flow system. Adv. Mater. 18, 1152-1156 (2006).
    • (2006) Adv. Mater. , vol.18 , pp. 1152-1156
    • Nisisako, T.1    Torii, T.2    Takahashi, T.3    Takizawa, Y.4
  • 43
    • 84856142118 scopus 로고    scopus 로고
    • High throughput production of single core double emulsions in a parallelized microfluidic device
    • Romanowsky, M. B., Abate, A. R., Rotem, A., Holtze, C., Weitz, D. A. High throughput production of single core double emulsions in a parallelized microfluidic device. Lab. Chip 12, 802 (2012).
    • (2012) Lab. Chip , vol.12 , pp. 802
    • Romanowsky, M.B.1    Abate, A.R.2    Rotem, A.3    Holtze, C.4    Weitz, D.A.5
  • 44
    • 84986243076 scopus 로고    scopus 로고
    • Startups use short-read data to expand long-read sequencing market
    • Eisenstein, M. Startups use short-read data to expand long-read sequencing market. Nat. Biotechnol. 33, 433-435 (2015).
    • (2015) Nat. Biotechnol. , vol.33 , pp. 433-435
    • Eisenstein, M.1
  • 45
    • 84960894307 scopus 로고    scopus 로고
    • Haplotyping germline and cancer genomes with high-throughput linked-read sequencing
    • Zheng, G. X. Y. et al. Haplotyping germline and cancer genomes with high-throughput linked-read sequencing. Nat. Biotechnol. 34, 303-311 (2016).
    • (2016) Nat. Biotechnol. , vol.34 , pp. 303-311
    • Zheng, G.X.Y.1
  • 46
    • 84941931026 scopus 로고    scopus 로고
    • Rapid, targeted and culture-free viral infectivity assay in drop-based microfluidics
    • Tao, Y. et al. Rapid, targeted and culture-free viral infectivity assay in drop-based microfluidics. Lab. Chip 15, 3934-3940 (2015).
    • (2015) Lab. Chip , vol.15 , pp. 3934-3940
    • Tao, Y.1
  • 47
    • 84943357780 scopus 로고    scopus 로고
    • Artifact-free quantification and sequencing of rare recombinant viruses using drop-based microfluidics
    • Tao, Y. et al. Artifact-free quantification and sequencing of rare recombinant viruses using drop-based microfluidics. Chembiochem. Eur. J. Chem. Biol. 16, 2167-2171 (2015).
    • (2015) Chembiochem. Eur. J. Chem. Biol. , vol.16 , pp. 2167-2171
    • Tao, Y.1
  • 48
    • 0032403465 scopus 로고    scopus 로고
    • Rapid prototyping of microfluidic systems in poly(dimethylsiloxane)
    • Duffy, D. C., McDonald, J. C., Schueller, O. J. A., Whitesides, G. M. Rapid prototyping of microfluidic systems in poly(dimethylsiloxane). Anal. Chem. 70, 4974-4984 (1998).
    • (1998) Anal. Chem. , vol.70 , pp. 4974-4984
    • Duffy, D.C.1    McDonald, J.C.2    Schueller, O.J.A.3    Whitesides, G.M.4
  • 49
    • 84913593681 scopus 로고    scopus 로고
    • Tn5 transposase and tagmentation procedures for massively scaled sequencing projects
    • Picelli, S. et al. Tn5 transposase and tagmentation procedures for massively scaled sequencing projects. Genome Res. 24, 2033-2040 (2014).
    • (2014) Genome Res. , vol.24 , pp. 2033-2040
    • Picelli, S.1
  • 50
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead, B., Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359 (2012).
    • (2012) Nat. Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 51
    • 84861760530 scopus 로고    scopus 로고
    • IDBA-UD: A de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
    • Peng, Y., Leung, H. C. M., Yiu, S. M., Chin, F. Y. L. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28, 1420-1428 (2012).
    • (2012) Bioinformatics , vol.28 , pp. 1420-1428
    • Peng, Y.1    Leung, H.C.M.2    Yiu, S.M.3    Chin, F.Y.L.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.