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Volumn 7, Issue 1, 2017, Pages

Massively parallel whole genome amplification for single-cell sequencing using droplet microfluidics

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL GENOME; BACTERIUM; CHEMISTRY; DNA SEQUENCE; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN GENOME; MICROBIOLOGY; MICROFLUIDICS; NEOPLASM; PROCEDURES; SINGLE CELL ANALYSIS; SOIL; TUMOR CELL CULTURE; WHOLE GENOME SEQUENCING;

EID: 85024126714     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/s41598-017-05436-4     Document Type: Article
Times cited : (103)

References (46)
  • 1
    • 84958606331 scopus 로고    scopus 로고
    • Single-cell genome sequencing: Current state of the science
    • Gawad, C., Koh, W. & Quake, S. R. Single-cell genome sequencing: current state of the science. Nat Rev Genet 17, 175-188 (2016).
    • (2016) Nat Rev Genet , vol.17 , pp. 175-188
    • Gawad, C.1    Koh, W.2    Quake, S.R.3
  • 2
    • 84929661801 scopus 로고    scopus 로고
    • Advances and applications of single-cell sequencing technologies
    • Wang, Y. & Navin, N. E. Advances and applications of single-cell sequencing technologies. Mol Cell 58, 598-609 (2015).
    • (2015) Mol Cell , vol.58 , pp. 598-609
    • Wang, Y.1    Navin, N.E.2
  • 3
    • 84881138595 scopus 로고    scopus 로고
    • Insights into the phylogeny and coding potential of microbial dark matter
    • Rinke, C. et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431-437 (2013).
    • (2013) Nature , vol.499 , pp. 431-437
    • Rinke, C.1
  • 4
    • 84906317195 scopus 로고    scopus 로고
    • Recent advances in genomic DNA sequencing of microbial species from single cells
    • Lasken, R. S. & McLean, J. S. Recent advances in genomic DNA sequencing of microbial species from single cells. Nat Rev Genet 15, 577-584 (2014).
    • (2014) Nat Rev Genet , vol.15 , pp. 577-584
    • Lasken, R.S.1    McLean, J.S.2
  • 5
    • 84887315590 scopus 로고    scopus 로고
    • Mosaic copy number variation in human neurons
    • McConnell, M. J. et al. Mosaic copy number variation in human neurons. Science 342, 632-637 (2013).
    • (2013) Science , vol.342 , pp. 632-637
    • McConnell, M.J.1
  • 6
    • 85027920141 scopus 로고    scopus 로고
    • Cancer genomics: One cell at a time
    • Navin, N. E. Cancer genomics: one cell at a time. Genome Biol 15, 452 (2014).
    • (2014) Genome Biol , vol.15 , pp. 452
    • Navin, N.E.1
  • 7
    • 84907889523 scopus 로고    scopus 로고
    • Microfluidic whole genome amplification device for single cell sequencing
    • Yu, Z., Lu, S. & Huang, Y. Microfluidic whole genome amplification device for single cell sequencing. Anal Chem 86, 9386-9390 (2014).
    • (2014) Anal Chem , vol.86 , pp. 9386-9390
    • Yu, Z.1    Lu, S.2    Huang, Y.3
  • 8
    • 34848895943 scopus 로고    scopus 로고
    • Nanoliter reactors improve multiple displacement amplification of genomes from single cells
    • Marcy, Y. et al. Nanoliter reactors improve multiple displacement amplification of genomes from single cells. PLoS Genet 3, 1702-1708 (2007).
    • (2007) PLoS Genet , vol.3 , pp. 1702-1708
    • Marcy, Y.1
  • 9
    • 84907194200 scopus 로고    scopus 로고
    • Parallel single cancer cell whole genome amplification using button-valve assisted mixing in nanoliter chambers
    • Yang, Y., Swennenhuis, J. F., Rho, H. S., Le Gac, S. & Terstappen, L. W. Parallel single cancer cell whole genome amplification using button-valve assisted mixing in nanoliter chambers. PLoS One 9, e107958 (2014).
    • (2014) PLoS One , vol.9 , pp. e107958
    • Yang, Y.1    Swennenhuis, J.F.2    Rho, H.S.3    Le Gac, S.4    Terstappen, L.W.5
  • 10
    • 84943170018 scopus 로고    scopus 로고
    • Single-cell genetic analysis using automated microfluidics to resolve somatic mosaicism
    • Szulwach, K. E. et al. Single-Cell Genetic Analysis Using Automated Microfluidics to Resolve Somatic Mosaicism. PLoS One 10, e0135007 (2015).
    • (2015) PLoS One , vol.10 , pp. e0135007
    • Szulwach, K.E.1
  • 11
    • 84920645442 scopus 로고    scopus 로고
    • A quantitative comparison of single-cell whole genome amplification methods
    • de Bourcy, C. F. et al. A quantitative comparison of single-cell whole genome amplification methods. PLoS One 9, e105585 (2014).
    • (2014) PLoS One , vol.9 , pp. e105585
    • De Bourcy, C.F.1
  • 12
    • 84890055556 scopus 로고    scopus 로고
    • Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells
    • Gole, J. et al. Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells. Nat Biotechnol 31, 1126-1132 (2013).
    • (2013) Nat Biotechnol , vol.31 , pp. 1126-1132
    • Gole, J.1
  • 13
    • 79952351866 scopus 로고    scopus 로고
    • Digital MDA for enumeration of total nucleic acid contamination
    • Blainey, P. C. & Quake, S. R. Digital MDA for enumeration of total nucleic acid contamination. Nucleic Acids Res 39, e19 (2011).
    • (2011) Nucleic Acids Res , vol.39 , pp. e19
    • Blainey, P.C.1    Quake, S.R.2
  • 14
    • 84964992835 scopus 로고    scopus 로고
    • Droplet-based microfluidics in drug discovery, transcriptomics and highthroughput molecular genetics
    • Shembekar, N., Chaipan, C., Utharala, R. & Merten, C. A. Droplet-based microfluidics in drug discovery, transcriptomics and highthroughput molecular genetics. Lab Chip 16, 1314-1331 (2016).
    • (2016) Lab Chip , vol.16 , pp. 1314-1331
    • Shembekar, N.1    Chaipan, C.2    Utharala, R.3    Merten, C.A.4
  • 15
    • 84942874388 scopus 로고    scopus 로고
    • Uniform and accurate single-cell sequencing based on emulsion whole-genome amplification
    • Fu, Y. et al. Uniform and accurate single-cell sequencing based on emulsion whole-genome amplification. Proc Natl Acad Sci USA 112, 11923-11928 (2015).
    • (2015) Proc Natl Acad Sci USA , vol.112 , pp. 11923-11928
    • Fu, Y.1
  • 16
    • 84946571003 scopus 로고    scopus 로고
    • Monodisperse picoliter droplets for low-bias and contamination-free reactions in single-cell whole genome amplification
    • Nishikawa, Y. et al. Monodisperse Picoliter Droplets for Low-Bias and Contamination-Free Reactions in Single-Cell Whole Genome Amplification. PLoS One 10, e0138733 (2015).
    • (2015) PLoS One , vol.10 , pp. e0138733
    • Nishikawa, Y.1
  • 17
    • 85016146681 scopus 로고    scopus 로고
    • Digital droplet multiple displacement amplification (ddMDA) for whole genome sequencing of limited DNA samples
    • Rhee, M., Light, Y. K., Meagher, R. J. & Singh, A. K. Digital Droplet Multiple Displacement Amplification (ddMDA) for Whole Genome Sequencing of Limited DNA Samples. PLoS One 11, e0153699 (2016).
    • (2016) PLoS One , vol.11 , pp. e0153699
    • Rhee, M.1    Light, Y.K.2    Meagher, R.J.3    Singh, A.K.4
  • 18
    • 84965129052 scopus 로고    scopus 로고
    • Enhanced sequencing coverage with digital droplet multiple displacement amplification
    • Sidore, A. M., Lan, F., Lim, S. W. & Abate, A. R. Enhanced sequencing coverage with digital droplet multiple displacement amplification. Nucleic Acids Res 44, e66 (2016).
    • (2016) Nucleic Acids Res , vol.44 , pp. e66
    • Sidore, A.M.1    Lan, F.2    Lim, S.W.3    Abate, A.R.4
  • 19
    • 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
  • 20
    • 69549097381 scopus 로고    scopus 로고
    • A fast and efficient microfluidic system for highly selective one-to-one droplet fusion
    • Mazutis, L., Baret, J. C. & Griffiths, A. D. A fast and efficient microfluidic system for highly selective one-to-one droplet fusion. Lab Chip 9, 2665-2672 (2009).
    • (2009) Lab Chip , vol.9 , pp. 2665-2672
    • Mazutis, L.1    Baret, J.C.2    Griffiths, A.D.3
  • 21
    • 84980398168 scopus 로고    scopus 로고
    • Virtual microfluidics for digital quantification and single-cell sequencing
    • Xu, L., Brito, I. L., Alm, E. J. & Blainey, P. C. Virtual microfluidics for digital quantification and single-cell sequencing. Nat Methods 13, 759-762 (2016).
    • (2016) Nat Methods , vol.13 , pp. 759-762
    • Xu, L.1    Brito, I.L.2    Alm, E.J.3    Blainey, P.C.4
  • 22
    • 84861328656 scopus 로고    scopus 로고
    • Artificial polyploidy improves bacterial single cell genome recovery
    • Dichosa, A. E. et al. Artificial polyploidy improves bacterial single cell genome recovery. PLoS One 7, e37387 (2012).
    • (2012) PLoS One , vol.7 , pp. e37387
    • Dichosa, A.E.1
  • 23
    • 84920678390 scopus 로고    scopus 로고
    • Reconstructing each cell's genome within complex microbial communities-dream or reality?
    • Clingenpeel, S., Clum, A., Schwientek, P., Rinke, C. & Woyke, T. Reconstructing each cell's genome within complex microbial communities-dream or reality? Front Microbiol 5, 771 (2014).
    • (2014) Front Microbiol , vol.5 , pp. 771
    • Clingenpeel, S.1    Clum, A.2    Schwientek, P.3    Rinke, C.4    Woyke, T.5
  • 24
    • 84937040910 scopus 로고    scopus 로고
    • CheckM: Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
    • Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25, 1043-1055 (2015).
    • (2015) Genome Res , vol.25 , pp. 1043-1055
    • Parks, D.H.1    Imelfort, M.2    Skennerton, C.T.3    Hugenholtz, P.4    Tyson, G.W.5
  • 26
    • 84906238686 scopus 로고    scopus 로고
    • Clonal evolution in breast cancer revealed by single nucleus genome sequencing
    • Wang, Y. et al. Clonal evolution in breast cancer revealed by single nucleus genome sequencing. Nature 512, 155-160 (2014).
    • (2014) Nature , vol.512 , pp. 155-160
    • Wang, Y.1
  • 27
    • 84882455458 scopus 로고    scopus 로고
    • Single-cell sequencing-based technologies will revolutionize whole-organism science
    • Shapiro, E., Biezuner, T. & Linnarsson, S. Single-cell sequencing-based technologies will revolutionize whole-organism science. Nat Rev Genet 14, 618-630 (2013).
    • (2013) Nat Rev Genet , vol.14 , pp. 618-630
    • Shapiro, E.1    Biezuner, T.2    Linnarsson, S.3
  • 28
    • 84942917849 scopus 로고    scopus 로고
    • The first five years of single-cell cancer genomics and beyond
    • Navin, N. E. The first five years of single-cell cancer genomics and beyond. Genome Res 25, 1499-1507 (2015).
    • (2015) Genome Res , vol.25 , pp. 1499-1507
    • Navin, N.E.1
  • 29
    • 84879517803 scopus 로고    scopus 로고
    • Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum
    • McLean, J. S. et al. Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum. Proc Natl Acad Sci USA 110, E2390-2399 (2013).
    • (2013) Proc Natl Acad Sci USA , vol.110 , pp. E2390-E2399
    • McLean, J.S.1
  • 30
    • 84899507119 scopus 로고    scopus 로고
    • Obtaining genomes from uncultivated environmental microorganisms using FACS-based single-cell genomics
    • Rinke, C. et al. Obtaining genomes from uncultivated environmental microorganisms using FACS-based single-cell genomics. Nat Protoc 9, 1038-1048 (2014).
    • (2014) Nat Protoc , vol.9 , pp. 1038-1048
    • Rinke, C.1
  • 31
    • 84979547050 scopus 로고    scopus 로고
    • Robust high-performance nanoliter-volume single-cell multiple displacement amplification on planar substrates
    • Leung, K. et al. Robust high-performance nanoliter-volume single-cell multiple displacement amplification on planar substrates. Proc Natl Acad Sci USA 113, 8484-8489 (2016).
    • (2016) Proc Natl Acad Sci USA , vol.113 , pp. 8484-8489
    • Leung, K.1
  • 32
    • 84922247524 scopus 로고    scopus 로고
    • Droplet-based microfluidics for high-throughput screening of a metagenomic library for isolation of microbial enzymes
    • Hosokawa, M. et al. Droplet-based microfluidics for high-throughput screening of a metagenomic library for isolation of microbial enzymes. Biosensors & bioelectronics 67, 379-385 (2015).
    • (2015) Biosensors & Bioelectronics , vol.67 , pp. 379-385
    • Hosokawa, M.1
  • 33
    • 78650594173 scopus 로고    scopus 로고
    • High-throughput injection with microfluidics using picoinjectors
    • Abate, A. R., Hung, T., Mary, P., Agresti, J. J. & Weitz, D. A. High-throughput injection with microfluidics using picoinjectors. Proc Natl Acad Sci USA 107, 19163-19166 (2010).
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 19163-19166
    • Abate, A.R.1    Hung, T.2    Mary, P.3    Agresti, J.J.4    Weitz, D.A.5
  • 34
    • 70349682763 scopus 로고    scopus 로고
    • Multi-step microfluidic droplet processing: Kinetic analysis of an in vitro translated enzyme
    • Mazutis, L. et al. Multi-step microfluidic droplet processing: kinetic analysis of an in vitro translated enzyme. Lab Chip 9, 2902-2908 (2009).
    • (2009) Lab Chip , vol.9 , pp. 2902-2908
    • Mazutis, L.1
  • 35
    • 33747130345 scopus 로고    scopus 로고
    • Miniaturising the laboratory in emulsion droplets
    • Griffiths, A. D. & Tawfik, D. S. Miniaturising the laboratory in emulsion droplets. Trends Biotechnol 24, 395-402 (2006).
    • (2006) Trends Biotechnol , vol.24 , pp. 395-402
    • Griffiths, A.D.1    Tawfik, D.S.2
  • 36
    • 84976609584 scopus 로고    scopus 로고
    • Droplet barcoding for massively parallel single-molecule deep sequencing
    • Lan, F., Haliburton, J. R., Yuan, A. & Abate, A. R. Droplet barcoding for massively parallel single-molecule deep sequencing. Nat Commun 7, 11784 (2016).
    • (2016) Nat Commun , vol.7 , pp. 11784
    • Lan, F.1    Haliburton, J.R.2    Yuan, A.3    Abate, A.R.4
  • 37
    • 85010982914 scopus 로고    scopus 로고
    • Sequencing thousands of single-cell genomes with combinatorial indexing
    • Vitak, S. A. et al. Sequencing thousands of single-cell genomes with combinatorial indexing. Nat Methods 14, 302-308 (2017).
    • (2017) Nat Methods , vol.14 , pp. 302-308
    • Vitak, S.A.1
  • 38
    • 84930006926 scopus 로고    scopus 로고
    • Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing
    • Cusanovich, D. A. et al. Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing. Science 348, 910-914 (2015).
    • (2015) Science , vol.348 , pp. 910-914
    • Cusanovich, D.A.1
  • 39
    • 85014379098 scopus 로고    scopus 로고
    • SAG-QC: Quality control of single amplified genome information by subtracting non-target sequences based on sequence compositions
    • Maruyama, T., Mori, T., Yamagishi, K. & Takeyama, H. SAG-QC: quality control of single amplified genome information by subtracting non-target sequences based on sequence compositions. BMC Bioinformatics 18, 152 (2017).
    • (2017) BMC Bioinformatics , vol.18 , pp. 152
    • Maruyama, T.1    Mori, T.2    Yamagishi, K.3    Takeyama, H.4
  • 40
    • 84930816939 scopus 로고    scopus 로고
    • ProDeGe: A computational protocol for fully automated decontamination of genomes
    • Tennessen, K. et al. ProDeGe: a computational protocol for fully automated decontamination of genomes. ISME J 10, 269-272 (2016).
    • (2016) ISME J , vol.10 , pp. 269-272
    • Tennessen, K.1
  • 41
    • 84878724342 scopus 로고    scopus 로고
    • Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage
    • Dodsworth, J. A. et al. Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage. Nat Commun 4, 1854 (2013).
    • (2013) Nat Commun , vol.4 , pp. 1854
    • Dodsworth, J.A.1
  • 42
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 43
    • 68549104404 scopus 로고    scopus 로고
    • The sequence alignment/map format and SAMtools
    • Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1
  • 45
    • 84876266928 scopus 로고    scopus 로고
    • QUAST: Quality assessment tool for genome assemblies
    • Gurevich, A., Saveliev, V., Vyahhi, N. & Tesler, G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29, 1072-1075 (2013).
    • (2013) Bioinformatics , vol.29 , pp. 1072-1075
    • Gurevich, A.1    Saveliev, V.2    Vyahhi, N.3    Tesler, G.4
  • 46
    • 77956295988 scopus 로고    scopus 로고
    • The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
    • McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20, 1297-1303 (2010).
    • (2010) Genome Res , vol.20 , pp. 1297-1303
    • McKenna, A.1


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