Digital droplet multiple displacement amplification (DDMDA) for whole genome sequencing of limited DNA samples

PLoS ONE

Volumn 11, Issue 5, 2016, Pages

  Rhee, Minsoung ^a,b   Light, Yooli K ^a   Meagher, Robert J ^a   Singh, Anup K ^a  

^a SANDIA NATIONAL LABORATORIES   (United States)

^b ILLUMINA INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPETITION; ENVIRONMENTAL MICROBIOLOGY; FORENSIC SCIENCE; MULTIPLE DISPLACEMENT AMPLIFICATION; WHOLE GENOME SEQUENCING; BACTERIAL GENOME; DNA SEQUENCE; ESCHERICHIA COLI; GENETICS; MICROFLUIDICS; NUCLEIC ACID AMPLIFICATION; PROCEDURES;

BACTERIAL DNA;

DNA, BACTERIAL; ESCHERICHIA COLI; GENOME, BACTERIAL; MICROFLUIDICS; NUCLEIC ACID AMPLIFICATION TECHNIQUES; SEQUENCE ANALYSIS, DNA;

EID: 85016146681     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0153699     Document Type: Article

References (42)

1. Gole J, Gore A, Richards A, Chiu Y- J, Fung H- L, Bushman D, et al. (2013) Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells. Nat Biotechnol 31: 1126–1132. doi: 10.1038/nbt.2720 PMID: 24213699
2. Zhang K, Martiny AC, Reppas NB, Barry KW, Malek J, Chisholm SW, et al. (2006) Sequencing genomes from single cells by polymerase cloning. Nat Biotechnol 24: 680–686. PMID: 16732271
3. Rodrigue S, Malmstrom RR, Berlin AM, Birren BW, Henn MR, Chisholm SW. (2009) Whole genome amplification and de novo assembly of single bacterial cells. PLoS ONE 4: e6864. doi: 10.1371/journal. pone.0006864 PMID: 19724646
4. Marcy Y, Ouverney C, Bik EM, Lösekann T, Ivanova N, Martin HG, et al. (2007) Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc Natl Acad Sci USA 104: 11889–11894. PMID: 17620602
5. Wang J, Fan HC, Behr B, Quake SR (2012) Genome-wide single-cell analysis of recombination activity and de novo mutation rates in human sperm. Cell 150: 402–412. doi: 10.1016/j.cell.2012.06.030 PMID: 22817899
6. Fitzsimons MS, Novotny M, Lo CC, Dichosa AE, Yee-Greenbaum JL, Snook JP, et al. (2013) Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome. Genome Res 23: 878–888. doi: 10.1101/gr.142208.112 PMID: 23493677
7. Motley ST, Picuri JM, Crowder CD, Minich JJ, Hofstadler SA, Eshoo MW. (2014) Improved Multiple Displacement Amplification (iMDA) and Ultraclean Reagents. BMC Genomics 15: 443. doi: 10.1186/1471-2164-15-443 PMID: 24906487
8. Asiello PJ, Baeumner AJ (2011) Miniaturized isothermal nucleic acid amplification, a review. Lap Chip 11: 1420–1430.
9. Zong C, Lu S, Chapman AR, Xie S (2012) Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science 338: 1622–1626. doi: 10.1126/science.1229164 PMID: 23258894
10. Blainey PC, Quake SR (2011) Digital MDA for enumeration of total nucleic acid contamination. Nucleic Acids Res 39: e19. doi: 10.1093/nar/gkq1074 PMID: 21071419
11. Esteban JA, Salas M, Blanco L (1993) Fidelity of phi 29 DNA polymerase comparison between protein-primed initiation and DNA polymerization. J Biol Chem 268: 2719–2726. PMID: 8428945
12. Paez JG, Lin M, Beroukhim R, Lee JC, Zhao X, Richter DJ, et al. (2004) Genome coverage and sequence fidelity of phi29 polymerase-based multiple strand displacement whole genome amplification. Nucleic Acids Res 32: e71. PMID: 15150323
13. Lizardi PM, Huangm X, Zhu Z, Bray-Ward P, Thomas DC, Ward DC. (1998) Mutation detection and single-molecule counting using isothermal rolling-circle amplification. Nat Genet 19: 225–232. PMID: 9662393
14. Dean FB, Nelson JR, Giesler TL, Lasken RS (2011) Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiplyprimed rolling circle amplification. Genome Res 11: 1095–1099.
15. Hosono S, Faruqi AF, Dean FB, Du Y, Sun Z, Wu X, et al. (2003) Unbiased whole genome amplification directly from clinical samples. Genome Res 13: 954–964. PMID: 12695328
16. Nelson JR, Cai YC, Giesler TL, Farchaus JW, Sundaram ST, Ortiz-Rivera M, et al. (2003) TempliPhi, phi29 DNA polymerase based rolling circle amplification of templates for DNA sequencing. Biotechniques 32: S44–S47.
17. Lage JM, Leamon JH, Pejovis T, Hamann S, Lacey M (2003) Whole genome analysis of genetic alterations in small DNA samples using hyperbranched strand displacement amplification and array-CGH. Genome Res 13: 294–307. PMID: 12566408
18. Woyke T, Tighe D, Mavromatis K, Clum A, Copeland A, Schackwitz W, et al. (2010) One bacterial cell, one complete genome. PLoS ONE 5: e10314. doi: 10.1371/journal.pone.0010314 PMID: 20428247
19. Yilmaz S, Singh AK (2012) Single cell genome sequencing. Curr Opin Biotech 23: 437–443. doi: 10. 1016/j.copbio.2011.11.018 PMID: 22154471
20. Raghunathan A, Ferguson HR Jr, Bornarth C. Song W. Driscoll M, Lasken RS. (2005) Genomic DNA amplification from a single bacterium. Appl Environ Microbiol 71: 3342–3347. PMID: 15933038
21. Hutchison CA III, Smith HO, Pfannkoch C, Venter JC (2005) Cell-free cloning using phi29 DNA polymerase. Proc Natl Acad Sci USA. 102: 17332–17336. PMID: 16286637
22. Marcy Y, Ishoey T, Lasken RS, Stockkwell TB, Walenz BP, Halpern AL, et al. (2007) Nanoliter reactors improve multiple displacement amplification of genomes from single cells. PLoS Genet 3: e155.
23. Rhee M, Light YK, Yilmaz S, Adams PD, Saxena D, Meagher RJ, et al. (2014) Pressure stabilizer for reproducible picoinjection in droplet microfluidic systems. Lab Chip 14: 4533–4539. doi: 10.1039/ c4lc00823e PMID: 25270338
24. Champlot S, Berthelot C, Pruvost M, Bennett EA, Grange T, Geigl E-M. (2010) An efficient multistrategy DNA decontamination procedure of PCR reagents for hypersensitive PCR applications. PLoS One 5: e13042. doi: 10.1371/journal.pone.0013042 PMID: 20927390
25. Woyke T, Sczyrba A, Lee J, Rinke C, Tighe D, Clingenpeel S, et al. (2011) Decontamination of MDA reagents for single cell whole genome amplification. PLoS One 6: e26161. doi: 10.1371/journal.pone. 0026161 PMID: 22028825
26. Bolger AM, Lohse M, Usadel B (2014) A flexible trimmer for Illumina Sequence Data. Bioinformatics 30: 2114–2120. doi: 10.1093/bioinformatics/btu170 PMID: 24695404
27. Langmead B, Salzberm SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Meth 9: 357–359.
28. Alikhan N, Petty NK, Zakour NLB, Beatson SA (2012) BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 12: 402.
29. Phanstiel DH (2014) Sushi: Tools for visualizing genomics data. R package version 1.4.0.
30. Quinlan A, Hail IM. (2010) BEDTools: a flexible suite of utilites for comparing genomic features. Bioinformatics 26: 1072–1075.
31. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19: 455–477. doi: 10.1089/cmb.2012.0021 PMID: 22506599
32. Gurevich A, Saveliev V, Vyahhi N, Tesler G. (2013) QUAST: quality assessment tool for genome assemblies, Bioinformatics 29: 1072–1075. doi: 10.1093/bioinformatics/btt086 PMID: 23422339
33. Lasken RS (2009) Genomic DNA amplification by the multiple displacement amplification (MDA) method. Biochem Soc Trans 37: 450–453. doi: 10.1042/BST0370450 PMID: 19290880
34. de Bourcy CFA, Vlaminck ID, Kanbar JN, Wang J, Gawad C, Quake SR (2014) A Quantitative Comparison of Single-Cell Whole Genome Amplification Methods. PLoS ONE 9: e105585. doi: 10.1371/ journal.pone.0105585 PMID: 25136831
35. Syvanen AC (2005) Toward genome-wide SNP genotyping. Nat Genet 37: S5–S10. PMID: 15920530
36. Dietmaier W, Hartmann A, Wallinger S, Heinmöller E, Kerner T, Endl E, et al. (1999) Multiple mutation analyses in single tumor cells with improved whole genome amplification. J Am J Path 1999, 154: 83–95. PMID: 9916922
37. Abulencia CB, Wyborski DL, Garcia JA, Podar M, Chen W, Chang SH, et al. (2006) Environmental whole-genome amplification to access microbial populations in contaminated sediments. Appl Environ Microbiol 72: 3291–3301. PMID: 16672469
38. Marine R, McCarren C, Vorrasane V, Nasko D, Crowgey E (2014) Caught in the middle with multiple displacement amplification: the myth of pooling for avoiding multiple displacement amplification bias in a metagenome. Microbiome 2: 3. doi: 10.1186/2049-2618-2-3 PMID: 24475755
39. Sidore AM, Lan F, Lim SW, Abate AR (2015) Enhanced sequencing coverage with digital droplet multiple displacement amplification. Nucleic Acids Res. doi: 10.1093/nar/gkv1493
40. Fu Y, Li C, Lu S, Zhou W, Tang F, Xie XS, Huang Y (2015) Uniform and accurate single-cell sequencing based on emulsion whole-genome amplification. Proc Natil Acad Sci USA 112: 11932–11928.
41. Rhee M, Liu P, Meagher RJ, Light YK, Singh AK (2014) Versatile on-demand droplet generation for controlled encapsulation. Biomicrofluidics 8: 034112. doi: 10.1063/1.4874715 PMID: 25379072
42. Niu X, deMello AJ (2012) Building droplet-based microfluidic systems for biological analysis. Biochem SocTrans 40: 615–623.