A quantitative comparison of single-cell whole genome amplification methods

PLoS ONE

Volumn 9, Issue 8, 2014, Pages

  De Bourcy, Charles F A ^a   De Vlaminck, Iwijn ^a,b,d   Kanbar, Jad N ^b,d   Wang, Jianbin ^b   Gawad, Charles ^a,b,c   Quake, Stephen R ^a,b,d  

^a STANFORD UNIVERSITY   (United States)

^b Stanford University   (United States)

^c STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d Howard Hughes MedicaInstitute ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMPLICON; ARTICLE; BACTERIAL GENOME; CLONAL VARIATION; CONTROLLED STUDY; COPY NUMBER VARIATION; CYTOLYSIS; DNA TEMPLATE; ESCHERICHIA COLI; GENE AMPLIFICATION; GENE DUPLICATION; GENETIC HETEROGENEITY; INTERMETHOD COMPARISON; MULTIPLE ANNEALING AND LOOPING BASED AMPLIFICATION CYCLES; MULTIPLE DISPLACEMENT AMPLIFICATION; NONHUMAN; NUCLEOTIDE SEQUENCE; QUANTITATIVE ANALYSIS; SINGLE CELL ANALYSIS; WHOLE GENOME AMPLIFICATION; GENETICS; GENOMICS; NUCLEIC ACID AMPLIFICATION; PROCEDURES; SINGLE NUCLEOTIDE POLYMORPHISM;

BACTERIAL DNA;

DNA COPY NUMBER VARIATIONS; DNA, BACTERIAL; ESCHERICHIA COLI; GENOME, BACTERIAL; GENOMICS; NUCLEIC ACID AMPLIFICATION TECHNIQUES; POLYMORPHISM, SINGLE NUCLEOTIDE; SINGLE-CELL ANALYSIS;

EID: 84920645442     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0105585     Document Type: Article

References (37)

1. Zong C, Lu S, Chapman AR, Xie XS (2012) Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science 338: 1622-1626.
2. Navin N, Kendall J, Troge J, Andrews P, Rodgers L, et al. (2011) Tumour evolution inferred by single-cell sequencing. Nature 472: 90-94.
3. Jan M, Snyder TM, Corces-Zimmerman MR, Vyas P, Weissman IL, et al. (2012) Clonal Evolution of Preleukemic Hematopoietic Stem Cells Precedes Human Acute Myeloid Leukemia. Science Translational Medicine 4: 149ra118.
4. Wells D, Delhanty JD (2000) Comprehensive chromosomal analysis of human preimplantation embryos using whole genome amplification and single cell comparative genomic hybridization. Mol Hum Reprod 6: 1055-1062.
5. McConnell MJ, Lindberg MR, Brennand KJ, Piper JC, Voet T, et al. (2013) Mosaic Copy Number Variation in Human Neurons. Science 342: 632-637.
6. Poduri A, Evrony GD, Cai X, Walsh CA (2013) Somatic Mutation, Genomic Variation, and Neurological Disease. Science 341.
7. Wang J, Fan HC, Behr B, Quake Stephen R (2012) Genome-wide Single-Cell Analysis of Recombination Activity and De Novo Mutation Rates in Human Sperm. Cell 150: 402-412.
8. Hou Y, Fan W, Yan L, Li R, Lian Y, et al. (2013) Genome Analyses of Single Human Oocytes. Cell 155: 1492-1506.
9. Kvist T, Ahring BK, Lasken RS, Westermann P (2007) Specific single-cell isolation and genomic amplification of uncultured microorganisms. Appl Microbiol Biotechnol 74: 926-935.
10. Marcy Y, Ouverney C, Bik EM, Lösekann T, Ivanova N, et al. (2007) Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proceedings of the National Academy of Sciences 104: 11889-11894. (Pubitemid 47185600)
11. Hongoh Y, Toyoda A (2011) Whole-genome sequencing of unculturable bacterium using whole-genome amplification. Methods Mol Biol 733: 25-33.
12. Dodsworth JA, Blainey PC, Murugapiran SK, Swingley WD, Ross CA, et al. (2013) Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage. Nat Commun 4: 1854.
13. Blainey PC, Quake SR (2014) Dissecting genomic diversity, one cell at a time. Nat Meth 11: 19-21.
14. Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, et al. (2013) Insights into the phylogeny and coding potential of microbial dark matter. Nature 499: 431-437.
15. Blainey PC (2013) The future is now: single-cell genomics of bacteria and archaea. FEMS Microbiol Rev 37: 407-427.
16. Dean FB, Hosono S, Fang L, Wu X, Faruqi AF, et al. (2002) Comprehensive human genome amplification using multiple displacement amplification. Proceedings of the National Academy of Sciences 99: 5261-5266. (Pubitemid 34411536)
17. Marcy Y, Ishoey T, Lasken RS, Stockwell TB, Walenz BP, et al. (2007) Nanoliter reactors improve multiple displacement amplification of genomes from single cells. PLoS Genet 3: 1702-1708. (Pubitemid 47510262)
18. Hutchison CA, 3rd, Smith HO, Pfannkoch C, Venter JC (2005) Cell-free cloning using phi29 DNA polymerase. Proc Natl Acad Sci U S A 102: 17332-17336. (Pubitemid 41740866)
19. Voet T, Kumar P, Van Loo P, Cooke SL, Marshall J, et al. (2013) Single-cell paired-end genome sequencing reveals structural variation per cell cycle. Nucleic Acids Res 41: 6119-6138.
20. Blainey PC, Mosier AC, Potanina A, Francis CA, Quake SR (2011) Genome of a Low-Salinity Ammonia-Oxidizing Archaeon Determined by Single-Cell and Metagenomic Analysis. PLoS One 6: e16626.
21. Youssef NH, Blainey PC, Quake SR, Elshahed MS (2011) Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone Spring, Oklahoma). Appl Environ Microbiol 77: 7804-7814.
22. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
23. Picard team (2009) Picard. http://picard.sourceforge.net.
24. Lasken RS (2009) Genomic DNA amplification by the multiple displacement amplification (MDA) method. Biochem Soc Trans 37: 450-453.
25. Schmitt MW, Kennedy SR, Salk JJ, Fox EJ, Hiatt JB, et al. (2012) Detection of ultra-rare mutations by next-generation sequencing. Proc Natl Acad Sci U S A 109: 14508-14513.
26. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, et al. (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19: 455-477.
27. Gurevich A, Saveliev V, Vyahhi N, Tesler G (2013) QUAST: quality assessment tool for genome assemblies. Bioinformatics 29: 1072-1075.
28. Hou Y, Song L, Zhu P, Zhang B, Tao Y, et al. (2012) Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm. Cell 148: 873-885.
29. Lasken RS (2012) Genomic sequencing of uncultured microorganisms from single cells. Nat Rev Micro 10: 631-640.
30. Gole J, Gore A, Richards A, Chiu Y-J, Fung H-L, et al. (2013) Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells. Nat Biotech 31: 1126-1132.
31. Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads.
32. Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE, et al. (2012) RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Res 40: W622-627.
33. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9: 357-359.
34. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
35. Larson D, Abbott T (2009) bam-readcount. https://github.com/genome/bam- readcount: GitHub repository.
36. Koboldt DC, Larson DE, Wilson RK (2002) Using VarScan 2 for Germline Variant Calling and Somatic Mutation Detection. Current Protocols in Bioinformatics: John Wiley & Sons, Inc.
37. Li H (2012) seqtk. https://github.com/lh3/seqtk: GitHub repository.