Journal
PLOS ONE
Volume 9, Issue 8, Pages -Publisher
PUBLIC LIBRARY SCIENCE
DOI: 10.1371/journal.pone.0105585
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Categories
Funding
- United States Department of Energy Joint Genome Institute Emerging Technologies Opportunity Program
- Office of Science of the United States Department of Energy [DE-AC02-05CH11231]
- National Science Foundation Partnerships for International Research and Education (PIRE) [0968421]
- International Fulbright Science and Technology Award
- Bureau of Educational and Cultural Affairs of the United States Department of State
- Melvin and Joan Lane Stanford Graduate Fellowship
- Leukemia and Lymphoma Society
- American Society of Hematology
- Child Health Research Institute at Stanford
- Office Of The Director
- Office Of Internatl Science &Engineering [0968421] Funding Source: National Science Foundation
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Single-cell sequencing is emerging as an important tool for studies of genomic heterogeneity. Whole genome amplification (WGA) is a key step in single-cell sequencing workflows and a multitude of methods have been introduced. Here, we compare three state-of-the-art methods on both bulk and single-cell samples of E. coli DNA: Multiple Displacement Amplification (MDA), Multiple Annealing and Looping Based Amplification Cycles (MALBAC), and the PicoPLEX single-cell WGA kit (NEB-WGA). We considered the effects of reaction gain on coverage uniformity, error rates and the level of background contamination. We compared the suitability of the different WGA methods for the detection of copy-number variations, for the detection of single-nucleotide polymorphisms and for de-novo genome assembly. No single method performed best across all criteria and significant differences in characteristics were observed; the choice of which amplifier to use will depend strongly on the details of the type of question being asked in any given experiment.
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