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Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Royal Inst Technol KTH, Div Prote & Nanobiotechnol, Sci Life Lab, Stockholm, Sweden..
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
Royal Inst Technol KTH, Div Prote & Nanobiotechnol, Sci Life Lab, Stockholm, Sweden..
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
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2016 (English)In: Microbiome, ISSN 0026-2633, E-ISSN 2049-2618, Vol. 4, 52Article in journal (Refereed) Published
Abstract [en]

Background: Whole genome amplification (WGA) is a challenging, key step in metagenomic studies of samples containing minute amounts of DNA, such as samples from low biomass environments. It is well known that multiple displacement amplification (MDA), the most commonly used WGA method for microbial samples, skews the genomic representation in the sample. We have combined MDA with droplet microfluidics to perform the reaction in a homogeneous emulsion. Each droplet in this emulsion can be considered an individual reaction chamber, allowing partitioning of the MDA reaction into millions of parallel reactions with only one or very few template molecules per droplet. Results: As a proof-of-concept, we amplified genomic DNA from a synthetic metagenome by MDA either in one bulk reaction or in emulsion and found that after sequencing, the species distribution was better preserved and the coverage depth was more evenly distributed across the genomes when the MDA reaction had been performed in emulsion. Conclusions: Partitioning MDA reactions into millions of reactions by droplet microfluidics is a straightforward way to improve the uniformity of MDA reactions for amplifying complex samples with limited amounts of DNA.

Place, publisher, year, edition, pages
2016. Vol. 4, 52
Keyword [en]
Whole genome amplification, Multiple displacement amplification, Metagenomics, Droplet microfluidics, Amplification bias
National Category
Microbiology
Identifiers
URN: urn:nbn:se:uu:diva-307271DOI: 10.1186/s40168-016-0197-7ISI: 000385047700001PubMedID: 27716450OAI: oai:DiVA.org:uu-307271DiVA: diva2:1046396
Funder
EU, European Research Council, 310039-PUZZLE_CELLSwedish Foundation for Strategic Research , SSF-FFL5Knut and Alice Wallenberg FoundationSwedish Research Council Formas
Available from: 2016-11-14 Created: 2016-11-11 Last updated: 2016-11-14Bibliographically approved

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Hammond, MariaHoma, FelixEttema, Thijs J. G.
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Molecular EvolutionScience for Life Laboratory, SciLifeLab
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