Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 562836
Title Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis
Author(s) Hammond, Maria; Homa, Felix; Andersson-Svahn, Helene; Ettema, Thijs J.G.; Joensson, Haakan N.
Source Microbiome 4 (2016). - ISSN 2049-2618
DOI https://doi.org/10.1186/s40168-016-0197-7
Publication type Refereed Article in a scientific journal
Publication year 2016
Keyword(s) Amplification bias - Droplet microfluidics - Metagenomics - Multiple displacement amplification - Whole genome amplification
Abstract

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.

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