Limited biological samples, like DNA from tiny model animals (e.g. worms and insects), dried blood spots and sorted cells, necessitates application of whole genome amplification (WGA) technologies to accommodate downstream molecular biology analyses such as Next Generation Sequencing or microarrays. Droplet based MDA ensures better biological representation of DNA from such limited sample types.
A unique advantage of Xdrop™ is that the DNA amplification takes place in tens of thousands of small volume droplets. The compartmentalization increases the sensitivity, allowing amplification to be initiated from femtogram amounts of target DNA. Performing the MDA in droplets has the additional advantage that it reduces the amplification bias between different DNA regions, due to the small reaction volume and one DNA molecule per droplet. Furthermore, the compartmentalization of single molecules drastically reduces the risk of chimeric molecules being generated by recombination of two similar molecules as compared to bulk MDA methods.
There are an abundant number of bulk-based systems available for WGA including isothermal and PCR based systems as well as combinations of these two. Unfortunately, the current available systems all generate errors, artifacts and amplification bias resulting in false mutations and/or allelic dropout. The Xdrop™ platform overcomes these issues in a simple and user-friendly way. DNA and reagents are partitioned into droplets, thus creating independent reaction chambers ensuring even chromosomal coverage of the entire genome (fig. A).
Samplix has compared Xdrop™ droplet MDA with selected bulk MDA methods and can confirm that bulk amplifications result in uneven amplification which can result in allelic drop-out being observed in downstream genome-wide analysis methods e.g. NGS and array-based copy number analysis. In contrast, droplet-based dMDA results in a more uniform amplification of all chromosomal areas from 100-1000-fold lower starting material.
Figure A. E.coli DNA was amplified using Xdrop™ dMDA (Samplix) and bulk amplification products from two other vendors. The amplified DNA was subsequently whole genome sequenced with on Illumina sequencing platform
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