Whole genome amplification (WGA) increases DNA in very limited samples to meet high input needs of downstream analyses like sequencing. Among other methods, multiple displacement amplification (MDA) has emerged as a relatively uncomplicated WGA method that uses random hexamer primers to amplify with high fidelity all DNA sequences in a bulk sample.
Though touted to be accurate, biases, allelic dropout, and intermolecular chimeric products are known issues of bulk MDA. The droplet MDA (dMDA) used in the Xdrop™ technology resolves these by encapsulating single-molecule amplification reactions in droplets.
We compared the performance of Xdrop™ droplet MDA (dMDA) to alternative WGA solutions based on bulk MDA. We used each solution to amplify serially diluted Escherichia coli DNA, from 0 (no-template control) to 1000 pg. Xdrop™ performed exceptionally well across the entire input range but exceled where the bulk methods reached their limits. Xdrop™ was also the only method to amplify 1 pg input DNA and the output covered 99% of the E. coli genome. View the complete dataset in our Application Note below.
Especially noteworthy is the extraordinary uniformity in genome coverage we achieved with Xdrop™.
Each molecule in a droplet was amplified individually and thus, when we pooled the contents to generate the sequencing library, all DNA molecules of the sample were represented in true proportions in the sequencing results. This was not the case for the bulk MDA solutions, where coverage was extremely variable and biased.
We corroborated the amplification efficiency of Xdrop™ dMDA with sub-picogram amounts of human DNA. Check out our scientific poster below for the details.