Introduction

What is SWGA?

Selective whole genome amplification (SWGA) is a method to selectively enrich for the DNA of a given organism from a mixture of DNA from that organism and contaminating DNA.

As an example, SWGA can be used to amplify the genome of Plasmodium falciparum from a mixture of human and P. falciparum DNA (Sundararaman, 2016). There are many ways to enrich for a target organism, both before and after DNA extraction. What makes SWGA unique is its universality. By choosing the right set of SWGA primers it should be possible to enrich for almost any target DNA from any contaminating DNA.

How does SWGA work?

SWGA uses the phi29 DNA polymerase, in combination with a specially designed set of primers to selectively amplify the DNA of a target organism (Leichty, 2014). 

SWGA is based on the same concept of commercially available phi29-based WGA kits such as GenomiPhi and REPLI-g, which use the phi29 DNA polymerase and random hexamers to amplify all DNA in a sample. SWGA modifies this approach by using specific primers that bind frequently to the target DNA and rarely to the contaminating DNA. This approach results in considerable amplification of the target DNA with little amplification to the contaminating DNA (Figure 1).

Figure 1: Selective whole genome amplification of target (Plasmodium) DNA from a mixture of Plasmodium and host DNA. SWGA primers (green lines) bind frequently to Plasmodium gDNA (red lines) and rarely to host gDNA (blue lines). These primers initiate amplification by the phi29 polymerase (yellow circle) synthesizing new DNA strands (black). When the phi29 polymerase reaches double stranded DNA, it displaces the complementary strand, creating new single stranded DNA that serves as a template for primer binding and amplification. This occurs frequently when primer binding sites are spaced close together (Plasmodium gDNA), but rarely when primer binding sites are spaced far apart (host gDNA).

How do you design SWGA primer sets?

The two main principles of primer set design are that the primers should bind more frequently to the target DNA than to the contaminating DNA and that primers should bind broadly across the target DNA. However, other primer and primer set characteristics are important such as melting temperature, the propensity to form homo-dimers or hetero-dimers, and the evenness of binding across the target genome.

With this in mind, we have designed a program swga to facilitate primer design which can be downloaded here.

I've designed my primer sets, now how do I do SWGA?

See the SWGA Protocol page for current best practices.

What samples can I use?

See the SWGA Sample Recommendations page.

Why a blog?

SWGA is in its infancy, meaning that best practices may change quickly. This blog will be updated as new information comes out. It will also serve as a repository for proven SWGA primer sets and answers to common questions. If you have experience that you would like to share, please feel free to get in contact with me.

References
Leichty AR, Brisson D. Selective whole genome amplification for resequencing target microbial species from complex natural samples. Genetics 198(2), 473-81 (2014).

Sundararaman SA, Plenderleith LJ, Liu W, Loy DE, Learn GH, Li Y, Shaw KS, Ayouba A, Peeters M, Speede S, Shaw GM, Bushman FD, Brisson D, Rayner JC, Sharp PM, Hahn BH. Genomes of cryptic chimpanzee Plasmodium species reveal key evolutionary events leading to human malaria. Nat Comms 7, 11078 (2016).