Amplicon sequencing toolkit

Amplicon Toolkit icon

The mission of the MalariaGEN Amplicon Sequencing Toolkit is to provide the protocols and tools needed to enable partners to utilise amplicon sequencing for malaria parasite and vector genomic surveillance in-country - from sample collection through to the production of actionable genetic data. While still being piloted at selected partner sites, our objective is to provide a public health, research and capacity-building framework to accommodate the growing and changing needs for parasite and vector surveillance data in malaria endemic regions, improving the delivery of translational research to policymakers at an unprecedented speed and scale.

The MalariaGEN Amplicon Sequencing Toolkit currently provides partners with the checklists, protocols and analytical methods needed to sequence and investigate targeted genes associated with drug or insecticide resistance. The amplicon process translates the raw sample data into accessible genetic report cards, and geo-temporal maps of resistance, that can inform regional malaria control.

We are working with partners at sentinel sites in The Gambia, Ghana, Mali, Vietnam and Indonesia to develop and implement the toolkit. When we are able to, we will make the protocols publicly available for use by other groups. In the first instance this will be with the laboratory protocols for P. falciaparum.

Until the DNA has been isolated and amplified, sample preparation and protocols differ for different species. Once the DNA is amplified, protocols for working with different species are the same.

For ease of use, we provide an end-to-end protocol for P. falciparum, P. vivax, and mosquitos separately, which include reagent and equipment lists. However, if you require the full list for the end-to-end process, or if you have any questions, please contact support [at]


P. falciparum Amplicon Toolkit protocols