Abstract
MalariaGEN is a data-sharing network that enables groups around the world to work together on the genomic epidemiology of malaria. Here we describe a new release of curated genome variation data on 7,000 Plasmodium falciparum samples from MalariaGEN partner studies in 28 malaria-endemic countries. High-quality genotype calls on 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using a standardised analysis pipeline. Copy number variants associated with drug resistance and structural variants that cause failure of rapid diagnostic tests were also analysed. Almost all samples showed genetic evidence of resistance to at least one antimalarial drug, and some samples from Southeast Asia carried markers of resistance to six commonly-used drugs. Genes expressed during the mosquito stage of the parasite life-cycle are prominent among loci that show strong geographic differentiation. By continuing to enlarge this open data resource we aim to facilitate research into the evolutionary processes affecting malaria control and to accelerate development of the surveillance toolkit required for malaria elimination.
Highlights
A major obstacle to malaria elimination is the great capacity of the parasite and vector populations to evolve in response to malaria control interventions
Deletions of hrp[3] only were more geographically widespread than hrp[2] deletions, being common in Ethiopia (43%, n=9/21) and in Senegal (7%, n=6/84), and at relatively low frequency (
After excluding variants and samples that failed to meet stringent quality control criteria, the dataset contains high-quality genotype calls for 3 million polymorphisms including single nucleotide polymorphisms (SNPs), indels, CNVs and large structural variations, in almost 6,000 samples
Summary
A major obstacle to malaria elimination is the great capacity of the parasite and vector populations to evolve in response to malaria control interventions. Current methods for genetic surveillance of the parasite population are largely based on targeted genotyping of specific loci, e.g. known markers of drug resistance. Whole genome sequencing of malaria parasites is currently more expensive and complex, at the stage of data analysis, but it is an important adjunct to targeted genotyping, as it provides a more comprehensive picture of parasite genetic variation. It is important for discovery of new drug resistance markers and for monitoring patterns of gene flow and evolutionary adaptation in the parasite population
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