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
Institut Pasteur, Paris, Keywords malaria, plasmodium falciparum, genomics, genomic epidemiology, evolution, data resource, population genetics, drug resistance, rapid diagnostic test failure
Each sample has been annotated to show its profile of resistance to six major antimalarial drugs and whether it carries structural variations that can cause Rapid diagnostic tests (RDTs) failure
Samples were collected by independent groups that were operative at a given time and in a given place with distinct objectives; while care needs to be taken when interpreting results spanning multiple years and geographical settings, this heterogeneity allows for the exploration of a wide range of epidemiological and transmission settings
Summary
Institut Pasteur, Paris, Keywords malaria, plasmodium falciparum, genomics, genomic epidemiology, evolution, data resource, population genetics, drug resistance, rapid diagnostic test failure. Data produced by the Pf Community Project have been used to address a broad range of research questions, both by the groups that generated samples and data and by the wider research community, and have generated over 50 previous publications (refs 5–55) These data have become a key resource for the epidemiology and population genetics of antimalarial drug resistance[9,10,11,12,13,14,15,16,17,18,19,20,21,22] and an important platform for the discovery of new genetic markers and mechanisms of resistance through genome-wide association studies[23,24,25,26,27] and combined genometranscriptome analysis[28]. We describe a new release of curated genome variation data on 7,113 samples of P. falciparum collected by 49 partner studies from 73 locations in Africa, Asia, South America and Oceania between 2002 and 2015 (Table 1, Supplementary Data; Supplementary Table 1 and 2)
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