Abstract

An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples

MalariaGen, Ahouidi A Ali M Almagro-Garcia J Amambua-Ngwa A Amaratunga C Amato R Amenga-Etego L Andagalu B Anderson TJC Andrianaranjaka V Apinjoh T Ariani C Ashley EA Auburn S Awandare GA Ba H Baraka V Barry AE Bejon P Bertin GI Boni MF Borrmann S Bousema T Branch O Bull PC Busby GBJ Chookajorn T Chotivanich K Claessens A Conway D Craig A D'Alessandro U Dama S Day NP Denis B Diakite M Djimde A Dolecek C Dondorp AM Drakeley C Drury E Duffy P Echeverry DF Egwang TG Erko B Fairhurst RM Faiz A Fanello CA Fukuda MM Gamboa D Ghansah A Golassa L Goncalves S Hamilton WL Harrison GLA Hart L Henrichs C Hien TT Hill CA Hodgson A Hubbart C Imwong M Ishengoma DS Jackson SA Jacob CG Jeffery B Jeffreys AE Johnson KJ Jyothi D Kamaliddin C Kamau E Kekre M Kluczynski K Kochakarn T Konate A Kwiatkowski DP Kyaw MP Lim P Lon C Loua KM Maiga-Ascofare O Malangone C Manske M Marfurt J Marsh K Mayxay M Miles A Miotto O Mobegi V Mokuolu OA Montgomery J Mueller I Newton PN Nguyen T Nguyen TN Noedl H Nosten F Noviyanti R Nzila A Ochola-Oyier LI Ocholla H Oduro A Omedo I Onyamboko MA Ouedraogo JB Oyebola K Pearson RD Peshu N Phyo AP Plowe CV Price RN Pukrittayakamee S Randrianarivelojosia M Rayner JC Ringwald P Rockett KA Rowlands K Ruiz L Saunders D Shayo A Siba P Simpson VJ Stalker J Su XZ Sutherland C Takala-Harrison S Tavul L Thathy V Tshefu A Verra F Vinetz J Wellems TE Wendler J White NJ Wright I Yavo W Ye H
Wellcome Open Res. 2021;642

Permenent descriptor

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.