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

MalariaGEN; Ahouidi, Ambroise; Ali, Mozam; Almagro-Garcia, Jacob; Amambua-Ngwa, AlfredORCID logo; Amaratunga, Chanaki; Amato, Roberto; Amenga-Etego, LucasORCID logo; Andagalu, Ben; Anderson, Tim JCORCID logo; +128 more...Andrianaranjaka, Voahangy; Apinjoh, Tobias; Ariani, Cristina; Ashley, Elizabeth AORCID logo; Auburn, Sarah; Awandare, Gordon A; Ba, HampateORCID logo; Baraka, VitoORCID logo; Barry, Alyssa E; Bejon, PhilipORCID logo; Bertin, Gwladys I; Boni, Maciej F; Borrmann, Steffen; Bousema, TeunORCID logo; Branch, Oralee; Bull, Peter C; Busby, George BJ; Chookajorn, ThanatORCID logo; Chotivanich, Kesinee; Claessens, AntoineORCID logo; Conway, DavidORCID logo; Craig, AlisterORCID logo; D'Alessandro, UmbertoORCID logo; Dama, Souleymane; Day, Nicholas PjORCID logo; Denis, Brigitte; Diakite, MahamadouORCID logo; Djimdé, AbdoulayeORCID logo; Dolecek, Christiane; Dondorp, Arjen MORCID logo; Drakeley, ChrisORCID logo; Drury, Eleanor; Duffy, Patrick; Echeverry, Diego F; Egwang, Thomas G; Erko, Berhanu; Fairhurst, Rick M; Faiz, Abdul; Fanello, Caterina AORCID logo; Fukuda, Mark M; Gamboa, DioniciaORCID logo; Ghansah, Anita; Golassa, Lemu; Goncalves, Sonia; Hamilton, William LORCID logo; Harrison, GL Abby; Hart, LeeORCID logo; Henrichs, Christa; Hien, Tran TinhORCID logo; Hill, Catherine A; Hodgson, Abraham; Hubbart, ChristinaORCID logo; Imwong, Mallika; Ishengoma, Deus SORCID logo; Jackson, Scott AORCID logo; Jacob, Chris G; Jeffery, Ben; Jeffreys, Anna EORCID logo; Johnson, Kimberly JORCID logo; Jyothi, DushyanthORCID logo; Kamaliddin, ClaireORCID logo; Kamau, EdwinORCID logo; Kekre, Mihir; Kluczynski, Krzysztof; Kochakarn, Theerarat; Konaté, Abibatou; Kwiatkowski, Dominic PORCID logo; Kyaw, Myat Phone; Lim, Pharath; Lon, Chanthap; Loua, Kovana MORCID logo; Maïga-Ascofaré, Oumou; Malangone, CinziaORCID logo; Manske, Magnus; Marfurt, Jutta; Marsh, KevinORCID logo; Mayxay, MayfongORCID logo; Miles, Alistair; Miotto, OlivoORCID logo; Mobegi, VictorORCID logo; Mokuolu, Olugbenga A; Montgomery, Jacqui; Mueller, Ivo; Newton, Paul N; Nguyen, Thuy; Nguyen, Thuy-Nhien; Noedl, Harald; Nosten, FrancoisORCID logo; Noviyanti, Rintis; Nzila, Alexis; Ochola-Oyier, Lynette I; Ocholla, Harold; Oduro, AbrahamORCID logo; Omedo, IreneORCID logo; Onyamboko, Marie A; Ouedraogo, Jean-Bosco; Oyebola, KolapoORCID logo; Pearson, Richard DORCID logo; Peshu, Norbert; Phyo, Aung PyaeORCID logo; Plowe, Chris V; Price, Ric NORCID logo; Pukrittayakamee, Sasithon; Randrianarivelojosia, Milijaona; Rayner, Julian CORCID logo; Ringwald, Pascal; Rockett, Kirk AORCID logo; Rowlands, Katherine; Ruiz, Lastenia; Saunders, David; Shayo, AlexORCID logo; Siba, Peter; Simpson, Victoria J; Stalker, Jim; Su, Xin-ZhuanORCID logo; Sutherland, ColinORCID logo; Takala-Harrison, Shannon; Tavul, Livingstone; Thathy, Vandana; Tshefu, Antoinette; Verra, Federica; Vinetz, Joseph; Wellems, Thomas EORCID logo; Wendler, Jason; White, Nicholas J; Wright, IanORCID logo; Yavo, William; and Ye, Htut (2021) An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples. Wellcome Open Research, 6. 42-. DOI: 10.12688/wellcomeopenres.16168.2
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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.


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