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

Author:

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

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.

Funder

Medical Research Council

Department for International Development, UK Government

Bill and Melinda Gates Foundation

Wellcome Trust

Publisher

F1000 Research Ltd

Subject

General Biochemistry, Genetics and Molecular Biology,Medicine (miscellaneous)

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