An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples
Authors:   MalariaGEN, Ahouidi Ambroise , Ali Mozam , Almagro-Garcia Jacob , Amambua-Ngwa Alfred , Amaratunga Chanaki , Amato Roberto , Amenga-Etego Lucas , Andagalu Ben , Anderson Tim J. C. , Andrianaranjaka Voahangy , Apinjoh Tobias , Ariani Cristina , Ashley Elizabeth A. , Auburn Sarah , Awandare Gordon A. , Ba Hampate , Baraka Vito , Barry Alyssa E. , Bejon Philip , Bertin Gwladys I. , Boni Maciej F. , Borrmann Steffen , Bousema Teun , Branch Oralee , Bull Peter C. , Busby George B. J. , Chookajorn Thanat , Chotivanich Kesinee , Claessens Antoine , Conway David , Craig Alister , D'Alessandro Umberto , Dama Souleymane , Day Nicholas P.J. , Denis Brigitte , Diakite Mahamadou , Djimdé Abdoulaye , Dolecek Christiane , Dondorp Arjen M. , Drakeley Chris , Drury Eleanor , Duffy Patrick , Echeverry Diego F. , Egwang Thomas G. , Erko Berhanu , Fairhurst Rick M. , Faiz Abdul , Fanello Caterina A. , Fukuda Mark M. , Gamboa Dionicia , Ghansah Anita , Golassa Lemu , Goncalves Sonia , Hamilton William L. , Harrison G. L. Abby , Hart Lee , Henrichs Christa , Hien Tran Tinh , Hill Catherine A. , Hodgson Abraham , Hubbart Christina , Imwong Mallika , Ishengoma Deus S. , Jackson Scott A. , Jacob Chris G. , Jeffery Ben , Jeffreys Anna E. , Johnson Kimberly J. , Jyothi Dushyanth , Kamaliddin Claire , Kamau Edwin , Kekre Mihir , Kluczynski Krzysztof , Kochakarn Theerarat , Konaté Abibatou , Kwiatkowski Dominic P. , Kyaw Myat Phone , Lim Pharath , Lon Chanthap , Loua Kovana M. , Maïga-Ascofaré Oumou , Malangone Cinzia , Manske Magnus , Marfurt Jutta , Marsh Kevin , Mayxay Mayfong , Miles Alistair , Miotto Olivo , Mobegi Victor , Mokuolu Olugbenga A. , Montgomery Jacqui , Mueller Ivo , Newton Paul N. , Nguyen Thuy , Nguyen Thuy-Nhien , Noedl Harald , Nosten François , Noviyanti Rintis , Nzila Alexis , Ochola-Oyier Lynette I. , Ocholla Harold , Oduro Abraham , Omedo Irene , Onyamboko Marie A. , Ouedraogo Jean-Bosco , Oyebola Kolapo , Pearson Richard D. , Peshu Norbert , Phyo Aung Pyae , Plowe Chris V. , Price Ric N. , Pukrittayakamee Sasithon , Randrianarivelojosia Milijaona , Rayner Julian C. , Ringwald Pascal , Rockett Kirk A. , Rowlands Katherine , Ruiz Lastenia , Saunders David , Shayo Alex , Siba Peter , Simpson Victoria J. , Stalker Jim , Su Xin-zhuan , Sutherland Colin , Takala-Harrison Shannon , Tavul Livingstone , Thathy Vandana , Tshefu Antoinette , Verra Federica , Vinetz Joseph , Wellems Thomas E. , Wendler Jason , White Nicholas J. , Wright Ian , Yavo William , Ye Htut 
Published: July 2021

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.