An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples
MalariaGEN(Cheikh Anta Diop University), Ambroise D. Ahouidi(Wellcome Sanger Institute), Mozam Ali(Wellcome Sanger Institute), Jacob Almagro‐Garcia(Wellcome Sanger Institute), Alfred Amambua‐Ngwa(Wellcome Sanger Institute), Chanaki Amaratunga(Wellcome Sanger Institute), Roberto Amato(University of Ghana), Lucas Amenga–Etego(University of Ghana), Ben Andagalu(Texas Biomedical Research Institute), Tim Anderson(Texas Biomedical Research Institute), Voahangy Andrianaranjaka(University of Antananarivo), Tobias O. Apinjoh(University of Buea), Cristina V. Ariani(Wellcome Sanger Institute), Elizabeth A. Ashley(University of Oxford), Sarah Auburn(University of Ghana), Gordon A. Awandare(University of Ghana), Hampaté Bâ(University of Antwerp), Vito Baraka(Burnet Institute), Alyssa E. Barry(Deakin University), Philip Bejon(Kenya Medical Research Institute), Gwladys Bertin(University of Oxford), Maciej F. Boni(University of Oxford), Steffen Borrmann(Radboud University Nijmegen), Teun Bousema(Radboud University Nijmegen), OraLee H. Branch(University of Cambridge), Peter C. Bull(University of Cambridge), George Busby(Mahidol University), Thanat Chookajorn(Mahidol University), Kesinee Chotivanich(Centre National de la Recherche Scientifique), Antoine Claessens(Centre National de la Recherche Scientifique), David J. Conway(University of Liverpool), Alister Craig(University of Liverpool), Umberto D’Alessandro(Université des Sciences, des Techniques et des Technologies de Bamako), Souleymane Dama(Université des Sciences, des Techniques et des Technologies de Bamako), Nicholas Day(University of Liverpool), Brigitte Denis(University of Liverpool), Mahamadou Diakité(Université des Sciences, des Techniques et des Technologies de Bamako), Abdoulaye Djimdé(University of Oxford), Christiane Dolecek(University of Oxford), Arjen M. Dondorp(London School of Hygiene & Tropical Medicine), Chris Drakeley(Wellcome Sanger Institute), Eleanor Drury(Wellcome Sanger Institute), Patrick Duffy(Centro Internacional de Entrenamiento e Investigaciones Medicas), Diego F. Echeverry, Thomas G. Egwang(Addis Ababa University), Berhanu Erko(National Institutes of Health), Rick M. Fairhurst(Child Health Research Foundation), Abdul Faiz(Mahidol Oxford Tropical Medicine Research Unit), Caterina Fanello(Armed Forces Research Institute of Medical Science), Mark M. Fukuda(Universidad Peruana Cayetano Heredia), Dionicia Gamboa(Noguchi Memorial Institute for Medical Research), Anita Ghansah(Addis Ababa University), Lemu Golassa(Wellcome Sanger Institute), Sónia Gonçalves(Cambridge University Hospitals NHS Foundation Trust), William L. Hamilton(Walter and Eliza Hall Institute of Medical Research), G. L. Abby Harrison(Walter and Eliza Hall Institute of Medical Research), Lee Hart(University of Oxford), Christa Henrichs(University of Oxford), Tran Tinh Hien(Purdue University West Lafayette), Catherine A. Hill(Ministry of Health), Abraham Hodgson(Centre for Human Genetics), Christina Hubbart(Mahidol University), Mallika Imwong(Mahidol University), Deus S. Ishengoma(University of Georgia), Scott A. Jackson(Wellcome Sanger Institute), Chris Jacob(Wellcome Sanger Institute), Ben Jeffery(Centre for Human Genetics), Anna E. Jeffreys(University of Oxford), Kimberly J. Johnson(Wellcome Sanger Institute), Dushyanth Jyothi(Wellcome Sanger Institute), Claire Kamaliddin(Institut de Recherche pour le Développement), Edwin Kamau(Wellcome Sanger Institute), Mihir Kekre(Wellcome Sanger Institute), Krzysztof Henryk Kluczynski(Mahidol University), Theerarat Kochakarn(Mahidol University), Abibatou Konaté(Centre for Human Genetics), Dominic Kwiatkowski(Wellcome Sanger Institute), Myat Phone Kyaw(National Institute of Allergy and Infectious Diseases), Pharath Lim(Armed Forces Research Institute of Medical Science), Chanthap Lon(Institut National de Santé Publique), Kovana Marcel Loua(Kwame Nkrumah University of Science and Technology), Oumou Maïga‐Ascofaré(Wellcome Sanger Institute), Claudio Malangone(Wellcome Sanger Institute), Magnus Manske(Wellcome Sanger Institute), Jutta Marfurt(African Academy of Sciences), Kevin Marsh(Mahosot Hospital), Mayfong Mayxay(Wellcome Sanger Institute), Alistair Miles(Wellcome Sanger Institute), Olivo Miotto(University of Nairobi), Victor A. Mobegi(University of Ilorin), Olugbenga Ayodeji Mokuolu(Monash University), Jacqui Montgomery(Walter and Eliza Hall Institute of Medical Research), Ivo Müeller(Walter and Eliza Hall Institute of Medical Research), Paul N. Newton(Wellcome Sanger Institute), Thuy Nguyen(Wellcome Sanger Institute), Thuy-Nhien Nguyen(Wellcome Sanger Institute), Harald Noedl(University of Oxford), François Nosten(Eijkman Institute for Molecular Biology), Rintis Noviyanti(King Fahd University of Petroleum and Minerals), Alexis Nzila(Kenya Medical Research Institute), Lynette Isabella Ochola‐Oyier(University of Nairobi), Harold Ocholla(Navrongo Health Research Centre), Abraham Oduro(Kenya Medical Research Institute), Irene Omedo(Kenya Medical Research Institute), Marie A. Onyamboko(Institut de Recherche en Sciences de la Santé), Jean‐Bosco Ouédraogo(University of Lagos), Kolapo Oyebola(Wellcome Sanger Institute), Richard D. Pearson(Wellcome Sanger Institute), Norbert Peshu(Kenya Medical Research Institute), Aung Pyae Phyo(University of Maryland, Baltimore), C V Plowe(University of Oxford), Ric N. Price(Mahidol University), Sasithon Pukrittayakamee(University of Antananarivo), Milijaona Randrianarivelojosia(Wellcome Sanger Institute), Julian C. Rayner(Wellcome Sanger Institute), Pascal Ringwald(Centre for Human Genetics), Kirk A. Rockett(Centre for Human Genetics), Katherine Rowlands(Universidad Nacional de la Amazonía Peruana), Lastenia Ruiz Mesía(Armed Forces Research Institute of Medical Science), David Saunders(Nelson Mandela African Institution of Science and Technology), Alex Shayo(Papua New Guinea Institute of Medical Research), Peter Siba(University of Oxford), Victoria Simpson(Wellcome Sanger Institute), Jim Stalker(Wellcome Sanger Institute), Xin‐zhuan Su(London School of Hygiene & Tropical Medicine), Colin Sutherland(University of Maryland, Baltimore), Shannon Takala‐Harrison(Papua New Guinea Institute of Medical Research), Livingstone Tavul(Columbia University Irving Medical Center), Vandana Thathy(Kenya Medical Research Institute), Antoinette Tshefu(Sapienza University of Rome), Federica Verra(Universidad Peruana Cayetano Heredia), Joseph M. Vinetz(National Institute of Allergy and Infectious Diseases), Thomas E. Wellems(Centre for Human Genetics), Jason Wendler(Mahidol Oxford Tropical Medicine Research Unit), Nicholas J. White(University of Oxford), I.G. Wright(University of Oxford), William Yavo(Myanmar Oxford Clinical Research Unit), Htut Ye(Yale University)
Cited by 197Open Access
Abstract
<ns3:p> 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 <ns3:italic>Plasmodium falciparum</ns3:italic> 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. </ns3:p>
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