An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples
MalariaGEN, Ambroise D. Ahouidi, Mozam Ali, Jacob Almagro‐Garcia, Alfred Amambua‐Ngwa, Chanaki Amaratunga, Roberto Amato, Lucas Amenga–Etego, Ben Andagalu, Tim Anderson, Voahangy Andrianaranjaka, Tobias O. Apinjoh, Cristina V. Ariani, Elizabeth A. Ashley, Sarah Auburn, Gordon A. Awandare, Hampaté Bâ, Vito Baraka, Alyssa E. Barry, Philip Bejon, Gwladys Bertin, Maciej F. Boni, Steffen Borrmann, Teun Bousema, OraLee H. Branch, Peter C. Bull, George Busby, Thanat Chookajorn, Kesinee Chotivanich, Antoine Claessens, David J. Conway, Alister Craig, Umberto D’Alessandro, Souleymane Dama, Nicholas Day, Brigitte Denis, Mahamadou Diakité, Abdoulaye Djimdé, Christiane Dolecek, Arjen M. Dondorp, Chris Drakeley, Eleanor Drury, Patrick Duffy, Diego F. Echeverry, Thomas G. Egwang, Berhanu Erko, Rick M. Fairhurst, Abdul Faiz, Caterina Fanello, Mark M. Fukuda, Dionicia Gamboa, Anita Ghansah, Lemu Golassa, Sónia Gonçalves, William L. Hamilton, G. L. Abby Harrison, Lee Hart, Christa Henrichs, Tran Tinh Hien, Catherine A. Hill, Abraham Hodgson, Christina Hubbart, Mallika Imwong, Deus S. Ishengoma, Scott A. Jackson, Chris Jacob, Ben Jeffery, Anna E. Jeffreys, Kimberly J. Johnson, Dushyanth Jyothi, Claire Kamaliddin, Edwin Kamau, Mihir Kekre, Krzysztof Henryk Kluczynski, Theerarat Kochakarn, Abibatou Konaté, Dominic Kwiatkowski, Myat Phone Kyaw, Pharath Lim, Chanthap Lon, Kovana Marcel Loua, Oumou Maïga‐Ascofaré, Claudio Malangone, Magnus Manske, Jutta Marfurt, Kevin Marsh, Mayfong Mayxay, Alistair Miles, Olivo Miotto, Victor A. Mobegi, Olugbenga Ayodeji Mokuolu, Jacqui Montgomery, Ivo Müeller, Paul N. Newton, Thuy Nguyen, Thuy-Nhien Nguyen, Harald Noedl, François Nosten, Rintis Noviyanti, Alexis Nzila
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>