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Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples

2023; Wellcome; Volume: 8; Linguagem: Inglês

10.12688/wellcomeopenres.18681.1

2398-502X

Muzamil Mahdi Abdel Hamid, Mohamed Hassan Abdelraheem, Desmond Omane Acheampong, Ambroise D. Ahouidi, Mozam Ali, Jacob Almagro‐Garcia, Alfred Amambua‐Ngwa, Chanaki Amaratunga, Lucas Amenga–Etego, Ben Andagalu, Tim Anderson, Voahangy Andrianaranjaka, Ifeyinwa Aniebo, Enoch Aninagyei, Felix Ansah, Patrick Ansah, Tobias O. Apinjoh, Paulo Arnaldo, Elizabeth A. Ashley, Sarah Auburn, Gordon A. Awandare, Hâmpaté Ba, Vito Baraka, Alyssa E. Barry, Philip Bejon, Gwladys Bertin, Maciej F. Boni, Steffen Borrmann, Teun Bousema, Marielle Karine Bouyou-Akotet, OraLee H. Branch, Peter C. Bull, H K Cheah, Keobouphaphone Chindavongsa, Thanat Chookajorn, Kesinee Chotivanich, Antoine Claessens, David J. Conway, Vladimir Corredor, Erin Courtier, Alister Craig, Umberto D’Alessandro, Souleymane Dama, Nicholas Day, Brigitte Denis, Mehul Dhorda, Mahamadou Diakité, Abdoulaye Djimdé, Christiane Dolecek, Arjen M. Dondorp, Seydou Doumbia, Chris Drakeley, Eleanor Drury, Patrick Duffy, Diego F. Echeverry, Thomas G. Egwang, Sónia Maria Enosse, Berhanu Erko, Rick M. Fairhurst, Abdul Faiz, Caterina Fanello, Mark Fleharty, Matthew Forbes, Mark M. Fukuda, Dionicia Gamboa, Anita Ghansah, Lemu Golassa, Sónia Gonçalves, G. L. Abby Harrison, Sara A. Healy, Jason A. Hendry, Anastasia Hernández-Koutoucheva, Tran Tinh Hien, Catherine A. St. Hill, Francis Hombhanje, Amanda Hott, Ye Htut, Mazza Hussein, Mallika Imwong, Deus S. Ishengoma, Scott A. Jackson, Chris Jacob, Julia Jeans, Kimberly J. Johnson, Claire Kamaliddin, Edwin Kamau, Jon Keatley, Theerarat Kochakarn, Drissa Konaté, Abibatou Konaté, Aminatou Koné, Dominic Kwiatkowski, Myat Phone Kyaw, Dennis E. Kyle, Mara Lawniczak, Samuel K. Lee, Martha Lemnge, Pharath Lim, Chanthap Lon, Kovana Marcel Loua, Celine I. Mandara, Jutta Marfurt, Kevin Marsh, Richard J. Maude, Mayfong Mayxay, Oumou Maïga‐Ascofaré, Olivo Miotto, Toshihiro Mita, Victor A. Mobegi, Abdelrahim Mohamed, Olugbenga Ayodeji Mokuolu, Jaqui Montgomery, Collins M. Morang’a, Ivo Müeller, Kathryn Murie, Paul N. Newton, Thang Ngo Duc, Thuy Nguyen, Thuy-Nhien Nguyen, Tuyen Nguyen Thi Kim, Hong Nguyen Van, Harald Noedl, François Nosten, Rintis Noviyanti, Vincent N. Ntui, Alexis Nzila, Lynette Isabella Ochola‐Oyier, Harold Ocholla, Abraham Oduro, Irene Omedo, Marie Onyamboko, Jean‐Bosco Ouédraogo, Kolapo Oyebola, Wellington Oyibo, Richard D. Pearson, Norbert Peshu, Aung Pyae Phyo, Christopher V. Plowe, Ric N. Price, Sasithon Pukrittayakamee, Huynh Hong Quang, Milijaona Randrianarivelojosia, Julian C. Rayner, Pascal Ringwald, Anna Rosanas‐Urgell, Eduard Rovira-Vallbona, Valentín Ruano-Rubio, Lastenia Ruiz Mesía, David Saunders, Alex Shayo, Peter Siba, Victoria J. Simpson, Mahamadou S. Sissoko, Christen Smith, Xin‐zhuan Su, Colin Sutherland, Shannon Takala‐Harrison, Arthur M. Talman, Livingstone Tavul, Ngo Viet Thanh, Vandana Thathy, Aung Myint Thu, Mahamoudou Touré, Antoinette Tshefu, Federica Verra, Joseph M. Vinetz, Thomas E. Wellems, Jason P. Wendler, Nicholas J. White, Georgia Whitton, William Yavo, Rob W. van der Pluijm,

Aquaculture disease management and microbiota

We describe the MalariaGEN Pf7 data resource, the seventh release of Plasmodium falciparum genome variation data from the MalariaGEN network. It comprises over 20,000 samples from 82 partner studies in 33 countries, including several malaria endemic regions that were previously underrepresented. For the first time we include dried blood spot samples that were sequenced after selective whole genome amplification, necessitating new methods to genotype copy number variations. We identify a large number of newly emerging crt mutations in parts of Southeast Asia, and show examples of heterogeneities in patterns of drug resistance within Africa and within the Indian subcontinent. We describe the profile of variations in the C-terminal of the csp gene and relate this to the sequence used in the RTS,S and R21 malaria vaccines. Pf7 provides high-quality data on genotype calls for 6 million SNPs and short indels, analysis of large deletions that cause failure of rapid diagnostic tests, and systematic characterisation of six major drug resistance loci, all of which can be freely downloaded from the MalariaGEN website.