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Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples
Authors :
MalariaGEN Abdel Hamid, Muzamil Mahdi Abdelraheem, Mohamed Hassan Acheampong, Desmond Omane Ahouidi, Ambroise Ali, Mozam Almagro-Garcia, Jacob Amambua-Ngwa, Alfred Amaratunga, Chanaki Amenga-Etego, Lucas Andagalu, Ben Anderson, Tim Andrianaranjaka, Voahangy Aniebo, Ifeyinwa Aninagyei, Enoch Ansah, Felix Ansah, Patrick O Apinjoh, Tobias Arnaldo, Paulo Ashley, Elizabeth Auburn, Sarah Awandare, Gordon A Ba, Hampate Baraka, Vito Barry, Alyssa Bejon, Philip Bertin, Gwladys I Boni, Maciej F Borrmann, Steffen Bousema, Teun Bouyou-Akotet, Marielle Branch, Oralee Bull, Peter C Cheah, Huch Chindavongsa, Keobouphaphone Chookajorn, Thanat Chotivanich, Kesinee Claessens, Antoine Conway, David J Corredor, Vladimir Courtier, Erin Craig, Alister D'Alessandro, Umberto Dama, Souleymane Day, Nicholas Denis, Brigitte Dhorda, Mehul Diakite, Mahamadou Djimde, Abdoulaye Dolecek, Christiane Dondorp, Arjen Doumbia, Seydou Drakeley, Chris Drury, Eleanor Duffy, Patrick Echeverry, Diego F Egwang, Thomas G Enosse, Sonia Maria Mauricio Erko, Berhanu Fairhurst, Rick M Faiz, Abdul Fanello, Caterina A Fleharty, Mark Forbes, Matthew Fukuda, Mark Gamboa, Dionicia Ghansah, Anita Golassa, Lemu Goncalves, Sonia Harrison, GL Abby Healy, Sara Anne Hendry, Jason A Hernandez-Koutoucheva, Anastasia Hien, Tran Tinh Hill, Catherine A Hombhanje, Francis Hott, Amanda Htut, Ye Hussein, Mazza Imwong, Mallika Ishengoma, Deus Jackson, Scott A Jacob, Chris G Jeans, Julia Johnson, Kimberly J Kamaliddin, Claire Kamau, Edwin Keatley, Jon Kochakarn, Theerarat Konate, Drissa S Konaté, Abibatou Kone, Aminatou Kwiatkowski, Dominic P Kyaw, Myat P Kyle, Dennis Lawniczak, Mara Lee, Samuel K Lemnge, Martha Lim, Pharath Lon, Chanthap Loua, Kovana M Mandara, Celine I Marfurt, Jutta Marsh, Kevin Maude, Richard James Mayxay, Mayfong Maïga-Ascofaré, Oumou Miotto, Olivo Mita, Toshihiro Mobegi, Victor Mohamed, Abdelrahim Osman Mokuolu, Olugbenga A Montgomery, Jaqui Morang'a, Collins Misita Mueller, Ivo Murie, Kathryn Newton, Paul N Ngo Duc, Thang Nguyen, Thuy Nguyen, Thuy-Nhien Nguyen Thi Kim, Tuyen Nguyen Van, Hong Noedl, Harald Nosten, Francois Noviyanti, Rintis Ntui, Vincent Ntui-Njock Nzila, Alexis Ochola-Oyier, Lynette Isabella Ocholla, Harold Oduro, Abraham Omedo, Irene Onyamboko, Marie A Ouedraogo, Jean-Bosco Oyebola, Kolapo Oyibo, Wellington Aghoghovwia Pearson, Richard Peshu, Norbert Phyo, Aung P Plowe, Christopher V Price, Ric N Pukrittayakamee, Sasithon Quang, Huynh Hong Randrianarivelojosia, Milijaona Rayner, Julian C Ringwald, Pascal Rosanas-Urgell, Anna Rovira-Vallbona, Eduard Ruano-Rubio, Valentin Ruiz, Lastenia Saunders, David Shayo, Alex Siba, Peter Simpson, Victoria J Sissoko, Mahamadou S Smith, Christen Su, Xin-Zhuan Sutherland, Colin Takala-Harrison, Shannon Talman, Arthur Tavul, Livingstone Thanh, Ngo Viet Thathy, Vandana Thu, Aung Myint Toure, Mahamoudou Tshefu, Antoinette Verra, Federica Vinetz, Joseph Wellems, Thomas E Wendler, Jason White, Nicholas J Whitton, Georgia Yavo, William Van Der Pluijm, Rob W Amenga-Etego, Lucas [0000-0003-4468-0506] Anderson, Tim [0000-0002-0191-0204] Ansah, Patrick O [0000-0002-3214-5621] Ashley, Elizabeth [0000-0002-7620-4822] Ba, Hampate [0000-0002-9299-5775] Baraka, Vito [0000-0001-9694-9293] Bejon, Philip [0000-0002-2135-7549] Bertin, Gwladys I [0000-0002-2218-9591] Boni, Maciej F [0000-0002-0830-9630] Bousema, Teun [0000-0003-2666-094X] Chookajorn, Thanat [0000-0003-2876-6203] Claessens, Antoine [0000-0002-4277-0914] Conway, David J [0000-0002-8711-3037] Craig, Alister [0000-0003-0914-6164] D'Alessandro, Umberto [0000-0001-6341-5009] Day, Nicholas [0000-0003-2309-1171] Diakite, Mahamadou [0000-0002-4268-8857] Djimde, Abdoulaye [0000-0003-0062-2283] Dondorp, Arjen [0000-0001-5190-2395] Drakeley, Chris [0000-0003-4863-075X] Echeverry, Diego F [0000-0003-0301-4478] Erko, Berhanu [0000-0003-1685-752X] Faiz, Abdul [0000-0002-3460-7535] Fanello, Caterina A [0000-0003-1932-9562] Gamboa, Dionicia [0000-0002-1420-7729] Golassa, Lemu [0000-0002-1216-8711] Healy, Sara Anne [0000-0003-3078-6094] Ishengoma, Deus [0000-0003-2040-3416] Jackson, Scott A [0000-0002-3172-1607] Kamaliddin, Claire [0000-0001-8198-6235] Kamau, Edwin [0000-0002-5761-7883] Konate, Drissa S [0000-0002-4177-9642] Kwiatkowski, Dominic P [0000-0002-5023-0176] Kyle, Dennis [0000-0002-0238-965X] Lawniczak, Mara [0000-0002-3006-2080] Loua, Kovana M [0000-0003-0571-0944] Marsh, Kevin [0000-0001-8377-5466] Mayxay, Mayfong [0000-0002-6056-4516] Miotto, Olivo [0000-0001-8060-6771] Mita, Toshihiro [0000-0001-8180-2344] Mobegi, Victor [0000-0002-1962-5583] Morang'a, Collins Misita [0000-0002-6988-150X] Nguyen, Thuy-Nhien [0000-0002-4101-5706] Nosten, Francois [0000-0002-7951-0745] Ntui, Vincent Ntui-Njock [0000-0002-7532-9930] Oduro, Abraham [0000-0002-4191-7419] Onyamboko, Marie A [0000-0002-7501-5931] Ouedraogo, Jean-Bosco [0000-0003-0412-8733] Oyebola, Kolapo [0000-0002-1003-2570] Pearson, Richard [0000-0002-7386-3566] Phyo, Aung P [0000-0002-0383-9624] Price, Ric N [0000-0003-2000-2874] Rayner, Julian C [0000-0002-9835-1014] Rosanas-Urgell, Anna [0000-0002-0432-5203] Shayo, Alex [0000-0002-7099-8537] Su, Xin-Zhuan [0000-0003-3246-3248] Vinetz, Joseph [0000-0001-8344-2004] Wellems, Thomas E [0000-0003-3899-8454] Apollo - University of Cambridge Repository
Publication Year :
2023
Publisher :
F1000 Research Ltd, 2023.
Abstract
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.
Details
Database :
OpenAIRE
Accession number :
edsair.doi.dedup.....8b9e5bb5dca504636fe25755ea3af9ea