Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples
In: EISSN: 2398-502X ; Wellcome Open Research ; https://hal.umontpellier.fr/hal-04110334 ; Wellcome Open Research, 2023, 2023
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academicJournal
Zugriff:
International audience ; 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.
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Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples
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Autor/in / Beteiligte Person: | 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, G ; 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, François ; 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 ; University of Khartoum ; University of Cape Coast Ghana ; Université Cheikh Anta Diop de Dakar Sénégal (UCAD) ; The Wellcome Trust Sanger Institute Cambridge ; London School of Hygiene and Tropical Medicine Fajara, Gambia ; London School of Hygiene and Tropical Medicine (LSHTM) ; National Institute of Allergy and Infectious Diseases Bethesda (NIAID-NIH) ; National Institutes of Health Bethesda, MD, USA (NIH) ; West African Centre for Cell Biology of Infectious Pathogens Legon, Ghana (WACCBIP) ; University of Ghana ; Navrongo Health Research Centre Navrongo, Ghana (NHRC) ; Kenya Medical Research Institute (KEMRI) ; Texas Biomedical Research Institute San Antonio, TX ; d'Antananarivo, Université ; University of Buéa ; Instituto Nacional de Saude Maputo, Mozambique (INS) ; Centre for Tropical Medicine and Global Health Oxford, UK ; Nuffield Department of Medicine Oxford, UK (Big Data Institute) ; University of Oxford-University of Oxford ; Mahidol Oxford Tropical Medicine Research Unit (MORU) ; University of Oxford-Mahidol University Bangkok -Wellcome Trust ; Menzies School of Health Research Australia ; Charles Darwin University Australia ; Nuffield Department of Clinical Medicine Oxford ; University of Oxford ; Institut de Recherche pour le Développement (IRD) ; Laboratory of Pathogen and Host Immunity Montpellier (LPHI) ; Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM) ; Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC) ; Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD France-Sud )-Université de Montpellier (UM) |
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Zeitschrift: | EISSN: 2398-502X ; Wellcome Open Research ; https://hal.umontpellier.fr/hal-04110334 ; Wellcome Open Research, 2023, 2023 |
Veröffentlichung: | HAL CCSD ; F1000Research, 2023 |
Medientyp: | academicJournal |
DOI: | 10.12688/wellcomeopenres.18681.1 |
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