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An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples

Ambroise Ahouidi Mozam Ali Jacob Almagro-Garcia Alfred Amambua-Ngwa Chanaki Amaratunga Roberto Amato Lucas Amenga-Etego Ben Andagalu Tim Anderson Voahangy Andrianaranjaka Tobias Apinjoh Cristina Ariani Elizabeth Ashley Sarah Auburn Gordon Awandare Hampate Ba Vito Baraka Alyssa Barry Philip Bejon Gwladys Bertin Maciej Boni Steffen Borrmann Teun Bousema Oralee Branch Peter Bull George Busby Thanat Chookajorn Kesinee Chotivanich Antoine Claessens 1 David Conway Alister Craig Umberto d'Alessandro Souleymane Dama Nicholas Pj Day Brigitte Denis Mahamadou Diakite Abdoulaye Djimdé Christiane Dolecek Arjen Dondorp Chris Drakeley Eleanor Drury Patrick Duffy Diego Echeverry Thomas Egwang Berhanu Erko Rick Fairhurst Abdul Faiz Caterina Fanello Mark Fukuda Dionicia Gamboa Anita Ghansah Lemu Golassa Sonia Goncalves William Hamilton G. Harrison Lee Hart Christa Henrichs Tran Tinh Hien Catherine Hill Abraham Hodgson Christina Hubbart Mallika Imwong Deus Ishengoma Scott Jackson Chris Jacob Ben Jeffery Anna Jeffreys Kimberly Johnson Dushyanth Jyothi Claire Kamaliddin Edwin Kamau Mihir Kekre Krzysztof Kluczynski Theerarat Kochakarn Abibatou Konaté Dominic Kwiatkowski Myat Phone Kyaw Pharath Lim Chanthap Lon Kovana Loua Oumou Maïga-Ascofaré Cinzia Malangone Magnus Manske Jutta Marfurt Kevin Marsh Mayfong Mayxay Alistair Miles Olivo Miotto Victor Mobegi Olugbenga Mokuolu Jacqui Montgomery Ivo Mueller Paul Newton Thuy Nguyen Thuy-Nhien Nguyen Harald Noedl Francois Nosten Rintis Noviyanti Alexis Nzila Lynette Ochola-Oyier Harold Ocholla Abraham Oduro Irene Omedo Marie Onyamboko Jean-Bosco Ouedraogo Kolapo Oyebola Richard Pearson Norbert Peshu Aung Pyae Phyo Chris Plowe Ric Price Sasithon Pukrittayakamee Milijaona Randrianarivelojosia Julian Rayner Pascal Ringwald Kirk Rockett Katherine Rowlands Lastenia Ruiz David Saunders Alex Shayo Peter Siba Victoria Simpson Jim Stalker Xin-Zhuan Su Colin Sutherland Shannon Takala-Harrison Livingstone Tavul Vandana Thathy Antoinette Tshefu Federica Verra Joseph Vinetz Thomas Wellems Jason Wendler Nicholas White Ian Wright William Yavo Htut Ye
1 LPHI - LPHI - Laboratory of Pathogen Host Interactions
Abstract : 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 Plasmodium falciparum 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.
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https://hal.umontpellier.fr/hal-03228653
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Soumis le : mardi 18 mai 2021 - 12:09:27
Dernière modification le : vendredi 22 octobre 2021 - 15:06:03

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UNIV-MONTPELLIER | LPHI | CNRS

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Ambroise Ahouidi, Mozam Ali, Jacob Almagro-Garcia, Alfred Amambua-Ngwa, Chanaki Amaratunga, et al.. An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples. Wellcome Open Research, F1000Research, 2021, 6, pp.42. ⟨10.12688/wellcomeopenres.16168.1⟩. ⟨hal-03228653⟩

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