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; 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

doi:10.12688/wellcomeopenres.16168.1

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

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Open Access

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, …

Wellcome Open Research, Vol.6

2021

DOI: https://doi.org/10.12688/wellcomeopenres.16168.1

Résumé

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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Titre: An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples
Créateurs - sans rôle: Ambroise Ahouidi - Cheikh Anta Diop University
Mozam Ali - Wellcome Sanger Institute
Jacob Almagro-Garcia - Wellcome Sanger Institute
Alfred Amambua-Ngwa - Genomics
Chanaki Amaratunga - National Institute of Allergy and Infectious Diseases
Roberto Amato - National Institute of Allergy and Infectious Diseases
Lucas Amenga-Etego
Ben Andagalu - University of Ghana
Tim Anderson - United States Army Medical Research Directorate - Africa
Voahangy Andrianaranjaka - Texas Biomedical Research Institute
Tobias Apinjoh - University of Antananarivo
Cristina Ariani - University of Buea
Elizabeth Ashley - Mahidol Oxford Tropical Medicine Research Unit
Sarah Auburn - Mahidol Oxford Tropical Medicine Research Unit
Gordon Awandare - University of Ghana
Hampate Ba - University of Ghana
Vito Baraka - National Institute for Medical Research
Alyssa Barry - Deakin University
Philip Bejon - Deakin University
Gwladys Bertin - Institut de Recherche pour le Développement
Maciej Boni - Institut de Recherche pour le Développement
Steffen Borrmann - Oxford University Clinical Research Unit
Teun Bousema - Radboud University Nijmegen
Oralee Branch - Radboud University Nijmegen
Peter Bull - Kenya Medical Research Institute
George Busby - University of Cambridge
Thanat Chookajorn - University of Oxford
Kesinee Chotivanich - Mahidol University
Antoine Claessens - Université de Montpellier, Laboratory of Pathogens and Host Immunity - LPHI
David Conway - Maladies Infectieuses et Vecteurs: Écologie, Génétique, Évolution et Contrôle
Alister Craig - Liverpool School of Tropical Medicine
Umberto d'Alessandro
Souleymane Dama - Université des Sciences, des Techniques et des Technologies de Bamako
Nicholas Pj Day - Mahidol Oxford Tropical Medicine Research Unit
Brigitte Denis - Malawi-Liverpool-Wellcome Trust Clinical Research Programme
Mahamadou Diakite - University of Liverpool
Abdoulaye Djimdé - Université des Sciences, des Techniques et des Technologies de Bamako
Christiane Dolecek - University of Oxford
Arjen Dondorp - Mahidol Oxford Tropical Medicine Research Unit
Chris Drakeley - London School of Hygiene & Tropical Medicine
Eleanor Drury - Wellcome Sanger Institute
Patrick Duffy - Wellcome Sanger Institute
Diego Echeverry - Centro Internacional de Entrenamiento e Investigaciones Medicas
Thomas Egwang - Universidad Peruana Cayetano Heredia
Berhanu Erko - Addis Ababa University
Rick Fairhurst - National Institutes of Health
Abdul Faiz - Child Health Research Foundation
Caterina Fanello - Mahidol Oxford Tropical Medicine Research Unit
Mark Fukuda - Mahidol Oxford Tropical Medicine Research Unit
Dionicia Gamboa - Universidad Peruana Cayetano Heredia
Anita Ghansah - Noguchi Memorial Institute for Medical Research
Lemu Golassa - Addis Ababa University
Sonia Goncalves - Wellcome Sanger Institute
William Hamilton - Cambridge University Hospitals NHS Foundation Trust
G. Harrison
Lee Hart - University of Oxford
Christa Henrichs - University of Oxford
Tran Tinh Hien - Genomics
Catherine Hill - Purdue University West Lafayette
Abraham Hodgson - Ghana Health Service
Christina Hubbart - University of Oxford
Mallika Imwong - Mahidol University
Deus Ishengoma - Mahidol University
Scott Jackson - University of Georgia
Chris Jacob - Wellcome Sanger Institute
Ben Jeffery - Wellcome Sanger Institute
Anna Jeffreys - University of Oxford
Kimberly Johnson - University of Oxford
Dushyanth Jyothi - University of Oxford
Claire Kamaliddin - Wellcome Sanger Institute
Edwin Kamau - Institut de Recherche pour le Développement
Mihir Kekre - Wellcome Sanger Institute
Krzysztof Kluczynski - University of Oxford
Theerarat Kochakarn - University of Oxford
Abibatou Konaté - Wellcome Sanger Institute
Dominic Kwiatkowski - University of Oxford
Myat Phone Kyaw - Wellcome Sanger Institute
Pharath Lim - Medical Care Development International
Chanthap Lon - Armed Forces Research Institute of Medical Science
Kovana Loua - Institut National de Santé Publique
Oumou Maïga-Ascofaré - Université des Sciences, des Techniques et des Technologies de Bamako
Cinzia Malangone
Magnus Manske - Wellcome Sanger Institute
Jutta Marfurt - Wellcome Sanger Institute
Kevin Marsh - University of Oxford
Mayfong Mayxay - University of Oxford
Alistair Miles - Wellcome Sanger Institute
Olivo Miotto - University of Oxford
Victor Mobegi - University of Nairobi
Olugbenga Mokuolu - University of Ilorin
Jacqui Montgomery - Monash University
Ivo Mueller - Barcelona Centre for International Affairs
Paul Newton - Walter and Eliza Hall Institute of Medical Research
Thuy Nguyen - Wellcome Sanger Institute
Thuy-Nhien Nguyen - Wellcome Sanger Institute
Harald Noedl - Wellcome Sanger Institute
Francois Nosten - Shoklo Malaria Research Unit
Rintis Noviyanti - University of Oxford
Alexis Nzila - King Fahd University of Petroleum and Minerals
Lynette Ochola-Oyier - Kenya Medical Research Institute
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
Détails de publication: Wellcome Open Research, Vol.6
Identifiants: 99151576709311
Unité académique: Laboratory of Pathogens and Host Immunity - LPHI
Langue: English
Type de ressource: Journal article
Champs locaux: hal-03228653