학술논문
An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples [version 1; peer review: 2 approved]
Document Type
article
Author
MalariaGEN; Ambroise Ahouidi; Mozam Ali; Jacob Almagro-Garcia; Alfred Amambua-Ngwa; Chanaki Amaratunga; Roberto Amato; Lucas Amenga-Etego; Ben Andagalu; Tim J. C. Anderson; Voahangy Andrianaranjaka; Tobias Apinjoh; Cristina Ariani; Elizabeth A. Ashley; Sarah Auburn; Gordon Awandare; Hampate Ba; Vito Baraka; Alyssa E. Barry; Philip Bejon; Gwladys I. Bertin; Maciej F. Boni; Steffen Borrmann; Teun Bousema; Oralee Branch; Peter C. Bull; George B. J. 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 M Dondorp; Chris Drakeley; Eleanor Drury; Patrick Duffy; Diego F. Echeverry; Thomas G. Egwang; Berhanu Erko; Rick M. Fairhurst; Abdul Faiz; Caterina A. Fanello; Mark M. Fukuda; Dionicia Gamboa; Anita Ghansah; Lemu Golassa; Sonia Goncalves; William L. Hamilton; G. L. Abby Harrison; Lee Hart; Christa Henrichs; Tran Tinh Hien; Catherine A. Hill; Abraham Hodgson; Christina Hubbart; Mallika Imwong; Deus S. Ishengoma; Scott A. Jackson; Chris G. Jacob; Ben Jeffery; Anna E. Jeffreys; Kimberly J. Johnson; Dushyanth Jyothi; Claire Kamaliddin; Edwin Kamau; Mihir Kekre; Krzysztof Kluczynski; Theerarat Kochakarn; Abibatou Konaté; Dominic P. Kwiatkowski; Myat Phone Kyaw; Pharath Lim; Chanthap Lon; Kovana M. Loua; Oumou Maïga-Ascofaré; Cinzia Malangone; Magnus Manske; Jutta Marfurt; Kevin Marsh; Mayfong Mayxay; Alistair Miles; Olivo Miotto; Victor Mobegi; Olugbenga A. Mokuolu; Jacqui Montgomery; Ivo Mueller; Paul N. Newton; Thuy Nguyen; Thuy-Nhien Nguyen; Harald Noedl; Francois Nosten; Rintis Noviyanti; Alexis Nzila; Lynette I. Ochola-Oyier; Harold Ocholla; Abraham Oduro; Irene Omedo; Marie A. Onyamboko; Jean-Bosco Ouedraogo; Kolapo Oyebola; Richard D. Pearson; Norbert Peshu; Aung Pyae Phyo; Chris V. Plowe; Ric N. Price; Sasithon Pukrittayakamee; Milijaona Randrianarivelojosia; Julian C. Rayner; Pascal Ringwald; Kirk A. Rockett; Katherine Rowlands; Lastenia Ruiz; David Saunders; Alex Shayo; Peter Siba; Victoria J. Simpson; Jim Stalker; Xin-zhuan Su; Colin Sutherland; Shannon Takala-Harrison; Livingstone Tavul; Vandana Thathy; Antoinette Tshefu; Federica Verra; Joseph Vinetz; Thomas E. Wellems; Jason Wendler; Nicholas J. White; Ian Wright; William Yavo; Htut Ye
Source
Wellcome Open Research, Vol 6 (2021)
Subject
Language
English
ISSN
2398-502X
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.