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

Issued Date

2021-01-01

Resource Type

Article

ISSN

2398502X

DOI

10.12688/wellcomeopenres.16168.2

Other identifier(s)

2-s2.0-85113375527

Rights

Mahidol University

Rights Holder(s)

SCOPUS

Bibliographic Citation

Wellcome Open Research. Vol.6, (2021), 1-31

Suggested Citation

Malaria Gen, 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 A. 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, François Nosten, Rintis Noviyanti, Alexis Nzila An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples. Wellcome Open Research. Vol.6, (2021), 1-31. doi:10.12688/wellcomeopenres.16168.2 Retrieved from: https://repository.li.mahidol.ac.th/handle/20.500.14594/76344

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Thesis

Title

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

Author(s)

Malaria Gen
 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 A. 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
 François Nosten
 Rintis Noviyanti
 Alexis Nzila

Other Contributor(s)

Mahidol Oxford Tropical Medicine Research Unit
 Oxford University Clinical Research Unit
 CSIR - Institute for Scientific and Technological Information
 Université de Montpellier
 Instituto de Salud Global de Barcelona
 Universidad Icesi
 The Wellcome Centre for Human Genetics
 Ministry of Health Laos
 Malawi-Liverpool-Wellcome Trust Clinical Research Programme
 Université d'Antananarivo
 University of Cocody
 Navrongo Health Research Center
 Ministry of Health Ghana
 Kwame Nkrumah University of Science and Technology
 National Institute for Medical Research Tanga
 Universite Cheikh Anta Diop
 Universidad Peruana Cayetano Heredia
 Addis Ababa University
 University of Buea
 African Academy of Sciences
 Kenya Medical Research Institute
 Eijkman Institute for Molecular Biology
 University of Nairobi Medical School
 Wellcome Trust Research Laboratories Nairobi
 Centro Internacional de Entrenamiento e Investigaciones Medicas
 Shoklo Malaria Research Unit
 London School of Hygiene & Tropical Medicine
 University of Cambridge
 University of Georgia
 IRD Institut de Recherche pour le Developpement
 Walter and Eliza Hall Institute of Medical Research
 University of Oxford
 Menzies School of Health Research
 NYU Grossman School of Medicine
 Texas Biomedical Research Institute
 Liverpool School of Tropical Medicine
 Bernhard Nocht Institut fur Tropenmedizin Hamburg
 Monash University
 Deakin University
 University of Ghana
 National Institute of Allergy and Infectious Diseases (NIAID)
 Eberhard Karls Universität Tübingen
 Cambridge University Hospitals NHS Foundation Trust
 Armed Forces Research Institute of Medical Sciences, Thailand
 Mahosot Hospital, Lao
 Universiteit Antwerpen
 Walter Reed Army Institute of Research
 Mahidol University
 University of Ilorin
 King Fahd University of Petroleum and Minerals
 Purdue University
 Nuffield Department of Medicine
 National Institutes of Health (NIH)
 Wellcome Sanger Institute
 Burnet Institute
 Radboud University Medical Center
 Medical Care Development International
 Malaria Research Initiative Bandarban (MARIB)
 Institut National de Santé Publique
 East African Consortium for Clinical Research (EACCR)
 Biotech Laboratories
 Institut National de Recherches en Santé Publique
 University of Sciences
 Dev Care Foundation
 University of Public Health

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.

Keyword(s)

Biochemistry, Genetics and Molecular Biology
 Medicine

Availability

URI

https://repository.li.mahidol.ac.th/handle/20.500.14594/76344

Collections

Scopus 2021