Wellcome Open Research (Jul 2021)
An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples [version 2; peer review: 2 approved]
- 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 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,
- 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
Affiliations
- MalariaGEN
- Ambroise Ahouidi
- Hopital Le Dantec, Universite Cheikh Anta Diop, Dakar, Senegal
- Mozam Ali
- Wellcome Sanger Institute, Hinxton, UK
- Jacob Almagro-Garcia
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
- Alfred Amambua-Ngwa
- Wellcome Sanger Institute, Hinxton, UK
- Chanaki Amaratunga
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
- Roberto Amato
- Wellcome Sanger Institute, Hinxton, UK
- Lucas Amenga-Etego
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
- Ben Andagalu
- United States Army Medical Research Directorate-Africa, Kenya Medical Research Institute/Walter Reed Project, Kisumu, Kenya
- Tim J. C. Anderson
- Texas Biomedical Research Institute, San Antonio, USA
- Voahangy Andrianaranjaka
- Université d'Antananarivo, Antananarivo, Madagascar
- Tobias Apinjoh
- University of Buea, Buea, Cameroon
- Cristina Ariani
- Wellcome Sanger Institute, Hinxton, UK
- Elizabeth A Ashley
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Sarah Auburn
- Menzies School of Health Research, Darwin, Australia
- Gordon A. Awandare
- University of Ghana, Legon, Ghana
- Hampate Ba
- Institut National de Recherche en Santé Publique, Nouakchott, Mauritania
- Vito Baraka
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania
- Alyssa E. Barry
- Deakin University, Geelong, Australia
- Philip Bejon
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
- Gwladys I. Bertin
- Institute of Research for Development (IRD), Paris, France
- Maciej F. Boni
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
- Steffen Borrmann
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
- Teun Bousema
- London School of Hygiene and Tropical Medicine, London, UK
- Oralee Branch
- NYU School of Medicine Langone Medical Center, New York, USA
- Peter C. Bull
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
- George B. J. Busby
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
- Thanat Chookajorn
- Mahidol University, Bangkok, Thailand
- Kesinee Chotivanich
- Mahidol University, Bangkok, Thailand
- Antoine Claessens
- Medical Research Council Unit The Gambia, at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
- David Conway
- London School of Hygiene and Tropical Medicine, London, UK
- Alister Craig
- Liverpool School of Tropical Medicine, Liverpool, UK
- Umberto D'Alessandro
- Medical Research Council Unit The Gambia, at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
- Souleymane Dama
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
- Nicholas PJ Day
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Brigitte Denis
- Malawi-Liverpool-Wellcome Trust Clinical Research, Blantyre, Malawi
- Mahamadou Diakite
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
- Abdoulaye Djimdé
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
- Christiane Dolecek
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Arjen M Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Chris Drakeley
- London School of Hygiene and Tropical Medicine, London, UK
- Eleanor Drury
- Wellcome Sanger Institute, Hinxton, UK
- Patrick Duffy
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
- Diego F. Echeverry
- Centro Internacional de Entrenamiento e Investigaciones Médicas - CIDEIM, Cali, Colombia
- Thomas G. Egwang
- Biotech Laboratories, Kampala, Uganda
- Berhanu Erko
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Rick M. Fairhurst
- National Institutes of Health (NIH), Bethesda, USA
- Abdul Faiz
- Dev Care Foundation, Dhaka, Bangladesh
- Caterina A. Fanello
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Mark M. Fukuda
- Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
- Dionicia Gamboa
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
- Anita Ghansah
- Nogouchi Memorial Institute for Medical Research, Legon-Accra, Ghana
- Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Sonia Goncalves
- Wellcome Sanger Institute, Hinxton, UK
- William L. Hamilton
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- G. L. Abby Harrison
- Walter and Eliza Hall Institute, Melbourne, Australia
- Lee Hart
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
- Christa Henrichs
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
- Tran Tinh Hien
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
- Catherine A. Hill
- Department of Entomology, Purdue University, West Lafayette, USA
- Abraham Hodgson
- Ghana Health Service, Ministry of Health, Accra, Ghana
- Christina Hubbart
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Mallika Imwong
- Mahidol University, Bangkok, Thailand
- Deus S. Ishengoma
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania
- Scott A. Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
- Chris G. Jacob
- Wellcome Sanger Institute, Hinxton, UK
- Ben Jeffery
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
- Anna E. Jeffreys
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Kimberly J. Johnson
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
- Dushyanth Jyothi
- Wellcome Sanger Institute, Hinxton, UK
- Claire Kamaliddin
- Institute of Research for Development (IRD), Paris, France
- Edwin Kamau
- Walter Reed Army Institute of Research, U.S. Military HIV Research Program, Silver Spring, MD, USA
- Mihir Kekre
- Wellcome Sanger Institute, Hinxton, UK
- Krzysztof Kluczynski
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
- Theerarat Kochakarn
- Wellcome Sanger Institute, Hinxton, UK
- Abibatou Konaté
- University Félix Houphouët-Boigny, Abidjan, Cote d'Ivoire
- Dominic P. Kwiatkowski
- Wellcome Sanger Institute, Hinxton, UK
- Myat Phone Kyaw
- The Myanmar Oxford Clinical Research Unit, University of Oxford, Yangon, Myanmar
- Pharath Lim
- Medical Care Development International, Maryland, USA
- Chanthap Lon
- Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
- Kovana M. Loua
- Institut National de Santé Publique, Conakry, Guinea
- Oumou Maïga-Ascofaré
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Cinzia Malangone
- Wellcome Sanger Institute, Hinxton, UK
- Magnus Manske
- Wellcome Sanger Institute, Hinxton, UK
- Jutta Marfurt
- Menzies School of Health Research, Darwin, Australia
- Kevin Marsh
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mayfong Mayxay
- Institute of Research and Education Development (IRED), University of Health Sciences, Ministry of Health, Vientiane, Lao People's Democratic Republic
- Alistair Miles
- Wellcome Sanger Institute, Hinxton, UK
- Olivo Miotto
- Wellcome Sanger Institute, Hinxton, UK
- Victor Mobegi
- School of Medicine, University of Nairobi, Nairobi, Kenya
- Olugbenga A. Mokuolu
- Department of Paediatrics and Child Health, University of Ilorin, Ilorin, Nigeria
- Jacqui Montgomery
- Institute of Vector-Borne Disease, Monash University, Clayton, Victoria, 3800, Australia
- Ivo Mueller
- Barcelona Centre for International Health Research, Barcelona, Spain
- Paul N. Newton
- Wellcome Trust-Mahosot Hospital-Oxford Tropical Medicine Research Collaboration, Vientiane, Lao People's Democratic Republic
- Thuy Nguyen
- Wellcome Sanger Institute, Hinxton, UK
- Thuy-Nhien Nguyen
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
- Harald Noedl
- MARIB - Malaria Research Initiative Bandarban, Bandarban, Bangladesh
- Francois Nosten
- Shoklo Malaria Research Unit, Bangkok, Thailand
- Rintis Noviyanti
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
- Alexis Nzila
- King Fahid University of Petroleum and Minerals (KFUMP), Dharhran, Saudi Arabia
- Lynette I. Ochola-Oyier
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
- Harold Ocholla
- KEMRI - Centres for Disease Control and Prevention (CDC) Research Program, Kisumu, Kenya
- Abraham Oduro
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
- Irene Omedo
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
- Marie A. Onyamboko
- Kinshasa School of Public Health, University of Kinshasa, Kinshasa, Congo, Democratic Republic
- Jean-Bosco Ouedraogo
- Institut de Recherche en Sciences de la Santé, Ouagadougou, Burkina Faso
- Kolapo Oyebola
- Nigerian Institute of Medical Research, Lagos, Nigeria
- Richard D. Pearson
- Wellcome Sanger Institute, Hinxton, UK
- Norbert Peshu
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
- Aung Pyae Phyo
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Chris V. Plowe
- School of Medicine, University of Maryland, Baltimore, MD, USA
- Ric N. Price
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Sasithon Pukrittayakamee
- Mahidol University, Bangkok, Thailand
- Milijaona Randrianarivelojosia
- Institut Pasteur de Madagascar, Antananarivo, Madagascar
- Julian C. Rayner
- Wellcome Sanger Institute, Hinxton, UK
- Pascal Ringwald
- World Health Organization (WHO), Geneva, Switzerland
- Kirk A. Rockett
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Katherine Rowlands
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Lastenia Ruiz
- Universidad Nacional de la Amazonia Peruana, Iquitos, Peru
- David Saunders
- Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
- Alex Shayo
- Nelson Mandela Institute of Science and Technology, Arusha, Tanzania
- Peter Siba
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
- Victoria J. Simpson
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
- Jim Stalker
- Wellcome Sanger Institute, Hinxton, UK
- Xin-zhuan Su
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
- Colin Sutherland
- London School of Hygiene and Tropical Medicine, London, UK
- Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland, School of Medicine, Baltimore, MD, USA
- Livingstone Tavul
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
- Vandana Thathy
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
- Antoinette Tshefu
- University of Kinshasa, Kinshasa, Congo, Democratic Republic
- Federica Verra
- Sapienza University of Rome, Rome, Italy
- Joseph Vinetz
- Yale School of Medicine, New Haven, CT, USA
- Thomas E. Wellems
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
- Jason Wendler
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Nicholas J. White
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Ian Wright
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
- William Yavo
- University Félix Houphouët-Boigny, Abidjan, Cote d'Ivoire
- Htut Ye
- Department of Medical Research, Yangon, Myanmar
- DOI
- https://doi.org/10.12688/wellcomeopenres.16168.2
- Journal volume & issue
-
Vol. 6
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.
