An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples
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. H...
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Biochemistry, Genetics and Molecular Biology Medicine 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 |
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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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Mahidol Oxford Tropical Medicine Research Unit |
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Mahidol Oxford Tropical Medicine Research Unit 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 |
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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 |
author_sort |
Malaria Gen |
title |
An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples |
title_short |
An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples |
title_full |
An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples |
title_fullStr |
An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples |
title_full_unstemmed |
An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples |
title_sort |
open dataset of plasmodium falciparum genome variation in 7,000 worldwide samples |
publishDate |
2022 |
url |
https://repository.li.mahidol.ac.th/handle/123456789/76344 |
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1763492413014278144 |
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th-mahidol.763442022-08-04T18:06:55Z An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples 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 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 Biochemistry, Genetics and Molecular Biology Medicine 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. 2022-08-04T08:13:43Z 2022-08-04T08:13:43Z 2021-01-01 Article Wellcome Open Research. Vol.6, (2021), 1-31 10.12688/wellcomeopenres.16168.2 2398502X 2-s2.0-85113375527 https://repository.li.mahidol.ac.th/handle/123456789/76344 Mahidol University SCOPUS https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85113375527&origin=inward |