Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples
MalariaGEN(University of Khartoum), Muzamil Mahdi Abdel Hamid(University of Khartoum), Mohamed Hassan Abdelraheem(University of Cape Coast), Desmond Omane Acheampong(Cheikh Anta Diop University), Ambroise D. Ahouidi(Wellcome Sanger Institute), Mozam Ali(Wellcome Sanger Institute), Jacob Almagro‐Garcia(Wellcome Sanger Institute), Alfred Amambua‐Ngwa(National Institute of Allergy and Infectious Diseases), Chanaki Amaratunga(University of Ghana), Lucas Amenga–Etego(Kenya Medical Research Institute), Ben Andagalu(Texas Biomedical Research Institute), Tim Anderson(University of Antananarivo), Voahangy Andrianaranjaka(Juntendo University Hospital), Ifeyinwa Aniebo(University of Nairobi), Enoch Aninagyei(University of Ghana), Felix Ansah(Navrongo Health Research Centre), Patrick Ansah(University of Buea), Tobias O. Apinjoh(Instituto Nacional de Saúde), Paulo Arnaldo(Mahidol Oxford Tropical Medicine Research Unit), Elizabeth A. Ashley(Menzies School of Health Research), Sarah Auburn(University of Ghana), Gordon A. Awandare(Centre for Human Genetics), Hampaté Bâ(Centre for Human Genetics), Vito Baraka(Centre for Human Genetics), Alyssa E. Barry(Centre for Human Genetics), Philip Bejon(Institut de Recherche pour le Développement), Gwladys Bertin(Centre for Human Genetics), Maciej F. Boni(Centre for Human Genetics), Steffen Borrmann(Centre for Human Genetics), Teun Bousema(Centre for Human Genetics), Marielle Karine Bouyou-Akotet(Centre for Human Genetics), OraLee H. Branch(Centre for Human Genetics), Peter C. Bull(Centre for Human Genetics), H K Cheah(Centre for Human Genetics), Keobouphaphone Chindavongsa(Centre for Human Genetics), Thanat Chookajorn(Centre for Human Genetics), Kesinee Chotivanich(Agropolis International), Antoine Claessens(Centre for Human Genetics), David J. Conway(Centre for Human Genetics), Vladimir Corredor(Myanmar Oxford Clinical Research Unit), Erin Courtier(Centre for Human Genetics), Alister Craig, Umberto D’Alessandro(Centre for Human Genetics), Souleymane Dama, Nicholas Day(Centre for Human Genetics), Brigitte Denis(Monash University), Mehul Dhorda(Centre for Human Genetics), Mahamadou Diakité(Centre for Human Genetics), Abdoulaye Djimdé(Centre for Human Genetics), Christiane Dolecek, Arjen M. Dondorp(Centre for Human Genetics), Seydou Doumbia(Centre for Human Genetics), Chris Drakeley(Myanmar Oxford Clinical Research Unit), Eleanor Drury(University of Georgia), Patrick Duffy(Centre for Human Genetics), Diego F. Echeverry(Centre for Human Genetics), Thomas G. Egwang(University of Ilorin), Sónia Maria Enosse(Centre for Human Genetics), Berhanu Erko(Centre for Human Genetics), Rick M. Fairhurst(Centre for Human Genetics), Abdul Faiz(Monash University), Caterina Fanello(Centre for Human Genetics), Mark Fleharty(Myanmar Oxford Clinical Research Unit), Matthew Forbes(Centre for Human Genetics), Mark M. Fukuda(Centre for Human Genetics), Dionicia Gamboa(Centre for Human Genetics), Anita Ghansah(Centre for Human Genetics), Lemu Golassa(Myanmar Oxford Clinical Research Unit), Sónia Gonçalves(Centre for Human Genetics), G. L. Abby Harrison(University of Georgia), Sara A. Healy(Centre for Human Genetics), Jason A. Hendry(Myanmar Oxford Clinical Research Unit), Anastasia Hernández-Koutoucheva, Tran Tinh Hien(Centre for Human Genetics), Catherine A. St. Hill(Centre for Human Genetics), Francis Hombhanje(Centre for Human Genetics), Amanda Hott(Centre for Human Genetics), Ye Htut(Centre for Human Genetics), Mazza Hussein(Centre for Human Genetics), Mallika Imwong(Centre for Human Genetics), Deus S. Ishengoma(Centre for Human Genetics), Scott A. Jackson(Myanmar Oxford Clinical Research Unit), Chris Jacob(Myanmar Oxford Clinical Research Unit), Julia Jeans(Myanmar Oxford Clinical Research Unit), Kimberly J. Johnson(Centre for Human Genetics), Claire Kamaliddin(Centre for Human Genetics), Edwin Kamau(Myanmar Oxford Clinical Research Unit), Jon Keatley(Centre for Human Genetics), Theerarat Kochakarn(Centre for Human Genetics), Drissa Konaté(Centre for Human Genetics), Abibatou Konaté(Centre for Human Genetics), Aminatou Koné(Myanmar Oxford Clinical Research Unit), Dominic Kwiatkowski(Centre for Human Genetics), Myat Phone Kyaw(Centre for Human Genetics), Dennis E. Kyle(Myanmar Oxford Clinical Research Unit), Mara Lawniczak(Centre for Human Genetics), Samuel K. Lee(Centre for Human Genetics), Martha Lemnge(University of Georgia), Pharath Lim(Centre for Human Genetics), Chanthap Lon(Centre for Human Genetics), Kovana Marcel Loua(Centre for Human Genetics), Celine I. Mandara(Centre for Human Genetics), Jutta Marfurt(Centre for Human Genetics), Kevin Marsh, Richard J. Maude, Mayfong Mayxay(Centre for Human Genetics), Oumou Maïga‐Ascofaré(Myanmar Oxford Clinical Research Unit), Olivo Miotto(Centre for Human Genetics), Toshihiro Mita(Centre for Human Genetics), Victor A. Mobegi(Centre for Human Genetics), Abdelrahim Osman Mohamed(Centre for Human Genetics), Olugbenga Ayodeji Mokuolu(Centre for Human Genetics), Jaqui Montgomery(University of Calgary), Collins M. Morang’a(Centre for Human Genetics), Ivo Müeller(Myanmar Oxford Clinical Research Unit), Kathryn Murie, Paul N. Newton(Centre for Human Genetics), Thang Ngo Duc(Myanmar Oxford Clinical Research Unit), Thuy Nguyen, Thuy-Nhien Nguyen(Centre for Human Genetics), Tuyen Nguyen Thi Kim(Centre for Human Genetics), Hong Nguyen Van(Centre for Human Genetics), Harald Noedl, François Nosten(Centre for Human Genetics), Rintis Noviyanti(University of Khartoum), Vincent N. Ntui(Centre for Human Genetics), Alexis Nzila, Lynette Isabella Ochola‐Oyier(Centre for Human Genetics), Harold Ocholla(Walter Reed Army Institute of Research), Abraham Oduro(Myanmar Oxford Clinical Research Unit), Irene Omedo(Centre for Human Genetics), Marie A. Onyamboko(Centre for Human Genetics), Jean‐Bosco Ouédraogo(Centre for Human Genetics), Kolapo Oyebola(Centre for Human Genetics), Wellington Oyibo(Myanmar Oxford Clinical Research Unit), Richard D. Pearson(Centre for Human Genetics), Norbert Peshu(Monash University), Aung Pyae Phyo(Centre for Human Genetics), Christopher V. Plowe(Monash University), Ric N. Price(Centre for Human Genetics), Sasithon Pukrittayakamee(Université Félix Houphouët-Boigny), Huynh Hong Quang(Université Félix Houphouët-Boigny), Milijaona Randrianarivelojosia(Université Félix Houphouët-Boigny), Julian C. Rayner(Université Félix Houphouët-Boigny), Pascal Ringwald(Université Félix Houphouët-Boigny), Anna Rosanas‐Urgell(Université Félix Houphouët-Boigny), Eduard Rovira-Vallbona(Centre for Human Genetics), Valentín Ruano-Rubio(Université Félix Houphouët-Boigny), Lastenia Ruiz Mesía(Université Félix Houphouët-Boigny), David Saunders(Université Félix Houphouët-Boigny), Alex Shayo(Université Félix Houphouët-Boigny), Peter Siba(Myanmar Oxford Clinical Research Unit), Victoria Simpson(Centre for Human Genetics), Mahamadou S. Sissoko(Myanmar Oxford Clinical Research Unit), Christen Smith(University of Georgia), Xin‐zhuan Su(Centre for Human Genetics), Colin Sutherland(Myanmar Oxford Clinical Research Unit), Shannon Takala‐Harrison(Agropolis International), Arthur M. Talman(Myanmar Oxford Clinical Research Unit), Livingstone Tavul, Ngo Viet Thanh(Myanmar Oxford Clinical Research Unit), Vandana Thathy(Myanmar Oxford Clinical Research Unit), Aung Myint Thu(Centre for Human Genetics), Mahamoudou Touré(Myanmar Oxford Clinical Research Unit), Antoinette Tshefu(University of Nairobi), Federica Verra(University of Khartoum), Joseph M. Vinetz(University of Georgia), Thomas E. Wellems(University of Ilorin), Jason Wendler, Nicholas J. White(Myanmar Oxford Clinical Research Unit), Georgia Whitton(Myanmar Oxford Clinical Research Unit), William Yavo(Monash University), Rob W. van der Pluijm
Cited by 146Open Access
Abstract
<ns3:p> We describe the MalariaGEN Pf7 data resource, the seventh release of <ns3:italic>Plasmodium falciparum</ns3:italic> genome variation data from the MalariaGEN network. It comprises over 20,000 samples from 82 partner studies in 33 countries, including several malaria endemic regions that were previously underrepresented. For the first time we include dried blood spot samples that were sequenced after selective whole genome amplification, necessitating new methods to genotype copy number variations. We identify a large number of newly emerging <ns3:italic>crt</ns3:italic> mutations in parts of Southeast Asia, and show examples of heterogeneities in patterns of drug resistance within Africa and within the Indian subcontinent. We describe the profile of variations in the C-terminal of the <ns3:italic>csp</ns3:italic> gene and relate this to the sequence used in the RTS,S and R21 malaria vaccines. Pf7 provides high-quality data on genotype calls for 6 million SNPs and short indels, analysis of large deletions that cause failure of rapid diagnostic tests, and systematic characterisation of six major drug resistance loci, all of which can be freely downloaded from the MalariaGEN website. </ns3:p>
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