Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples.

Autor:	Abdel Hamid MM; Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan., Abdelraheem MH; Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan.; Nuclear Applications In Biological Sciences, Sudan Atomic Energy Commission, Khartoum, Sudan., Acheampong DO; Department of Biomedical Sciences, School of Allied Health Sciences, University of Cape Coast, Cape Coast, Ghana., Ahouidi A; Health Research Epidemiological Surveillance and Training Institute (IRESSEF), Université Cheikh Anta Diop, Dakar, Senegal., Ali M; Wellcome Sanger Institute, Hinxton, UK., Almagro-Garcia J; Wellcome Sanger Institute, Hinxton, UK., Amambua-Ngwa A; Wellcome Sanger Institute, Hinxton, UK.; Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia., Amaratunga C; National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA., Amenga-Etego L; West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Legon, Ghana.; Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana., Andagalu B; United States Army Medical Research Directorate-Africa, Kenya Medical Research Institute/Walter Reed Project, Kisumu, Kenya., Anderson T; Texas Biomedical Research Institute, San Antonio, USA., Andrianaranjaka V; Université d'Antananarivo, Antananarivo, Madagascar., Aniebo I; Health Strategy and Delivery Foundation, Lagos, Nigeria., Aninagyei E; Department of Biomedical Sciences, School of Basic and Biomedical Sciences, University of Health & Allied Sciences, Ho, Ghana., Ansah F; West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Legon, Ghana., Ansah PO; Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana., Apinjoh T; University of Buea, Buea, Cameroon., Arnaldo P; Instituto Nacional de Saúde (INS), Maputo, Mozambique., Ashley E; Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand.; Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK., Auburn S; Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia.; Nuffield Department of Medicine, University of Oxford, UK., Awandare GA; West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Legon, Ghana., Ba H; Institut National de Recherche en Santé Publique, Nouakchott, Mauritania., Baraka V; National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania.; Department of Epidemiology, International Health Unit, Universiteit Antwerpen, Antwerp, Belgium., Barry A; Walter and Eliza Hall Institute, Melbourne, Australia.; Deakin University, Geelong, Australia.; Burnet Institute, Melbourne, Australia., Bejon P; KEMRI Wellcome Trust Research Programme, Kilifi, Kenya., Bertin GI; Institute of Research for Development (IRD), Paris, France., Boni MF; Nuffield Department of Medicine, University of Oxford, UK.; Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam., Borrmann S; Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany., Bousema T; London School of Hygiene and Tropical Medicine, London, UK.; Radboud University Medical Center, Nijmegen, The Netherlands., Bouyou-Akotet M; Department of Parasitology-Mycology, Université des Sciences de la Santé, Libreville, Gabon., Branch O; NYU School of Medicine Langone Medical Center, New York, USA., Bull PC; KEMRI Wellcome Trust Research Programme, Kilifi, Kenya.; Department of Pathology, University of Cambridge, Cambridge, UK., Cheah H; National Center for Parasitology, Entomology and Malaria Control, Phnom Penh, Cambodia., Chindavongsa K; Center of Malariology, Parasitology and Entomology (CMPE), Vientiane, Lao People's Democratic Republic., Chookajorn T; Mahidol University, Bangkok, Thailand., Chotivanich K; Mahidol University, Bangkok, Thailand., Claessens A; Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia.; LPHI, MIVEGEC, INSERM, CNRS, IRD, University of Montpellier, Montpellier, France., Conway DJ; London School of Hygiene and Tropical Medicine, London, UK., Corredor V; National University of Colombia, Bogota, Colombia., Courtier E; Wellcome Sanger Institute, Hinxton, UK., Craig A; Liverpool School of Tropical Medicine, Liverpool, UK.; Malawi-Liverpool-Wellcome Trust Clinical Research Program, Blantyre, Malawi., D'Alessandro U; Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia., Dama S; Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali., Day N; Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand.; Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK., Denis B; Malawi-Liverpool-Wellcome Trust Clinical Research Program, Blantyre, Malawi., Dhorda M; Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand.; WorldWide Antimalarial Resistance Network - Asia Regional Centre, Bangkok, Thailand., Diakite M; Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali.; University Clinical Research Center (UCRC), Bamako, Mali., Djimde A; Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali., Dolecek C; Nuffield Department of Medicine, University of Oxford, UK., Dondorp A; Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand.; Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK., Doumbia S; Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali.; University Clinical Research Center (UCRC), Bamako, Mali., Drakeley C; London School of Hygiene and Tropical Medicine, London, UK., Drury E; Wellcome Sanger Institute, Hinxton, UK., Duffy P; National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA., Echeverry DF; Departamento de Microbiología, Universidad del Valle, Cali, Colombia.; Centro Internacional de Entrenamiento e Investigaciones Médicas - CIDEIM, Cali, Colombia., Egwang TG; Biotech Laboratories, Kampala, Uganda., Enosse SMM; Instituto Nacional de Saúde (INS), Maputo, Mozambique., Erko B; Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia., Fairhurst RM; National Institutes of Health (NIH), Maryland, USA., Faiz A; Dev Care Foundation, Dhaka, Bangladesh., Fanello CA; Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand., Fleharty M; Broad Institute of Harvard and MIT and Harvard, Cambridge, MA, USA., Forbes M; Wellcome Sanger Institute, Hinxton, UK., Fukuda M; Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand., Gamboa D; Laboratorio ICEMR-Amazonia, Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru., Ghansah A; Nogouchi Memorial Institute for Medical Research, Legon-Accra, Ghana., Golassa L; Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia., Goncalves S; Wellcome Sanger Institute, Hinxton, UK., Harrison GLA; Walter and Eliza Hall Institute, Melbourne, Australia., Healy SA; National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA., Hendry JA; Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK., Hernandez-Koutoucheva A; Wellcome Sanger Institute, Hinxton, UK., Hien TT; Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK.; Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam., Hill CA; Department of Entomology, Purdue University, West Lafayette, USA., Hombhanje F; Centre for Health Research & Diagnostics, Divine Word University, Madang, Papua New Guinea., Hott A; University of South Florida, Tampa, USA., Htut Y; Department of Medical Research, Yangon, Myanmar., Hussein M; Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan., Imwong M; Mahidol University, Bangkok, Thailand., Ishengoma D; National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania.; East African Consortium for Clinical Research (EACCR), Dar es Salaam, Tanzania., Jackson SA; Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA., Jacob CG; Wellcome Sanger Institute, Hinxton, UK., Jeans J; Wellcome Sanger Institute, Hinxton, UK., Johnson KJ; Wellcome Sanger Institute, Hinxton, UK., Kamaliddin C; Institute of Research for Development (IRD), Paris, France.; The University of Calgary, Calgary, Canada., Kamau E; U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA., Keatley J; Wellcome Sanger Institute, Hinxton, UK., Kochakarn T; Mahidol University, Bangkok, Thailand., Konate DS; Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali., Konaté A; University Félix Houphouët-Boigny, Abidjan, Cote d'Ivoire., Kone A; Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali., Kwiatkowski DP; Wellcome Sanger Institute, Hinxton, UK., Kyaw MP; Myanmar Oxford Clinical Research Unit, University of Oxford, Yangon, Myanmar.; University of Public Health, Yangon, Myanmar., Kyle D; University of South Florida, Tampa, USA.; University of Georgia, Athens, USA., Lawniczak M; Wellcome Sanger Institute, Hinxton, UK., Lee SK; Broad Institute of Harvard and MIT and Harvard, Cambridge, MA, USA., Lemnge M; National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania., Lim P; National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA.; Medical Care Development International, Maryland, USA., Lon C; National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia., Loua KM; University Gamal Abdel Nasser of Conakry, Conakry, Guinea.; Institut National de Santé Publique, Conakry, Guinea., Mandara CI; National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania., Marfurt J; Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia., Marsh K; Nuffield Department of Medicine, University of Oxford, UK.; KEMRI Wellcome Trust Research Programme, Kilifi, Kenya., Maude RJ; Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand.; Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK.; Harvard TH Chan School of Public Health, Harvard University, Boston, USA., Mayxay M; Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK.; Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic.; Institute of Research and Education Development (IRED), University of Health Sciences, Ministry of Health, Vientiane, Lao People's Democratic Republic., Maïga-Ascofaré O; Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali.; Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.; Research in Tropical Medicine, Kwame Nkrumah University of Sciences and Technology, Kumasi, Ghana., Miotto O; Wellcome Sanger Institute, Hinxton, UK.; Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand.; MRC Centre for Genomics and Global Health, Big Data Institute, Oxford University, Oxford, UK., Mita T; Juntendo University, Tokyo, Japan., Mobegi V; Department of Biochemistry and Centre for Biotechnology and Bioinformatics, University of Nairobi, Nairobi, Kenya., Mohamed AO; Faculty of Medicine, University of Khartoum, Khartoum, Sudan., Mokuolu OA; Department of Paediatrics and Child Health, University of Ilorin, Ilorin, Nigeria., Montgomery J; Malawi-Liverpool-Wellcome Trust Clinical Research Program, Blantyre, Malawi.; World Mosquito Program, Monash University, Melbourne, Australia., Morang'a CM; West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Legon, Ghana., Mueller I; Walter and Eliza Hall Institute, Melbourne, Australia.; University of Melbourne, Melbourne, Australia., Murie K; Wellcome Sanger Institute, Hinxton, UK., Newton PN; Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK.; Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic., Ngo Duc T; National Institute of Malariology, Parasitology and Entomology (NIMPE), Hanoi, Vietnam., Nguyen T; Wellcome Sanger Institute, Hinxton, UK., Nguyen TN; Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK.; Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam., Nguyen Thi Kim T; Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam., Nguyen Van H; National Institute of Malariology, Parasitology and Entomology (NIMPE), Hanoi, Vietnam., Noedl H; MARIB - Malaria Research Initiative Bandarban, Bandarban, Bangladesh.; Medical University of Vienna, Vienna, Austria., Nosten F; Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK.; Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand., Noviyanti R; Eijkman Institute for Molecular Biology, Jakarta, Indonesia., Ntui VN; University of Buea, Buea, Cameroon., Nzila A; King Fahid University of Petroleum and Minerals (KFUMP), Dhahran, Saudi Arabia., Ochola-Oyier LI; KEMRI Wellcome Trust Research Programme, Kilifi, Kenya., Ocholla H; KEMRI Centres for Disease Control and Prevention (CDC) Research Program, Kisumu, Kenya.; Centre for Bioinformatics and Biotechnology, University of Nairobi, Nairobi, Kenya., Oduro A; Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana., Omedo I; Wellcome Sanger Institute, Hinxton, UK.; KEMRI Wellcome Trust Research Programme, Kilifi, Kenya., Onyamboko MA; Kinshasa School of Public Health, University of Kinshasa, Kinshasa, Congo, Democratic Republic., Ouedraogo JB; Institut de Recherche en Sciences de la Santé, Ouagadougou, Burkina Faso., Oyebola K; Nigerian Institute of Medical Research, Lagos, Nigeria.; Parasitology and Bioinformatics Unit, Faculty of Science, University of Lagos, Lagos, Nigeria., Oyibo WA; College of Medicine, University of Lagos, Lagos, Nigeria., Pearson R; Wellcome Sanger Institute, Hinxton, UK., Peshu N; KEMRI Wellcome Trust Research Programme, Kilifi, Kenya., Phyo AP; Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand.; Shoklo Malaria Research Unit, Bangkok, Thailand., Plowe CV; University of Maryland School of Medicine, Maryland, USA., Price RN; Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand.; Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK.; Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia., Pukrittayakamee S; Mahidol University, Bangkok, Thailand., Quang HH; Institute of Malariology, Parasitology, and Entomology (IMPE) Quy Nhon, Ministry of Health, Quy Nhon, Vietnam., Randrianarivelojosia M; Institut Pasteur de Madagascar, Antananarivo, Madagascar.; Universités d'Antananarivo et de Mahajanga, Antananarivo, Madagascar., Rayner JC; Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK., Ringwald P; World Health Organization (WHO), Geneva, Switzerland., Rosanas-Urgell A; Institute of Tropical Medicine Antwerp, Antwerp, Belgium., Rovira-Vallbona E; Institute of Tropical Medicine Antwerp, Antwerp, Belgium., Ruano-Rubio V; Broad Institute of Harvard and MIT and Harvard, Cambridge, MA, USA., Ruiz L; Universidad Nacional de la Amazonia Peruana, Iquitos, Peru., Saunders D; Department of Medicine, Uniformed Services University, Bethesda, MD, USA., Shayo A; Nelson Mandela Institute of Science and Technology, Arusha, Tanzania., Siba P; Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea., Simpson VJ; Wellcome Sanger Institute, Hinxton, UK., Sissoko MS; Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali., Smith C; Wellcome Sanger Institute, Hinxton, UK., Su XZ; National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA., Sutherland C; London School of Hygiene and Tropical Medicine, London, UK., Takala-Harrison S; Center for Vaccine Development and Global Health, University of Maryland, School of Medicine, Baltimore, MD, USA., Talman A; MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France., Tavul L; Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea., Thanh NV; Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam., Thathy V; KEMRI Wellcome Trust Research Programme, Kilifi, Kenya.; Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA., Thu AM; Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand., Toure M; Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali., Tshefu A; University of Kinshasa, Kinsasha, Congo, Democratic Republic., Verra F; Sapienza University of Rome, Rome, Italy., Vinetz J; Laboratorio ICEMR-Amazonia, Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru.; Yale School of Medicine, New Haven, CT, USA., Wellems TE; National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA., Wendler J; National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA.; Seattle Children's Hospital, Seattle, USA., White NJ; Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand.; Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK., Whitton G; Wellcome Sanger Institute, Hinxton, UK., Yavo W; University Félix Houphouët-Boigny, Abidjan, Cote d'Ivoire.; Malaria Research and Control Center of the National Institute of Public Health, Abidjan, Cote d'Ivoire., van der Pluijm RW; Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand.
Jazyk:	angličtina
Zdroj:	Wellcome open research [Wellcome Open Res] 2023 Jan 16; Vol. 8, pp. 22. Date of Electronic Publication: 2023 Jan 16 (Print Publication: 2023).
DOI:	10.12688/wellcomeopenres.18681.1
Abstrakt:	We describe the MalariaGEN Pf7 data resource, the seventh release of Plasmodium falciparum 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 crt 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 csp 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. Competing Interests: No competing interests were disclosed. (Copyright: © 2023 MalariaGEN et al.)
Databáze:	MEDLINE
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