Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples
Issued Date
2023-01-01
Resource Type
eISSN
2398502X
Scopus ID
2-s2.0-85150355807
Journal Title
Wellcome Open Research
Volume
8
Rights Holder(s)
SCOPUS
Bibliographic Citation
Wellcome Open Research Vol.8 (2023)
Suggested Citation
Abdel Hamid M.M., Abdelraheem M.H., Acheampong D.O., Ahouidi A., Ali M., Almagro-Garcia J., Amambua-Ngwa A., Amaratunga C., Amenga-Etego L., Andagalu B., Anderson T., Andrianaranjaka V., Aniebo I., Aninagyei E., Ansah F., Ansah P.O., Apinjoh T., Arnaldo P., Ashley E., Auburn S., Awandare G.A., Ba H., Baraka V., Barry A., Bejon P., Bertin G.I., Boni M.F., Borrmann S., Bousema T., Bouyou-Akotet M., Branch O., Bull P.C., Cheah H., Chindavongsa K., Chookajorn T., Chotivanich K., Claessens A., Conway D.J., Corredor V., Courtier E., Craig A., D'Alessandro U., Dama S., Day N., Denis B., Dhorda M., Diakite M., Djimde A., Dolecek C., Dondorp A., Doumbia S., Drakeley C., Drury E., Duffy P., Echeverry D.F., Egwang T.G., Enosse S.M.M., Erko B., Fairhurst R.M., Faiz A., Fanello C.A., Fleharty M., Forbes M., Fukuda M., Gamboa D., Ghansah A., Golassa L., Goncalves S., Harrison G.L.A., Healy S.A., Hendry J.A., Hernandez-Koutoucheva A., Hien T.T., Hill C.A., Hombhanje F., Hott A., Htut Y., Hussein M., Imwong M., Ishengoma D., Jackson S.A., Jacob C.G., Jeans J., Johnson K.J., Kamaliddin C., Kamau E., Keatley J., Kochakarn T., Konate D.S., Konaté A., Kone A., Kwiatkowski D.P., Kyaw M.P., Kyle D., Lawniczak M., Lee S.K., Lemnge M., Lim P., Lon C., Loua K.M. Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples. Wellcome Open Research Vol.8 (2023). doi:10.12688/wellcomeopenres.18681.1 Retrieved from: https://repository.li.mahidol.ac.th/handle/20.500.14594/82323
Title
Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples
Author(s)
Abdel Hamid M.M.
Abdelraheem M.H.
Acheampong D.O.
Ahouidi A.
Ali M.
Almagro-Garcia J.
Amambua-Ngwa A.
Amaratunga C.
Amenga-Etego L.
Andagalu B.
Anderson T.
Andrianaranjaka V.
Aniebo I.
Aninagyei E.
Ansah F.
Ansah P.O.
Apinjoh T.
Arnaldo P.
Ashley E.
Auburn S.
Awandare G.A.
Ba H.
Baraka V.
Barry A.
Bejon P.
Bertin G.I.
Boni M.F.
Borrmann S.
Bousema T.
Bouyou-Akotet M.
Branch O.
Bull P.C.
Cheah H.
Chindavongsa K.
Chookajorn T.
Chotivanich K.
Claessens A.
Conway D.J.
Corredor V.
Courtier E.
Craig A.
D'Alessandro U.
Dama S.
Day N.
Denis B.
Dhorda M.
Diakite M.
Djimde A.
Dolecek C.
Dondorp A.
Doumbia S.
Drakeley C.
Drury E.
Duffy P.
Echeverry D.F.
Egwang T.G.
Enosse S.M.M.
Erko B.
Fairhurst R.M.
Faiz A.
Fanello C.A.
Fleharty M.
Forbes M.
Fukuda M.
Gamboa D.
Ghansah A.
Golassa L.
Goncalves S.
Harrison G.L.A.
Healy S.A.
Hendry J.A.
Hernandez-Koutoucheva A.
Hien T.T.
Hill C.A.
Hombhanje F.
Hott A.
Htut Y.
Hussein M.
Imwong M.
Ishengoma D.
Jackson S.A.
Jacob C.G.
Jeans J.
Johnson K.J.
Kamaliddin C.
Kamau E.
Keatley J.
Kochakarn T.
Konate D.S.
Konaté A.
Kone A.
Kwiatkowski D.P.
Kyaw M.P.
Kyle D.
Lawniczak M.
Lee S.K.
Lemnge M.
Lim P.
Lon C.
Loua K.M.
Abdelraheem M.H.
Acheampong D.O.
Ahouidi A.
Ali M.
Almagro-Garcia J.
Amambua-Ngwa A.
Amaratunga C.
Amenga-Etego L.
Andagalu B.
Anderson T.
Andrianaranjaka V.
Aniebo I.
Aninagyei E.
Ansah F.
Ansah P.O.
Apinjoh T.
Arnaldo P.
Ashley E.
Auburn S.
Awandare G.A.
Ba H.
Baraka V.
Barry A.
Bejon P.
Bertin G.I.
Boni M.F.
Borrmann S.
Bousema T.
Bouyou-Akotet M.
Branch O.
Bull P.C.
Cheah H.
Chindavongsa K.
Chookajorn T.
Chotivanich K.
Claessens A.
Conway D.J.
Corredor V.
Courtier E.
Craig A.
D'Alessandro U.
Dama S.
Day N.
Denis B.
Dhorda M.
Diakite M.
Djimde A.
Dolecek C.
Dondorp A.
Doumbia S.
Drakeley C.
Drury E.
Duffy P.
Echeverry D.F.
Egwang T.G.
Enosse S.M.M.
Erko B.
Fairhurst R.M.
Faiz A.
Fanello C.A.
Fleharty M.
Forbes M.
Fukuda M.
Gamboa D.
Ghansah A.
Golassa L.
Goncalves S.
Harrison G.L.A.
Healy S.A.
Hendry J.A.
Hernandez-Koutoucheva A.
Hien T.T.
Hill C.A.
Hombhanje F.
Hott A.
Htut Y.
Hussein M.
Imwong M.
Ishengoma D.
Jackson S.A.
Jacob C.G.
Jeans J.
Johnson K.J.
Kamaliddin C.
Kamau E.
Keatley J.
Kochakarn T.
Konate D.S.
Konaté A.
Kone A.
Kwiatkowski D.P.
Kyaw M.P.
Kyle D.
Lawniczak M.
Lee S.K.
Lemnge M.
Lim P.
Lon C.
Loua K.M.
Author's Affiliation
WorldWide Antimalarial Resistance Network
Université de Conakry
Mahidol Oxford Tropical Medicine Research Unit
Oxford University Clinical Research Unit
University of Health and Allied Sciences, Ghana
CSIR - Institute for Scientific and Technological Information
Laboratory of Pathogen Host Interactions
The Wellcome Centre for Human Genetics
Ministry of Health Myanmar
Instituto Nacional de Saude Maputo
Malawi-Liverpool-Wellcome Trust Clinical Research Programme
Université d'Antananarivo
Universite des Sciences de la Sante Liberville
University of Cocody
University of Cape Coast Ghana
Navrongo Health Research Center
Sudan Atomic Energy Commission
Institute of Endemic Diseases Sudan
National Institute for Medical Research Tanga
Universite Cheikh Anta Diop
Universidad Peruana Cayetano Heredia
Addis Ababa University
University of Buea
Kenya Medical Research Institute
Universidad del Valle, Cali
Wellcome Trust Research Laboratories Nairobi
Universidad Nacional de Colombia
Centro Internacional de Entrenamiento e Investigaciones Medicas
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
Deakin University
University of Ghana
National Institute of Allergy and Infectious Diseases (NIAID)
Eberhard Karls Universität Tübingen
Armed Forces Research Institute of Medical Sciences, Thailand
Universiteit Antwerpen
Walter Reed Army Institute of Research
Mahidol University
Purdue University
Nuffield Department of Medicine
University of South Florida, Tampa
National Institutes of Health (NIH)
Wellcome Sanger Institute
Burnet Institute
Radboud University Medical Center
University of Calgary
Broad Institute
University of Sciences
Institut National de Santé Publique
Dev Care Foundation
East African Consortium for Clinical Research (EACCR)
Biotech Laboratories
University Clinical Research Center (UCRC)
Institut National de Recherche en Santé Publique
Health Strategy and Delivery Foundation
National Center for Parasitology
University of Public Health
Medical Care Development International
Divine Word University
Centre of Malariology
Université de Conakry
Mahidol Oxford Tropical Medicine Research Unit
Oxford University Clinical Research Unit
University of Health and Allied Sciences, Ghana
CSIR - Institute for Scientific and Technological Information
Laboratory of Pathogen Host Interactions
The Wellcome Centre for Human Genetics
Ministry of Health Myanmar
Instituto Nacional de Saude Maputo
Malawi-Liverpool-Wellcome Trust Clinical Research Programme
Université d'Antananarivo
Universite des Sciences de la Sante Liberville
University of Cocody
University of Cape Coast Ghana
Navrongo Health Research Center
Sudan Atomic Energy Commission
Institute of Endemic Diseases Sudan
National Institute for Medical Research Tanga
Universite Cheikh Anta Diop
Universidad Peruana Cayetano Heredia
Addis Ababa University
University of Buea
Kenya Medical Research Institute
Universidad del Valle, Cali
Wellcome Trust Research Laboratories Nairobi
Universidad Nacional de Colombia
Centro Internacional de Entrenamiento e Investigaciones Medicas
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
Deakin University
University of Ghana
National Institute of Allergy and Infectious Diseases (NIAID)
Eberhard Karls Universität Tübingen
Armed Forces Research Institute of Medical Sciences, Thailand
Universiteit Antwerpen
Walter Reed Army Institute of Research
Mahidol University
Purdue University
Nuffield Department of Medicine
University of South Florida, Tampa
National Institutes of Health (NIH)
Wellcome Sanger Institute
Burnet Institute
Radboud University Medical Center
University of Calgary
Broad Institute
University of Sciences
Institut National de Santé Publique
Dev Care Foundation
East African Consortium for Clinical Research (EACCR)
Biotech Laboratories
University Clinical Research Center (UCRC)
Institut National de Recherche en Santé Publique
Health Strategy and Delivery Foundation
National Center for Parasitology
University of Public Health
Medical Care Development International
Divine Word University
Centre of Malariology
Other Contributor(s)
Abstract
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.