Pf8: an open dataset of Plasmodium falciparum genome variation in 33,325 worldwide samples
Issued Date
2025-01-01
Resource Type
eISSN
2398502X
Scopus ID
2-s2.0-105024496716
Journal Title
Wellcome Open Research
Volume
10
Rights Holder(s)
SCOPUS
Bibliographic Citation
Wellcome Open Research Vol.10 (2025)
Suggested Citation
Abdel Hamid M.M., Abdelraheem M.H., Acheampong D.O., Adam I., Aide P., Ajibaye O., Ali M., Almagro-Garcia J., Amambua-Ngwa A., Amenga-Etego L., Aniebo I., Aninagyei E., Ansah F., Apinjoh T.O., Ariani C.V., Auburn S., Awandare G.A., Balmer A., Bejon P., Boene S., Bwire G., Candrinho B., Chidimatembue A., Chindavongsa K., Comiche K., Conway D., Dara A., Diakite M., Djimde A., Dondorp A., Doumbia S., Drury E., Fanello C.A., Ferdig M., Figueroa K., Gamboa D., Golassa L., Gonçalves S., Guindo M.d.A., Hamaluba M., Hanboonkunupakarn B., Howe K., Hussien M., Imwong M., Ishengoma D., Jeans J., Kabaghe A., Kamuhabwa A., Kindermans J.M., Konate D.S., Kwiatkowski D.P., Lee C., Lee S.K., Lee S.J., Ley B., Llanos-Cuentas A., Marfurt J., Matambisso G., Maude R.R., Maude R.J., Mayor A., Mayxay M., Maïga-Ascofaré O., McCann R.S., Miles A., Miotto O., Mohamed A.O., Morang’a C.M., Murie K., Ngasala B.E., Nguyen T.N., Nolasco O., Nosten F., Noviyanti R., O'Connor Í., Oboh M., Ochola-Oyier L.I., Olufunke Falade C., Olukosi A., Olumide A., Olusola F.I., Onyamboko M.A., Oriero E.C., Oyibo W.A., Pannebaker D., Pearson R.D., Phiri K., van der Pluijm R.W., Price R.N., Quang H.H., Rajkumar Devaraju V., Randrianarivelojosia M., Ranford-Cartwright L., Rayner J.C., Rovira-Vallbona E., Rowlands K., Ruano-Rubio V., Sanchez J.F., Saúte F., Shettima S. Pf8: an open dataset of Plasmodium falciparum genome variation in 33,325 worldwide samples. Wellcome Open Research Vol.10 (2025). doi:10.12688/wellcomeopenres.24031.1 Retrieved from: https://repository.li.mahidol.ac.th/handle/123456789/113585
Title
Pf8: an open dataset of Plasmodium falciparum genome variation in 33,325 worldwide samples
Author(s)
Abdel Hamid M.M.
Abdelraheem M.H.
Acheampong D.O.
Adam I.
Aide P.
Ajibaye O.
Ali M.
Almagro-Garcia J.
Amambua-Ngwa A.
Amenga-Etego L.
Aniebo I.
Aninagyei E.
Ansah F.
Apinjoh T.O.
Ariani C.V.
Auburn S.
Awandare G.A.
Balmer A.
Bejon P.
Boene S.
Bwire G.
Candrinho B.
Chidimatembue A.
Chindavongsa K.
Comiche K.
Conway D.
Dara A.
Diakite M.
Djimde A.
Dondorp A.
Doumbia S.
Drury E.
Fanello C.A.
Ferdig M.
Figueroa K.
Gamboa D.
Golassa L.
Gonçalves S.
Guindo M.d.A.
Hamaluba M.
Hanboonkunupakarn B.
Howe K.
Hussien M.
Imwong M.
Ishengoma D.
Jeans J.
Kabaghe A.
Kamuhabwa A.
Kindermans J.M.
Konate D.S.
Kwiatkowski D.P.
Lee C.
Lee S.K.
Lee S.J.
Ley B.
Llanos-Cuentas A.
Marfurt J.
Matambisso G.
Maude R.R.
Maude R.J.
Mayor A.
Mayxay M.
Maïga-Ascofaré O.
McCann R.S.
Miles A.
Miotto O.
Mohamed A.O.
Morang’a C.M.
Murie K.
Ngasala B.E.
Nguyen T.N.
Nolasco O.
Nosten F.
Noviyanti R.
O'Connor Í.
Oboh M.
Ochola-Oyier L.I.
Olufunke Falade C.
Olukosi A.
Olumide A.
Olusola F.I.
Onyamboko M.A.
Oriero E.C.
Oyibo W.A.
Pannebaker D.
Pearson R.D.
Phiri K.
van der Pluijm R.W.
Price R.N.
Quang H.H.
Rajkumar Devaraju V.
Randrianarivelojosia M.
Ranford-Cartwright L.
Rayner J.C.
Rovira-Vallbona E.
Rowlands K.
Ruano-Rubio V.
Sanchez J.F.
Saúte F.
Shettima S.
Abdelraheem M.H.
Acheampong D.O.
Adam I.
Aide P.
Ajibaye O.
Ali M.
Almagro-Garcia J.
Amambua-Ngwa A.
Amenga-Etego L.
Aniebo I.
Aninagyei E.
Ansah F.
Apinjoh T.O.
Ariani C.V.
Auburn S.
Awandare G.A.
Balmer A.
Bejon P.
Boene S.
Bwire G.
Candrinho B.
Chidimatembue A.
Chindavongsa K.
Comiche K.
Conway D.
Dara A.
Diakite M.
Djimde A.
Dondorp A.
Doumbia S.
Drury E.
Fanello C.A.
Ferdig M.
Figueroa K.
Gamboa D.
Golassa L.
Gonçalves S.
Guindo M.d.A.
Hamaluba M.
Hanboonkunupakarn B.
Howe K.
Hussien M.
Imwong M.
Ishengoma D.
Jeans J.
Kabaghe A.
Kamuhabwa A.
Kindermans J.M.
Konate D.S.
Kwiatkowski D.P.
Lee C.
Lee S.K.
Lee S.J.
Ley B.
Llanos-Cuentas A.
Marfurt J.
Matambisso G.
Maude R.R.
Maude R.J.
Mayor A.
Mayxay M.
Maïga-Ascofaré O.
McCann R.S.
Miles A.
Miotto O.
Mohamed A.O.
Morang’a C.M.
Murie K.
Ngasala B.E.
Nguyen T.N.
Nolasco O.
Nosten F.
Noviyanti R.
O'Connor Í.
Oboh M.
Ochola-Oyier L.I.
Olufunke Falade C.
Olukosi A.
Olumide A.
Olusola F.I.
Onyamboko M.A.
Oriero E.C.
Oyibo W.A.
Pannebaker D.
Pearson R.D.
Phiri K.
van der Pluijm R.W.
Price R.N.
Quang H.H.
Rajkumar Devaraju V.
Randrianarivelojosia M.
Ranford-Cartwright L.
Rayner J.C.
Rovira-Vallbona E.
Rowlands K.
Ruano-Rubio V.
Sanchez J.F.
Saúte F.
Shettima S.
Author's Affiliation
University of Oxford
Université Paris Cité
UCSF School of Medicine
Harvard T.H. Chan School of Public Health
University of Notre Dame
London School of Hygiene & Tropical Medicine
Mahidol University
University of Ibadan
Broad Institute
Addis Ababa University
Nuffield Department of Medicine
University of Ghana
College of Medical, Veterinary & Life Sciences
Kwame Nkrumah University of Science & Technology
Wellcome Sanger Institute
Khartoum University
Universidad Peruana Cayetano Heredia
Instituto de Salud Global de Barcelona
Faculty of Tropical Medicine, Mahidol University
University of Cape Coast Ghana
Faculty of Medicine Ramathibodi Hospital, Mahidol University
Menzies School of Health Research
Muhimbili University of Health and Allied Sciences
Kamuzu University of Health Sciences
Bernhard Nocht Institut fur Tropenmedizin Hamburg
University of Buea
Cambridge Institute for Medical Research
Mahidol Oxford Tropical Medicine Research Unit
College of Medicine, University of Ibadan
Université de Kinshasa
Wellcome Trust Research Laboratories Nairobi
University of Health and Allied Sciences, Ghana
Oxford University Clinical Research Unit
National Institute for Medical Research Tanga
College of Medicine, University of Lagos
University of Khartoum Faculty of Medicine
Center for Vaccine Development and Global Health (CVD)
Université des Sciences, des Techniques et des Technologies de Bamako
Nigerian Institute of Medical Research
Institut Pasteur de Madagascar
Centro de Investigação em Saúde de Manhiça CISM
Modibbo Adama University of Technology, Yola
Naval Medical Research Unit South
Mahosot Hospital, Lao
Medecins Sans Frontieres, Brussels
Eijkman Institute for Molecular Biology
Navrongo Health Research Center
Institute of Endemic Diseases Sudan
First Technical University
Sudan Atomic Energy Commission
Université de Toliara
Ministry of Health Laos
Centre of Malariology
National Malaria Control Programme
Health Strategy and Delivery Foundation
University Clinical Research Center
The Kinshasa Medical Oxford Research Unit
Université Paris Cité
UCSF School of Medicine
Harvard T.H. Chan School of Public Health
University of Notre Dame
London School of Hygiene & Tropical Medicine
Mahidol University
University of Ibadan
Broad Institute
Addis Ababa University
Nuffield Department of Medicine
University of Ghana
College of Medical, Veterinary & Life Sciences
Kwame Nkrumah University of Science & Technology
Wellcome Sanger Institute
Khartoum University
Universidad Peruana Cayetano Heredia
Instituto de Salud Global de Barcelona
Faculty of Tropical Medicine, Mahidol University
University of Cape Coast Ghana
Faculty of Medicine Ramathibodi Hospital, Mahidol University
Menzies School of Health Research
Muhimbili University of Health and Allied Sciences
Kamuzu University of Health Sciences
Bernhard Nocht Institut fur Tropenmedizin Hamburg
University of Buea
Cambridge Institute for Medical Research
Mahidol Oxford Tropical Medicine Research Unit
College of Medicine, University of Ibadan
Université de Kinshasa
Wellcome Trust Research Laboratories Nairobi
University of Health and Allied Sciences, Ghana
Oxford University Clinical Research Unit
National Institute for Medical Research Tanga
College of Medicine, University of Lagos
University of Khartoum Faculty of Medicine
Center for Vaccine Development and Global Health (CVD)
Université des Sciences, des Techniques et des Technologies de Bamako
Nigerian Institute of Medical Research
Institut Pasteur de Madagascar
Centro de Investigação em Saúde de Manhiça CISM
Modibbo Adama University of Technology, Yola
Naval Medical Research Unit South
Mahosot Hospital, Lao
Medecins Sans Frontieres, Brussels
Eijkman Institute for Molecular Biology
Navrongo Health Research Center
Institute of Endemic Diseases Sudan
First Technical University
Sudan Atomic Energy Commission
Université de Toliara
Ministry of Health Laos
Centre of Malariology
National Malaria Control Programme
Health Strategy and Delivery Foundation
University Clinical Research Center
The Kinshasa Medical Oxford Research Unit
Corresponding Author(s)
Other Contributor(s)
Abstract
We describe the Pf8 data resource, the latest MalariaGEN release of curated genome variation data on over 33,000 Plasmodium falciparum samples from 99 partner studies and 122 locations over more than 50 years. This release provides open access to raw sequencing data and genotypes at over 12 million genomic positions. For the first time, it includes copy-number variation (CNV) calls in the drug-resistance associated genes gch1 and crt. As in Pf7, CNV calls are provided for mdr1 and plasmepsin2/3, along with calls for deletion in hrp2 and hrp3, genes associated with rapid diagnostic test failures. This data resource additionally features derived datasets, interactive web applications for exploring patterns of drug resistance and variation in over 5,000 genes, an updated Python package providing methods for accessing and analysing the data, and open access analysis notebooks that can be used as starting points for further analyses. In addition, informative example analyses show contrasting profiles of the decline of chloroquine resistance-associated mutations in Africa, and variation in copy number variation across 10 distinct sub-populations. To the best of our knowledge, Pf8 is the largest open data set of genome variation in any eukaryotic species, making it an invaluable foundational resource for understanding evolution, including that of pathogens.