Pf8: an open dataset of Plasmodium falciparum genome variation in 33,325 worldwide samples

Malaria Genomic Epidemiology Network (MalariaGEN)

doi:10.12688/wellcomeopenres.24031.1

Pf8: an open dataset of Plasmodium falciparum genome variation in 33,325 worldwide samples

Malaria Genomic Epidemiology Network (MalariaGEN)

West African Center for Cell Biology of Infectious Pathogens

Institute of Endemic Diseases Sudan
Sudan Atomic Energy Commission
University of Cape Coast Ghana
University of Khartoum
Centro de Investigação em Saúde da Manhiça (CISM)
Nigerian Institute of Medical Research
Wellcome Sanger Institute
London School of Hygiene & Tropical Medicine
University for Development Studies Ghana
Health Strategy and Delivery Foundation
University of Health and Allied Sciences
University of Ghana
University of Buea
Charles Darwin University
Nuffield Department of Medicine
Wellcome Trust Research Laboratories Nairobi
University of Oxford
Muhimbili University of Health and Allied Sciences
National Malaria Control Programme
Centre of Malariology
University of Science
University Clinical Research Center
Mahidol-Oxford Tropical Medicine Research Unit
University of Notre Dame
Universidad Peruana Cayetano Heredia
Addis Ababa University
Faculty of Tropical Medicine, Mahidol University
Mahidol University
National Institute for Medical Research Tanzania
Kamuzu University of Health Sciences
Médecins Sans Frontières
Broad Institute
Faculty of Medicine Ramathibodi Hospital, Mahidol University
Harvard T.H. Chan School of Public Health
Universitat de Barcelona
Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU)
Ministry of Health Laos
Bernhard Nocht Insitute for Tropical Medicine
Kwame Nkrumah University of Science and Technology
University of Maryland, Baltimore
University of California at San Francisco
Eijkman Institute for Molecular Biology
College of Medicine, University of Ibadan
First Technical University
University of Ibadan
Université de Kinshasa
The Kinshasa Medical Oxford Research Unit
College of Medicine, University of Lagos
American Embassy Unit
Université Paris Cité
Ministry of Health Vietnam
Institut Pasteur de Madagascar
Université de Toliara
University of Glasgow
Cambridge Institute for Medical Research
Modibbo Adama University of Technology, Yola
Wageningen University & Research
University of Amsterdam
National Institute of Allergy and Infectious Diseases Division of Intramural Research National Institutes of Health
Seattle Children's Hospital

Research output: Contribution to journal › Article › peer-review

2 Citations (Scopus)

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.

Original language	English
Article number	325
Journal	Wellcome Open Research
Volume	10
DOIs	https://doi.org/10.12688/wellcomeopenres.24031.1
Publication status	Published - 2025

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

Plasmodium falciparum
data resource
genomic epidemiology
genomic surveillance
genomics
malaria
open data sharing

Access to Document

10.12688/wellcomeopenres.24031.1

Cite this

@article{11a46e8412cb47ecac8afe489b068ac0,

title = "Pf8: an open dataset of Plasmodium falciparum genome variation in 33,325 worldwide samples",

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.",

keywords = "Plasmodium falciparum, data resource, genomic epidemiology, genomic surveillance, genomics, malaria, open data sharing",

author = "\{Malaria Genomic Epidemiology Network (MalariaGEN)\} and \{Abdel Hamid\}, \{Muzamil Mahdi\} and Abdelraheem, \{Mohamed Hassan\} and Acheampong, \{Desmond Omane\} and Ishag Adam and Pedro Aide and Olusola Ajibaye and Mozam Ali and Jacob Almagro-Garcia and Alfred Amambua-Ngwa and Lucas Amenga-Etego and Ifeyinwa Aniebo and Enoch Aninagyei and Felix Ansah and Apinjoh, \{Tobias O.\} and Ariani, \{Cristina V.\} and Sarah Auburn and Awandare, \{Gordon A.\} and Andrew Balmer and Philip Bejon and Simone Boene and George Bwire and Baltazar Candrinho and Arlindo Chidimatembue and Keobouphaphone Chindavongsa and Kiba Comiche and David Conway and Antoine Dara and Mahamadou Diakite and Abdoulaye Djimde and Arjen Dondorp and Seydou Doumbia and Eleanor Drury and Fanello, \{Caterina A.\} and Mike Ferdig and Katherine Figueroa and Dionicia Gamboa and Lemu Golassa and S{\'o}nia Gon{\c c}alves and Guindo, \{Merepen dite Agnes\} and Mainga Hamaluba and Borimas Hanboonkunupakarn and Kevin Howe and Maazza Hussien and Mallika Imwong and Deus Ishengoma and Julia Jeans and Alinune Kabaghe and Appolinary Kamuhabwa and Kindermans, \{Jean Marie\} and Konate, \{Drissa S.\}",

note = "Publisher Copyright: Copyright: {\textcopyright} 2025 Malaria Genomic Epidemiology Network (MalariaGEN) et al.",

year = "2025",

doi = "10.12688/wellcomeopenres.24031.1",

language = "English",

volume = "10",

journal = "Wellcome Open Research",

issn = "2398-502X",

publisher = "F1000 Research Ltd",

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TY - JOUR

T1 - Pf8

T2 - an open dataset of Plasmodium falciparum genome variation in 33,325 worldwide samples

AU - Malaria Genomic Epidemiology Network (MalariaGEN)

AU - Abdel Hamid, Muzamil Mahdi

AU - Abdelraheem, Mohamed Hassan

AU - Acheampong, Desmond Omane

AU - Adam, Ishag

AU - Aide, Pedro

AU - Ajibaye, Olusola

AU - Ali, Mozam

AU - Almagro-Garcia, Jacob

AU - Amambua-Ngwa, Alfred

AU - Amenga-Etego, Lucas

AU - Aniebo, Ifeyinwa

AU - Aninagyei, Enoch

AU - Ansah, Felix

AU - Apinjoh, Tobias O.

AU - Ariani, Cristina V.

AU - Auburn, Sarah

AU - Awandare, Gordon A.

AU - Balmer, Andrew

AU - Bejon, Philip

AU - Boene, Simone

AU - Bwire, George

AU - Candrinho, Baltazar

AU - Chidimatembue, Arlindo

AU - Chindavongsa, Keobouphaphone

AU - Comiche, Kiba

AU - Conway, David

AU - Dara, Antoine

AU - Diakite, Mahamadou

AU - Djimde, Abdoulaye

AU - Dondorp, Arjen

AU - Doumbia, Seydou

AU - Drury, Eleanor

AU - Fanello, Caterina A.

AU - Ferdig, Mike

AU - Figueroa, Katherine

AU - Gamboa, Dionicia

AU - Golassa, Lemu

AU - Gonçalves, Sónia

AU - Guindo, Merepen dite Agnes

AU - Hamaluba, Mainga

AU - Hanboonkunupakarn, Borimas

AU - Howe, Kevin

AU - Hussien, Maazza

AU - Imwong, Mallika

AU - Ishengoma, Deus

AU - Jeans, Julia

AU - Kabaghe, Alinune

AU - Kamuhabwa, Appolinary

AU - Kindermans, Jean Marie

AU - Konate, Drissa S.

PY - 2025

Y1 - 2025

N2 - 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.

AB - 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.

KW - Plasmodium falciparum

KW - data resource

KW - genomic epidemiology

KW - genomic surveillance

KW - genomics

KW - malaria

KW - open data sharing

UR - https://www.scopus.com/pages/publications/105024496716

U2 - 10.12688/wellcomeopenres.24031.1

DO - 10.12688/wellcomeopenres.24031.1

M3 - Article

AN - SCOPUS:105024496716

SN - 2398-502X

VL - 10

JO - Wellcome Open Research

JF - Wellcome Open Research

M1 - 325

ER -