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

Muzamil Mahdi Abdel Hamid ; Mohamed Hassan Abdelraheem ; Desmond Omane Acheampong

; Ishag Adam ; Pedro Aide ; Olusola Ajibaye

; Mozam Ali ; Jacob Almagro-Garcia ; Alfred Amambua-Ngwa ; Lucas Amenga-Etego

; +104 more... Ifeyinwa Aniebo ; Enoch Aninagyei

; Felix Ansah ; Tobias O Apinjoh ; Cristina V Ariani ; Sarah Auburn ; Gordon A Awandare ; Andrew Balmer ; Philip Bejon

; Simone Boene

; George Bwire ; Baltazar Candrinho ; Arlindo Chidimatembue ; Keobouphaphone Chindavongsa ; Kiba Comiche ; David Conway

; Antoine Dara ; Mahamadou Diakite

; Abdoulaye Djimde

; Arjen Dondorp

; Seydou Doumbia ; Eleanor Drury ; Caterina A Fanello

; Mike Ferdig ; Katherine Figueroa ; Dionicia Gamboa ; Lemu Golassa ; Sónia Gonçalves ; Merepen dite Agnes Guindo ; Mainga Hamaluba

; Borimas Hanboonkunupakarn ; Kevin Howe ; Maazza Hussien ; Mallika Imwong ; Deus Ishengoma ; Julia Jeans ; Alinune Kabaghe ; Appolinary Kamuhabwa ; Jean-Marie Kindermans ; Drissa S Konate

; Dominic P Kwiatkowski ; Chiyun Lee ; Samuel K Lee ; Sue J Lee

; Benedikt Ley

; Alejandro Llanos-Cuentas

; Jutta Marfurt ; Glória Matambisso ; Rapeephan Rattanawongnara Maude ; Richard James Maude

; Alfredo Mayor ; Mayfong Mayxay

; Oumou Maïga-Ascofaré ; Robert S McCann ; Alistair Miles ; Olivo Miotto ; Abdelrahim Osman Mohamed

; Collins Misita Morang’a

; Kathryn Murie ; Billy Ephraim Ngasala

; Thuy-Nhien Nguyen

; Oscar Nolasco ; Francois Nosten

; Rintis Noviyanti ; Ísla O'Connor ; Mary Oboh ; Lynette Isabella Ochola-Oyier ; Catherine Olufunke Falade ; Adeola Olukosi ; Ajibola Olumide ; Fiyinfoluwa I Olusola ; Marie A Onyamboko

; Eniyou Cheryll Oriero ; Wellington Aghoghovwia Oyibo ; Danielle Pannebaker ; Richard D Pearson

; Kamija Phiri

; Rob W van der Pluijm ; Ric N Price

; Huynh Hong Quang ; Vinoth Rajkumar Devaraju ; Milijaona Randrianarivelojosia

; Lisa Ranford-Cartwright

; Julian C Rayner

; Eduard Rovira-Vallbona

; Katherine Rowlands ; Valentin Ruano-Rubio ; Juan F Sanchez ; Francisco Saúte ; Shuwaram Shettima ; Clemente da Silva ; Victoria J Simpson ; Simon Suddaby ; Willem Takken ; Aung Myint Thu ; Mahamoudou Toure ; Eyyub Unlu ; Hugo O Valdivia

; Michele van Vugt ; Naomi Waithira

; Thomas Wellems

; Jason Wendler ; Nina White

; Rachel Wuendrich Ogidan ; (2025) Pf8: an open dataset of Plasmodium falciparum genome variation in 33,325 worldwide samples. Wellcome Open Research, 10. p. 325. ISSN 2398-502X DOI: 10.12688/wellcomeopenres.24031.1

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<ns7:p>We describe the Pf8 data resource, the latest MalariaGEN release of curated genome variation data on over 33,000 <ns7:italic>Plasmodium falciparum</ns7:italic> 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 <ns7:italic>gch1</ns7:italic> and <ns7:italic>crt</ns7:italic>. As in Pf7, CNV calls are provided for <ns7:italic>mdr1</ns7:italic> and <ns7:italic>plasmepsin2/3</ns7:italic>, along with calls for deletion in <ns7:italic>hrp2</ns7:italic> and <ns7:italic>hrp3,</ns7:italic> 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.</ns7:p>