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

Abdel Hamid, MM; Abdelraheem, MH; Acheampong, DOORCID logo; Adam, I; Aide, P; Ajibaye, OORCID logo; Ali, M; Almagro-Garcia, J; Amambua-Ngwa, A; Amenga-Etego, LORCID logo; +104 more...Aniebo, I; Aninagyei, EORCID logo; Ansah, F; Apinjoh, TO; Ariani, CV; Auburn, S; Awandare, GA; Balmer, A; Bejon, PORCID logo; Boene, SORCID logo; Bwire, G; Candrinho, B; Chidimatembue, A; Chindavongsa, K; Comiche, K; Conway, DORCID logo; Dara, A; Diakite, MORCID logo; Djimde, AORCID logo; Dondorp, AORCID logo; Doumbia, S; Drury, E; Fanello, CAORCID logo; Ferdig, M; Figueroa, K; Gamboa, D; Golassa, L; Gonçalves, S; Guindo, MdA; Hamaluba, MORCID logo; Hanboonkunupakarn, B; Howe, K; Hussien, M; Imwong, M; Ishengoma, D; Jeans, J; Kabaghe, A; Kamuhabwa, A; Kindermans, J; Konate, DSORCID logo; Kwiatkowski, DP; Lee, C; Lee, SK; Lee, SJORCID logo; Ley, BORCID logo; Llanos-Cuentas, AORCID logo; Marfurt, J; Matambisso, G; Maude, RR; Maude, RJORCID logo; Mayor, A; Mayxay, MORCID logo; Maïga-Ascofaré, O; McCann, RS; Miles, A; Miotto, O; Mohamed, AOORCID logo; Morang’a, CMORCID logo; Murie, K; Ngasala, BEORCID logo; Nguyen, TORCID logo; Nolasco, O; Nosten, FORCID logo; Noviyanti, R; O'Connor, Í; Oboh, M; Ochola-Oyier, LI; Olufunke Falade, C; Olukosi, A; Olumide, A; Olusola, FI; Onyamboko, MAORCID logo; Oriero, EC; Oyibo, WA; Pannebaker, D; Pearson, RDORCID logo; Phiri, KORCID logo; van der Pluijm, RW; Price, RNORCID logo; Quang, HH; Rajkumar Devaraju, V; Randrianarivelojosia, MORCID logo; Ranford-Cartwright, LORCID logo; Rayner, JCORCID logo; Rovira-Vallbona, EORCID logo; Rowlands, K; Ruano-Rubio, V; Sanchez, JF; Saúte, F; Shettima, S; da Silva, C; Simpson, VJ; Suddaby, S; Takken, W; Thu, AM; Toure, M; Unlu, E; Valdivia, HOORCID logo; van Vugt, M; Waithira, NORCID logo; Wellems, TORCID logo; Wendler, J; White, NORCID logo; Wuendrich Ogidan, R and (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>


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