Медицинская библиотека · Wellcome open research · 2025

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

Malaria Genomic Epidemiology Network (MalariaGEN), Abdel Hamid Muzamil Mahdi, Abdelraheem Mohamed Hassan, Acheampong Desmond Omane, Adam Ishag, Aide Pedro, Ajibaye Olusola, Ali Mozam, Almagro-Garcia Jacob, Amambua-Ngwa Alfred, Amenga-Etego Lucas, Aniebo Ifeyinwa, Aninagyei Enoch, Ansah Felix, Apinjoh Tobias O, Ariani Cristina V, Auburn Sarah, Awandare Gordon A, Balmer Andrew, Bejon Philip, Boene Simone, Bwire George, Candrinho Baltazar, Chidimatembue Arlindo, Chindavongsa Keobouphaphone, Comiche Kiba, Conway David, Dara Antoine, Diakite Mahamadou, Djimde Abdoulaye, Dondorp Arjen, Doumbia Seydou, Drury Eleanor, Fanello Caterina A, Ferdig Mike, Figueroa Katherine, Gamboa Dionicia, Golassa Lemu, Gonçalves Sónia, Guindo Merepen Dite Agnes, Hamaluba Mainga, Hanboonkunupakarn Borimas, Howe Kevin, Hussien Maazza, Imwong Mallika, Ishengoma Deus, Jeans Julia, Kabaghe Alinune, Kamuhabwa Appolinary, Kindermans Jean-Marie, Konate Drissa S, Kwiatkowski Dominic P, Lee Chiyun, Lee Samuel K, Lee Sue J, Ley Benedikt, Llanos-Cuentas Alejandro, Marfurt Jutta, Matambisso Glória, Maude Rapeephan Rattanawongnara, Maude Richard James, Mayor Alfredo, Mayxay Mayfong, Maïga-Ascofaré Oumou, McCann Robert S, Miles Alistair, Miotto Olivo, Mohamed Abdelrahim Osman, Morang'a Collins Misita, Murie Kathryn, Ngasala Billy Ephraim, Nguyen Thuy-Nhien, Nolasco Oscar, Nosten Francois, Noviyanti Rintis, O'Connor Ísla, Oboh Mary, Ochola-Oyier Lynette Isabella, Olufunke Falade Catherine, Olukosi Adeola, Olumide Ajibola, Olusola Fiyinfoluwa I, Onyamboko Marie A, Oriero Eniyou Cheryll, Oyibo Wellington Aghoghovwia, Pannebaker Danielle, Pearson Richard D, Phiri Kamija, van der Pluijm Rob W, Price Ric N, Quang Huynh Hong, Rajkumar Devaraju Vinoth, Randrianarivelojosia Milijaona, Ranford-Cartwright Lisa, Rayner Julian C, Rovira-Vallbona Eduard, Rowlands Katherine, Ruano-Rubio Valentin, Sanchez Juan F, Saúte Francisco, Shettima Shuwaram, da Silva Clemente, Simpson Victoria J, Suddaby Simon, Takken Willem, Thu Aung Myint, Toure Mahamoudou, Unlu Eyyub, Valdivia Hugo O, van Vugt Michele, Waithira Naomi, Wellems Thomas, Wendler Jason, White Nina, Wuendrich Ogidan Rachel

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Аннотация

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.

Для цитирования: Malaria Genomic Epidemiology Network (MalariaGEN), Abdel Hamid Muzamil Mahdi, Abdelraheem Mohamed Hassan, Acheampong Desmond Omane, Adam Ishag, Aide Pedro, Ajibaye Olusola, Ali Mozam, Almagro-Garcia Jacob, Amambua-Ngwa Alfred, Amenga-Etego Lucas, Aniebo Ifeyinwa, Aninagyei Enoch, Ansah Felix, Apinjoh Tobias O, Ariani Cristina V, Auburn Sarah, Awandare Gordon A, Balmer Andrew, Bejon Philip, Boene Simone, Bwire George, Candrinho Baltazar, Chidimatembue Arlindo, Chindavongsa Keobouphaphone, Comiche Kiba, Conway David, Dara Antoine, Diakite Mahamadou, Djimde Abdoulaye, Dondorp Arjen, Doumbia Seydou, Drury Eleanor, Fanello Caterina A, Ferdig Mike, Figueroa Katherine, Gamboa Dionicia, Golassa Lemu, Gonçalves Sónia, Guindo Merepen Dite Agnes, Hamaluba Mainga, Hanboonkunupakarn Borimas, Howe Kevin, Hussien Maazza, Imwong Mallika, Ishengoma Deus, Jeans Julia, Kabaghe Alinune, Kamuhabwa Appolinary, Kindermans Jean-Marie, Konate Drissa S, Kwiatkowski Dominic P, Lee Chiyun, Lee Samuel K, Lee Sue J, Ley Benedikt, Llanos-Cuentas Alejandro, Marfurt Jutta, Matambisso Glória, Maude Rapeephan Rattanawongnara, Maude Richard James, Mayor Alfredo, Mayxay Mayfong, Maïga-Ascofaré Oumou, McCann Robert S, Miles Alistair, Miotto Olivo, Mohamed Abdelrahim Osman, Morang'a Collins Misita, Murie Kathryn, Ngasala Billy Ephraim, Nguyen Thuy-Nhien, Nolasco Oscar, Nosten Francois, Noviyanti Rintis, O'Connor Ísla, Oboh Mary, Ochola-Oyier Lynette Isabella, Olufunke Falade Catherine, Olukosi Adeola, Olumide Ajibola, Olusola Fiyinfoluwa I, Onyamboko Marie A, Oriero Eniyou Cheryll, Oyibo Wellington Aghoghovwia, Pannebaker Danielle, Pearson Richard D, Phiri Kamija, van der Pluijm Rob W, Price Ric N, Quang Huynh Hong, Rajkumar Devaraju Vinoth, Randrianarivelojosia Milijaona, Ranford-Cartwright Lisa, Rayner Julian C, Rovira-Vallbona Eduard, Rowlands Katherine, Ruano-Rubio Valentin, Sanchez Juan F, Saúte Francisco, Shettima Shuwaram, da Silva Clemente, Simpson Victoria J, Suddaby Simon, Takken Willem, Thu Aung Myint, Toure Mahamoudou, Unlu Eyyub, Valdivia Hugo O, van Vugt Michele, Waithira Naomi, Wellems Thomas, Wendler Jason, White Nina, Wuendrich Ogidan Rachel. Pf8: an open dataset of Plasmodium falciparum genome variation in 33,325 worldwide samples.. Wellcome open research. 2025. DOI: 10.12688/wellcomeopenres.24031.1.

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