Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples

Muzamil Mahdi Abdel Hamid, Mohamed Hassan Abdelraheem, Desmond Omane Acheampong, Ambroise Ahouidi, Mozam Ali, Jacob Almagro-Garcia, Alfred Amambua-Ngwa, Chanaki Amaratunga, Lucas Amenga-Etego, Ben Andagalu, Tim Anderson, Voahangy Andrianaranjaka, Ifeyinwa Aniebo, Enoch Aninagyei, Felix Ansah, Patrick O. Ansah, Tobias Apinjoh, Paulo Arnaldo, Elizabeth Ashley, Sarah AuburnGordon A. Awandare, Hampate Ba, Vito Baraka, Alyssa Barry, Philip Bejon, Gwladys I. Bertin, Maciej F. Boni, Steffen Borrmann, Teun Bousema, Marielle Bouyou-Akotet, Oralee Branch, Peter C. Bull, Huch Cheah, Keobouphaphone Chindavongsa, Thanat Chookajorn, Kesinee Chotivanich, Antoine Claessens, David J. Conway, Vladimir Corredor, Erin Courtier, Alister Craig, Umberto D'Alessandro, Souleymane Dama, Nicholas Day, Brigitte Denis, Mehul Dhorda, Mahamadou Diakite, Abdoulaye Djimde, Christiane Dolecek, Arjen Dondorp, Seydou Doumbia, Chris Drakeley, Eleanor Drury, Patrick Duffy, Diego F. Echeverry, Thomas G. Egwang, Sonia Maria Mauricio Enosse, Berhanu Erko, Rick M. Fairhurst, Abdul Faiz, Caterina A. Fanello, Mark Fleharty, Matthew Forbes, Mark Fukuda, Dionicia Gamboa, Anita Ghansah, Lemu Golassa, Sonia Goncalves, G. L.Abby Harrison, Sara Anne Healy, Jason A. Hendry, Anastasia Hernandez-Koutoucheva, Tran Tinh Hien, Catherine A. Hill, Francis Hombhanje, Amanda Hott, Ye Htut, Mazza Hussein, Mallika Imwong, Deus Ishengoma, Scott A. Jackson, Chris G. Jacob, Julia Jeans, Kimberly J. Johnson, Claire Kamaliddin, Edwin Kamau, Jon Keatley, Theerarat Kochakarn, Drissa S. Konate, Abibatou Konaté, Aminatou Kone, Dominic P. Kwiatkowski, Myat P. Kyaw, Dennis Kyle, Mara Lawniczak, Samuel K. Lee, Martha Lemnge, Pharath Lim, Chanthap Lon, Kovana M. Loua, Celine I. Mandara, Jutta Marfurt, Kevin Marsh, Richard James Maude, Mayfong Mayxay, Oumou Maïga-Ascofaré, Olivo Miotto, Toshihiro Mita, Victor Mobegi, Abdelrahim Osman Mohamed, Olugbenga A. Mokuolu, Jaqui Montgomery, Collins Misita Morang’a, Ivo Mueller, Kathryn Murie, Paul N. Newton, Thang Ngo Duc, Thuy Nguyen, Thuy Nhien Nguyen, Tuyen Nguyen Thi Kim, Hong Nguyen Van, Harald Noedl, Francois Nosten, Rintis Noviyanti, Vincent Ntui Njock Ntui, Alexis Nzila, Lynette Isabella Ochola-Oyier, Harold Ocholla, Abraham Oduro, Irene Omedo, Marie A. Onyamboko, Jean Bosco Ouedraogo, Kolapo Oyebola, Wellington Aghoghovwia Oyibo, Richard Pearson, Norbert Peshu, Aung P. Phyo, Christopher V. Plowe, Ric N. Price, Sasithon Pukrittayakamee, Huynh Hong Quang, Milijaona Randrianarivelojosia, Julian C. Rayner, Pascal Ringwald, Anna Rosanas-Urgell, Eduard Rovira-Vallbona, Valentin Ruano-Rubio, Lastenia Ruiz, David Saunders, Alex Shayo, Peter Siba, Victoria J. Simpson, Mahamadou S. Sissoko, Christen Smith, Xin Zhuan Su, Colin Sutherland, Shannon Takala-Harrison, Arthur Talman, Livingstone Tavul, Ngo Viet Thanh, Vandana Thathy, Aung Myint Thu, Mahamoudou Toure, Antoinette Tshefu, Federica Verra, Joseph Vinetz, Thomas E. Wellems, Jason Wendler, Nicholas J. White, Georgia Whitton, William Yavo, Rob W. van der Pluijm

Research output: Contribution to journalArticlepeer-review

4 Scopus citations


We describe the MalariaGEN Pf7 data resource, the seventh release of Plasmodium falciparum genome variation data from the MalariaGEN network.  It comprises over 20,000 samples from 82 partner studies in 33 countries, including several malaria endemic regions that were previously underrepresented.  For the first time we include dried blood spot samples that were sequenced after selective whole genome amplification, necessitating new methods to genotype copy number variations.  We identify a large number of newly emerging crt mutations in parts of Southeast Asia, and show examples of heterogeneities in patterns of drug resistance within Africa and within the Indian subcontinent.  We describe the profile of variations in the C-terminal of the csp gene and relate this to the sequence used in the RTS,S and R21 malaria vaccines.  Pf7 provides high-quality data on genotype calls for 6 million SNPs and short indels, analysis of large deletions that cause failure of rapid diagnostic tests, and systematic characterisation of six major drug resistance loci, all of which can be freely downloaded from the MalariaGEN website.

Original languageEnglish
Article number22
JournalWellcome Open Research
StatePublished - 2023

Bibliographical note

Funding Information:
This study was conducted by MalariaGEN, and was made possible by clinical parasite samples contributed by partner studies, whose investigators are represented in the author list and in the associated data release ( ). This research was supported in part by the Intramural Research Programme of the NIH, NIAID. In addition, the authors would like to thank the following individuals who contributed to partner studies, making this study possible: Dr Eugene Laman for work in sample collection in the Republic of Guinea; Dr Abderahmane Tandia and Dr Yacine Deh and Dr Samuel Assefa for work in sample collection in Mauritania; Dr Ibrahim Sanogo, Dr Sekou F. Traore and Dr Merepen dite Agnes Guindo for work in sample collection in Mali; Dr James Abugri and Dr Nicholas Amoako for work coordinating sample collection in Ghana. Genome sequencing was undertaken by the Wellcome Sanger Institute and we thank the staff of the Wellcome Sanger Institute Sample Logistics, Sequencing, and Informatics facilities for their contribution. The views expressed here are solely those of the authors and do not reflect the views, policies or positions of the U.S. Government or Department of Defense. Material has been reviewed by the Walter Reed Army Institute of Research. There is no objection to its presentation and/or publication. The opinions or assertions contained herein are the private views of the author, and are not to be construed as official, or as reflecting true views of the Department of the Army or the Department of Defense. The investigators have adhered to the policies for protection of human subjects as prescribed in AR 70–25. PR is a staff member of the World Health Organization. PR alone is responsible for the views expressed in this publication and they do not necessarily represent the decisions, policy or views of the World Health Organization.

Publisher Copyright:
Copyright: © 2023 MalariaGEN et al.


  • data resource
  • genomic epidemiology
  • genomics
  • malaria
  • plasmodium falciparum

ASJC Scopus subject areas

  • Medicine (miscellaneous)
  • Biochemistry, Genetics and Molecular Biology (all)


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