Abstract
| Original language | English |
|---|---|
| Article number | 22 |
| Journal | Wellcome open research |
| Volume | 8 |
| DOIs | |
| Publication status | Published - 2023 |
| Externally published | Yes |
Keywords
- data resource
- genomic epidemiology
- genomics
- malaria
- plasmodium falciparum
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In: Wellcome open research, Vol. 8, 22, 2023.
Research output: Contribution to journal › Article › Academic › peer-review
TY - JOUR
T1 - Pf7
T2 - an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples
AU - Abdel Hamid, Muzamil Mahdi
AU - Abdelraheem, Mohamed Hassan
AU - Acheampong, Desmond Omane
AU - Ahouidi, Ambroise
AU - Ali, Mozam
AU - Almagro-Garcia, Jacob
AU - Amambua-Ngwa, Alfred
AU - Amaratunga, Chanaki
AU - Amenga-Etego, Lucas
AU - Andagalu, Ben
AU - Anderson, Tim
AU - Andrianaranjaka, Voahangy
AU - Aniebo, Ifeyinwa
AU - Aninagyei, Enoch
AU - Ansah, Felix
AU - Ansah, Patrick O.
AU - Apinjoh, Tobias
AU - Arnaldo, Paulo
AU - Ashley, Elizabeth
AU - Auburn, Sarah
AU - Awandare, Gordon A.
AU - Ba, Hampate
AU - Baraka, Vito
AU - Barry, Alyssa
AU - Bejon, Philip
AU - Bertin, Gwladys I.
AU - Boni, Maciej F.
AU - Borrmann, Steffen
AU - Bousema, Teun
AU - Bouyou-Akotet, Marielle
AU - Branch, Oralee
AU - Bull, Peter C.
AU - Cheah, Huch
AU - Chindavongsa, Keobouphaphone
AU - Chookajorn, Thanat
AU - Chotivanich, Kesinee
AU - Claessens, Antoine
AU - Conway, David J.
AU - Corredor, Vladimir
AU - Courtier, Erin
AU - Craig, Alister
AU - D'Alessandro, Umberto
AU - Dama, Souleymane
AU - Day, Nicholas
AU - Denis, Brigitte
AU - Dhorda, Mehul
AU - Diakite, Mahamadou
AU - Djimde, Abdoulaye
AU - Dolecek, Christiane
AU - Dondorp, Arjen
AU - Doumbia, Seydou
AU - Drakeley, Chris
AU - Drury, Eleanor
AU - Duffy, Patrick
AU - Echeverry, Diego F.
AU - Egwang, Thomas G.
AU - Enosse, Sonia Maria Mauricio
AU - Erko, Berhanu
AU - Fairhurst, Rick M.
AU - Faiz, Abdul
AU - Fanello, Caterina A.
AU - Fleharty, Mark
AU - Forbes, Matthew
AU - Fukuda, Mark
AU - Gamboa, Dionicia
AU - Ghansah, Anita
AU - Golassa, Lemu
AU - Goncalves, Sonia
AU - Harrison, G. L. Abby
AU - Healy, Sara Anne
AU - Hendry, Jason A.
AU - Hernandez-Koutoucheva, Anastasia
AU - Hien, Tran Tinh
AU - Hill, Catherine A.
AU - Hombhanje, Francis
AU - Hott, Amanda
AU - Htut, Ye
AU - Hussein, Mazza
AU - Imwong, Mallika
AU - Ishengoma, Deus
AU - Jackson, Scott A.
AU - Jacob, Chris G.
AU - Jeans, Julia
AU - Johnson, Kimberly J.
AU - Kamaliddin, Claire
AU - Kamau, Edwin
AU - Keatley, Jon
AU - Kochakarn, Theerarat
AU - Konate, Drissa S.
AU - Konaté, Abibatou
AU - Kone, Aminatou
AU - Kwiatkowski, Dominic P.
AU - Kyaw, Myat P.
AU - Kyle, Dennis
AU - Lawniczak, Mara
AU - Lee, Samuel K.
AU - Lemnge, Martha
AU - Lim, Pharath
AU - Lon, Chanthap
AU - Loua, Kovana M.
AU - Mandara, Celine I.
AU - Marfurt, Jutta
AU - Marsh, Kevin
AU - Maude, Richard James
AU - Mayxay, Mayfong
AU - Maïga-Ascofaré, Oumou
AU - Miotto, Olivo
AU - Mita, Toshihiro
AU - Mobegi, Victor
AU - Mohamed, Abdelrahim Osman
AU - Mokuolu, Olugbenga A.
AU - Montgomery, Jaqui
AU - Morang’a, Collins Misita
AU - Mueller, Ivo
AU - Murie, Kathryn
AU - Newton, Paul N.
AU - Ngo Duc, Thang
AU - Nguyen, Thuy
AU - Nguyen, Thuy-Nhien
AU - Nguyen Thi Kim, Tuyen
AU - Nguyen van, Hong
AU - Noedl, Harald
AU - Nosten, Francois
AU - Noviyanti, Rintis
AU - Ntui, Vincent Ntui-Njock
AU - Nzila, Alexis
AU - Ochola-Oyier, Lynette Isabella
AU - Ocholla, Harold
AU - Oduro, Abraham
AU - Omedo, Irene
AU - Onyamboko, Marie A.
AU - Ouedraogo, Jean-Bosco
AU - Oyebola, Kolapo
AU - Oyibo, Wellington Aghoghovwia
AU - Pearson, Richard
AU - Peshu, Norbert
AU - Phyo, Aung P.
AU - Plowe, Christopher V.
AU - Price, Ric N.
AU - Pukrittayakamee, Sasithon
AU - Quang, Huynh Hong
AU - Randrianarivelojosia, Milijaona
AU - Rayner, Julian C.
AU - Ringwald, Pascal
AU - Rosanas-Urgell, Anna
AU - Rovira-Vallbona, Eduard
AU - Ruano-Rubio, Valentin
AU - Ruiz, Lastenia
AU - Saunders, David
AU - Shayo, Alex
AU - Siba, Peter
AU - Simpson, Victoria J.
AU - Sissoko, Mahamadou S.
AU - Smith, Christen
AU - Su, Xin-Zhuan
AU - Sutherland, Colin
AU - Takala-Harrison, Shannon
AU - Talman, Arthur
AU - Tavul, Livingstone
AU - Thanh, Ngo Viet
AU - Thathy, Vandana
AU - Thu, Aung Myint
AU - Toure, Mahamoudou
AU - Tshefu, Antoinette
AU - Verra, Federica
AU - Vinetz, Joseph
AU - Wellems, Thomas E.
AU - Wendler, Jason
AU - White, Nicholas J.
AU - Whitton, Georgia
AU - Yavo, William
AU - van der Pluijm, Rob W.
N1 - 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 ( https://www.malariagen.net/resource/34 ). 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.
PY - 2023
Y1 - 2023
N2 - 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.
AB - 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.
KW - data resource
KW - genomic epidemiology
KW - genomics
KW - malaria
KW - plasmodium falciparum
UR - http://www.scopus.com/inward/record.url?scp=85150355807&partnerID=8YFLogxK
U2 - https://doi.org/10.12688/wellcomeopenres.18681.1
DO - https://doi.org/10.12688/wellcomeopenres.18681.1
M3 - Article
C2 - 36864926
SN - 2398-502X
VL - 8
JO - Wellcome open research
JF - Wellcome open research
M1 - 22
ER -