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An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples

Ahouidi, Ambroise, Ali, Mozam, Almagro-Garcia, Jacob, Amambua-Ngwa, Alfred, Amaratunga, Chanaki, Amato, Roberto, Amenga-Etego, Lucas, Andagalu, Ben, Anderson, Tim JC, Andrianaranjaka, Voahangy, Apinjoh, Tobias, Ariani, Cristina, Ashley, Elizabeth A, Auburn, Sarah, Awandare, Gordon, Ba, Hampdate, Baraka, Vito, Barry, Alyssa E, Bejon, Philip, Bertin, Gwladys I, Boni, Maciej F, Borrmann, Steffen, Bousema, Teun, Branch, Oralee, Bull, Peter C, Busby, George BJ, Chookajorn, Thanat, Chotivanich, Kesinee, Claessens, Antoine, Conway, David, Craig, Alister, D'Alessandro, Umberto, Dama, Souleymane, Day, Nicholas PJ, Denis, Brigitte, Diakite, Mahamadou, Djimdé, Abdoulaye, Dolecek, Christiane, Dondorp, Arjen M, Drakeley, Chris, Drury, Eleanor, Duffy, Patrick, Echeverry, Diego F, Egwang, Thomas G, Erko, Berhanu, Fairhurst, Rick M, Faiz, Abdul, Fanello, Caterina A, Fukuda, Mark M, Gamboa, Dionica, Ghansah, Anita, Golassa, Lemu, Goncalves, Sonia, Hamilton, William L, Harrison, GL Abby, Hart, Lee, Henrichs, Christa, Hien, Tran Tinh, Hill, Catherine A, Hodgson, Abraham, Hubbart, Christina, Imwong, Mallika, Ishengoma, Deus S, Jackson, Scott A, Jacob, Chris G, Jeffery, Ben, Jeffreys, Anna E, Johnson, Kimberly J, Jyothi, Dushyanth, Kamaliddin, Claire, Kamau, Edwin, Kekre, Mihir, Kluczynski, Krzysztof, Kochakarn, Theerarat, Konaté, Abibatou, Kwiatkowski, Dominic P, Kyaw, Myat Phone, Lim, Pharath, Lon, Chanthap, Loua, Kovana M, Maïga-Ascofaré, Oumou, Malangone, Cinzia, Manske, Magnus, Marfurt, Jutta, Marsh, Kevin, Mayxay, Mayfong, Miles, Alistair, Miotto, Olivo, Mobegi, Victor, Mokuolu, Olugbenga A, Montgomery, Jacqui, Mueller, Ivo, Newton, Paul N, Nguyen, Thuy, Nguyen, Thuy-Nhien, Noedl, Harald, Nosten, Francois, Noviyanti, Rintis, Nzila, Alexis and Ochola-Oyier, Lynette I 2021, An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples, Wellcome Open Research, vol. 6, pp. 1-31, doi: 10.12688/wellcomeopenres.16168.2.

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Title An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples
Author(s) Ahouidi, Ambroise
Ali, Mozam
Almagro-Garcia, Jacob
Amambua-Ngwa, Alfred
Amaratunga, Chanaki
Amato, Roberto
Amenga-Etego, Lucas
Andagalu, Ben
Anderson, Tim JC
Andrianaranjaka, Voahangy
Apinjoh, Tobias
Ariani, Cristina
Ashley, Elizabeth A
Auburn, Sarah
Awandare, Gordon
Ba, Hampdate
Baraka, Vito
Barry, Alyssa EORCID iD for Barry, Alyssa E
Bejon, Philip
Bertin, Gwladys I
Boni, Maciej F
Borrmann, Steffen
Bousema, Teun
Branch, Oralee
Bull, Peter C
Busby, George BJ
Chookajorn, Thanat
Chotivanich, Kesinee
Claessens, Antoine
Conway, David
Craig, Alister
D'Alessandro, Umberto
Dama, Souleymane
Day, Nicholas PJ
Denis, Brigitte
Diakite, Mahamadou
Djimdé, Abdoulaye
Dolecek, Christiane
Dondorp, Arjen M
Drakeley, Chris
Drury, Eleanor
Duffy, Patrick
Echeverry, Diego F
Egwang, Thomas G
Erko, Berhanu
Fairhurst, Rick M
Faiz, Abdul
Fanello, Caterina A
Fukuda, Mark M
Gamboa, Dionica
Ghansah, Anita
Golassa, Lemu
Goncalves, Sonia
Hamilton, William L
Harrison, GL Abby
Hart, Lee
Henrichs, Christa
Hien, Tran Tinh
Hill, Catherine A
Hodgson, Abraham
Hubbart, Christina
Imwong, Mallika
Ishengoma, Deus S
Jackson, Scott A
Jacob, Chris G
Jeffery, Ben
Jeffreys, Anna E
Johnson, Kimberly J
Jyothi, Dushyanth
Kamaliddin, Claire
Kamau, Edwin
Kekre, Mihir
Kluczynski, Krzysztof
Kochakarn, Theerarat
Konaté, Abibatou
Kwiatkowski, Dominic P
Kyaw, Myat Phone
Lim, Pharath
Lon, Chanthap
Loua, Kovana M
Maïga-Ascofaré, Oumou
Malangone, Cinzia
Manske, Magnus
Marfurt, Jutta
Marsh, Kevin
Mayxay, Mayfong
Miles, Alistair
Miotto, Olivo
Mobegi, Victor
Mokuolu, Olugbenga A
Montgomery, Jacqui
Mueller, Ivo
Newton, Paul N
Nguyen, Thuy
Nguyen, Thuy-Nhien
Noedl, Harald
Nosten, Francois
Noviyanti, Rintis
Nzila, Alexis
Ochola-Oyier, Lynette I
Journal name Wellcome Open Research
Volume number 6
Article ID 42
Start page 1
End page 31
Total pages 31
Publisher Wellcome Trust
Place of publication [London, Eng.]
Publication date 2021
ISSN 2398-502X
Keyword(s) data resource
drug resistance
genomic epidemiology
plasmodium falciparum
population genetics
rapid diagnostic test failure
Summary MalariaGEN is a data-sharing network that enables groups around the world to work together on the genomic epidemiology of malaria. Here we describe a new release of curated genome variation data on 7,000 Plasmodium falciparum samples from MalariaGEN partner studies in 28 malaria-endemic countries. High-quality genotype calls on 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using a standardised analysis pipeline. Copy number variants associated with drug resistance and structural variants that cause failure of rapid diagnostic tests were also analysed.  Almost all samples showed genetic evidence of resistance to at least one antimalarial drug, and some samples from Southeast Asia carried markers of resistance to six commonly-used drugs. Genes expressed during the mosquito stage of the parasite life-cycle are prominent among loci that show strong geographic differentiation. By continuing to enlarge this open data resource we aim to facilitate research into the evolutionary processes affecting malaria control and to accelerate development of the surveillance toolkit required for malaria elimination.
Language eng
DOI 10.12688/wellcomeopenres.16168.2
Indigenous content off
HERDC Research category C1 Refereed article in a scholarly journal
Free to Read? Yes
Persistent URL

Document type: Journal Article
Collections: Faculty of Health
School of Medicine
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