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

MalariaGEN; Abdel Hamid, MM; Abdelraheem, MH; Acheampong, DO; Ahouidi, A; Ali, M; Almagro-Garcia, J; Amambua-Ngwa, AORCID logo; Amaratunga, C; Amenga-Etego, LORCID logo; +163 more...Andagalu, B; Anderson, TORCID logo; Andrianaranjaka, V; Aniebo, I; Aninagyei, E; Ansah, F; Ansah, POORCID logo; Apinjoh, T; Arnaldo, P; Ashley, EORCID logo; Auburn, S; Awandare, GA; Ba, HORCID logo; Baraka, VORCID logo; Barry, A; Bejon, PORCID logo; Bertin, GIORCID logo; Boni, MFORCID logo; Borrmann, S; Bousema, TORCID logo; Bouyou-Akotet, M; Branch, O; Bull, PC; Cheah, H; Chindavongsa, K; Chookajorn, TORCID logo; Chotivanich, K; Claessens, AORCID logo; Conway, DJORCID logo; Corredor, V; Courtier, E; Craig, AORCID logo; D'Alessandro, UORCID logo; Dama, S; Day, NORCID logo; Denis, B; Dhorda, M; Diakite, MORCID logo; Djimde, AORCID logo; Dolecek, C; Dondorp, AORCID logo; Doumbia, S; Drakeley, CORCID logo; Drury, E; Duffy, P; Echeverry, DFORCID logo; Egwang, TG; Enosse, SMM; Erko, BORCID logo; Fairhurst, RM; Faiz, AORCID logo; Fanello, CAORCID logo; Fleharty, M; Forbes, M; Fukuda, M; Gamboa, DORCID logo; Ghansah, A; Golassa, LORCID logo; Goncalves, S; Harrison, GA; Healy, SAORCID logo; Hendry, JA; Hernandez-Koutoucheva, A; Hien, TT; Hill, CA; Hombhanje, F; Hott, A; Htut, Y; Hussein, M; Imwong, M; Ishengoma, DORCID logo; Jackson, SAORCID logo; Jacob, CG; Jeans, J; Johnson, KJ; Kamaliddin, CORCID logo; Kamau, EORCID logo; Keatley, J; Kochakarn, T; Konate, DSORCID logo; Konaté, A; Kone, A; Kwiatkowski, DPORCID logo; Kyaw, MP; Kyle, DORCID logo; Lawniczak, MORCID logo; Lee, SK; Lemnge, M; Lim, P; Lon, C; Loua, KMORCID logo; Mandara, CI; Marfurt, J; Marsh, KORCID logo; Maude, RJ; Mayxay, MORCID logo; Maïga-Ascofaré, O; Miotto, OORCID logo; Mita, TORCID logo; Mobegi, VORCID logo; Mohamed, AO; Mokuolu, OA; Montgomery, J; Morang'a, CMORCID logo; Mueller, I; Murie, K; Newton, PN; Ngo Duc, T; Nguyen, T; Nguyen, TORCID logo; Nguyen Thi Kim, T; Nguyen Van, H; Noedl, H; Nosten, FORCID logo; Noviyanti, R; Ntui, VNORCID logo; Nzila, A; Ochola-Oyier, LI; Ocholla, H; Oduro, AORCID logo; Omedo, I; Onyamboko, MAORCID logo; Ouedraogo, JORCID logo; Oyebola, KORCID logo; Oyibo, WA; Pearson, RORCID logo; Peshu, N; Phyo, APORCID logo; Plowe, CV; Price, RNORCID logo; Pukrittayakamee, S; Quang, HH; Randrianarivelojosia, M; Rayner, JCORCID logo; Ringwald, P; Rosanas-Urgell, AORCID logo; Rovira-Vallbona, E; Ruano-Rubio, V; Ruiz, L; Saunders, D; Shayo, AORCID logo; Siba, P; Simpson, VJ; Sissoko, MS; Smith, C; Su, XORCID logo; Sutherland, CORCID logo; Takala-Harrison, S; Talman, A; Tavul, L; Thanh, NV; Thathy, V; Thu, AM; Toure, M; Tshefu, A; Verra, F; Vinetz, JORCID logo; Wellems, TEORCID logo; Wendler, J; White, NJ; Whitton, G; Yavo, W; van der Pluijm, RW and (2023) Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples. Wellcome open research, 8. 22-. ISSN 2398-502X DOI: 10.12688/wellcomeopenres.18681.1
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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.


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