Abstract

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 A Amaratunga C Amenga-Etego L Andagalu B Anderson T Andrianaranjaka V Aniebo I Aninagyei E Ansah F Ansah PO Apinjoh T Arnaldo P Ashley E Auburn S Awandare GA Ba H Baraka V Barry A Bejon P Bertin GI Boni MF Borrmann S Bousema T Bouyou-Akotet M Branch O Bull PC Cheah H Chindavongsa K Chookajorn T Chotivanich K Claessens A Conway DJ Corredor V Courtier E Craig A D'Alessandro U Dama S Day N Denis B Dhorda M Diakite M Djimde A Dolecek C Dondorp A Doumbia S Drakeley C Drury E Duffy P Echeverry DF Egwang TG Enosse SMM Erko B Fairhurst RM Faiz A Fanello CA Fleharty M Forbes M Fukuda M Gamboa D Ghansah A Golassa L Goncalves S Harrison GLA Healy SA Hendry JA Hernandez-Koutoucheva A Hien TT Hill CA Hombhanje F Hott A Htut Y Hussein M Imwong M Ishengoma D Jackson SA Jacob CG Jeans J Johnson KJ Kamaliddin C Kamau E Keatley J Kochakarn T Konate DS Konate A Kone A Kwiatkowski DP Kyaw MP Kyle D Lawniczak M Lee SK Lemnge M Lim P Lon C Loua KM Mandara CI Marfurt J Marsh K Maude RJ Mayxay M Maiga-Ascofare O Miotto O Mita T Mobegi V Mohamed AO Mokuolu OA Montgomery J Morang'a CM Mueller I Murie K Newton PN Ngo Duc T Nguyen T Nguyen TN Nguyen Thi Kim T Nguyen Van H Noedl H Nosten F Noviyanti R Ntui VN Nzila A Ochola-Oyier LI Ocholla H Oduro A Omedo I Onyamboko MA Ouedraogo JB Oyebola K Oyibo WA Pearson R Peshu N Phyo AP Plowe CV Price RN Pukrittayakamee S Quang HH Randrianarivelojosia M Rayner JC Ringwald P Rosanas-Urgell A Rovira-Vallbona E Ruano-Rubio V Ruiz L Saunders D Shayo A Siba P Simpson VJ Sissoko MS Smith C Su XZ Sutherland C Takala-Harrison S Talman A Tavul L Thanh NV Thathy V Thu AM Toure M Tshefu A Verra F Vinetz J Wellems TE Wendler J White NJ Whitton G Yavo W van der Pluijm RW
Wellcome Open Res. 2023;822

Permenent descriptor

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.