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

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.