학술논문
Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples [version 1; peer review: 2 approved]
Document Type
article
Author
Mohamed Hassan Abdelraheem; Sonia Goncalves; Lemu Golassa; Tim Anderson; Desmond Omane Acheampong; Enoch Aninagyei; Ifeyinwa Aniebo; Patrick O Ansah; Felix Ansah; Gordon A Awandare; Paulo Arnaldo; Maciej F Boni; Gwladys I Bertin; Peter C Bull; Marielle Bouyou-Akotet; Keobouphaphone Chindavongsa; Edwin Kamau; Huch Cheah; Claire Kamaliddin; Vladimir Corredor; David J Conway; Nicholas Day; Abibatou Konaté; Erin Courtier; Theerarat Kochakarn; Arjen Dondorp; Abdoulaye Djimde; Diego F Echeverry; Seydou Doumbia; Mara Lawniczak; Pharath Lim; Sonia Maria Mauricio Enosse; Oumou Maïga-Ascofaré; Thomas G Egwang; Aung Myint Thu; Mark Fleharty; Jutta Marfurt; Caterina A Fanello; Mark Fukuda; Victor Mobegi; Matthew Forbes; Sara Anne Healy; G L Abby Harrison; Anastasia Hernandez-Koutoucheva; Jason A Hendry; Ivo Mueller; Francis Hombhanje; Harald Noedl; Catherine A Hill; Thuy-Nhien Nguyen; Mazza Hussein; Amanda Hott; Rintis Noviyanti; Scott A Jackson; Abraham Oduro; Deus Ishengoma; Harold Ocholla; Julia Jeans; Jean-Bosco Ouedraogo; Chris G Jacob; Drissa S Konate; Jon Keatley; Francois Nosten; Kolapo Oyebola; Myat P Kyaw; Aminatou Kone; Norbert Peshu; Samuel K Lee; Dennis Kyle; Kovana M Loua; Milijaona Randrianarivelojosia; Martha Lemnge; Sasithon Pukrittayakamee; Richard James Maude; Pascal Ringwald; Celine I Mandara; Abdelrahim Osman Mohamed; Toshihiro Mita; Jaqui Montgomery; Julian C Rayner; David Saunders; Olugbenga A Mokuolu; Lastenia Ruiz; Kathryn Murie; Peter Siba; Collins Misita Morang’a; Alex Shayo; Tuyen Nguyen Thi Kim; Thang Ngo Duc; Vincent Ntui-Njock Ntui; Colin Sutherland; Hong Nguyen Van; Xin-zhuan Su; Marie A Onyamboko; Livingstone Tavul; Irene Omedo; Richard Pearson; Antoinette Tshefu; Wellington Aghoghovwia Oyibo; Vandana Thathy; Chris Drakeley; Huynh Hong Quang; Joseph Vinetz; Christopher V Plowe; Federica Verra; Eduard Rovira-Vallbona; Jason Wendler; Anna Rosanas-Urgell; Teun Bousema; Thuy Nguyen; Mahamadou S. Sissoko; Valentin Ruano-Rubio; Alexis Nzila; Shannon Takala-Harrison; Christen Smith; William Yavo; Ngo Viet Thanh; Arthur Talman; Georgia Whitton; Mahamoudou Toure; Rob W van der Pluijm; Sarah Auburn; Antoine Claessens; Mahamadou Diakite; Kesinee Chotivanich; Mehul Dhorda; Olivo Miotto; Mallika Imwong; Mayfong Mayxay; Alfred Amambua-Ngwa; Philip Bejon; Elizabeth Ashley; Alyssa Barry; Rick M. Fairhurst; Ye Htut; Tran Tinh Hien; Kimberly J Johnson; Dominic P Kwiatkowski; Umberto D'Alessandro; Chanthap Lon; Paul N Newton; Aung P Phyo; Ric N Price; Victoria J Simpson; Kevin Marsh; Nicholas J White; Thomas E Wellems; Lynette Isabella Ochola-Oyier; Mozam Ali; Ambroise Ahouidi; Jacob Almagro-Garcia; Ben Andagalu; Lucas Amenga-Etego; Voahangy Andrianaranjaka; Tobias Apinjoh; Vito Baraka; Hampate Ba; Steffen Borrmann; Oralee Branch; Thanat Chookajorn; Souleymane Dama; Chanaki Amaratunga; Alister Craig; Brigitte Denis; Eleanor Drury; Christiane Dolecek; Patrick Duffy; Berhanu Erko; Abdul Faiz; Muzamil Mahdi Abdel Hamid; Anita Ghansah; Dionicia Gamboa
Source
Wellcome Open Research, Vol 8 (2023)
Subject
Language
English
ISSN
2398-502X
Abstract
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.