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

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

doi:10.12688/wellcomeopenres.18681.1

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

Journal article

Open access

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

Muzamil Mahdi Abdel Hamid, Mohamed Hassan Abdelraheem, Desmond Omane Acheampong, Ambroise Ahouidi, Mozam Ali, Jacob Almagro-Garcia, Alfred Amambua-Ngwa, Chanaki Amaratunga, Lucas Amenga-Etego, Ben Andagalu, …

Wellcome Open Research, Vol.8

01/2023

DOI: https://doi.org/10.12688/wellcomeopenres.18681.1

PMCID: PMC9971654

PMID: 36864926

Abstract

data resource

genomic epidemiology

genomics

malaria

plasmodium falciparum

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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Title: Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples
Creators - without role: Muzamil Mahdi Abdel Hamid - University of Khartoum
Mohamed Hassan Abdelraheem - University of Khartoum
Desmond Omane Acheampong - University of Cape Coast
Ambroise Ahouidi - Cheikh Anta Diop University
Mozam Ali - Wellcome Sanger Institute
Jacob Almagro-Garcia - Wellcome Sanger Institute
Alfred Amambua-Ngwa - Wellcome Sanger Institute
Chanaki Amaratunga - National Institute of Allergy and Infectious Diseases
Lucas Amenga-Etego - Navrongo Health Research Centre
Ben Andagalu - Kenya Medical Research Institute
Tim Anderson - Texas Biomedical Research Institute
Voahangy Andrianaranjaka - University of Antananarivo
Ifeyinwa Aniebo - Juntendo University Hospital
Enoch Aninagyei - University of Nairobi
Felix Ansah - University of Ghana
Patrick O Ansah - Navrongo Health Research Centre
Tobias Apinjoh - University of Buea
Paulo Arnaldo - Instituto Nacional de Saúde
Elizabeth Ashley - Mahidol Oxford Tropical Medicine Research Unit
Sarah Auburn - Royal Darwin Hospital
Gordon A Awandare - University of Ghana
Hampate Ba - University of Oxford
Vito Baraka - Centre for Human Genetics
Alyssa Barry - Centre for Human Genetics
Philip Bejon - Centre for Human Genetics
Gwladys I Bertin - Institut de Recherche pour le Développement
Maciej F Boni - University of Oxford
Steffen Borrmann - Centre for Human Genetics
Teun Bousema - Centre for Human Genetics
Marielle Bouyou-Akotet - University of Oxford
Oralee Branch - University of Oxford
Peter C Bull - Centre for Human Genetics
Huch Cheah - University of Oxford
Keobouphaphone Chindavongsa - Centre for Human Genetics
Thanat Chookajorn - Centre for Human Genetics
Kesinee Chotivanich - Centre for Human Genetics
Antoine Claessens - Université de Montpellier, Laboratory of Pathogens and Host Immunity - LPHI
David J Conway - University of Oxford
Vladimir Corredor - Centre for Human Genetics
Erin Courtier - Myanmar Oxford Clinical Research Unit
Alister Craig - Centre for Human Genetics
Umberto d'Alessandro
Souleymane Dama - Centre for Human Genetics
Nicholas Day
Brigitte Denis - Centre for Human Genetics
Mehul Dhorda - Monash University
Mahamadou Diakite - Centre for Human Genetics
Abdoulaye Djimde - University of Oxford
Christiane Dolecek - Centre for Human Genetics
Arjen Dondorp
Seydou Doumbia - Centre for Human Genetics
Chris Drakeley - Centre for Human Genetics
Eleanor Drury - Myanmar Oxford Clinical Research Unit
Patrick Duffy - Applied Genetic Technologies
Diego F Echeverry - University of Oxford
Thomas G Egwang - Centre for Human Genetics
Sonia Maria Mauricio Enosse - University of Ilorin
Berhanu Erko - Centre for Human Genetics
Rick M Fairhurst - Centre for Human Genetics
Abdul Faiz - University of Oxford
Caterina A Fanello - Monash University
Mark Fleharty - Centre for Human Genetics
Matthew Forbes - Myanmar Oxford Clinical Research Unit
Mark Fukuda - University of Oxford
Dionicia Gamboa - University of Oxford
Anita Ghansah - Centre for Human Genetics
Lemu Golassa - University of Oxford
Sonia Goncalves - Myanmar Oxford Clinical Research Unit
G Harrison
Sara Anne Healy - Applied Genetic Technologies
Jason A Hendry - Centre for Human Genetics
Anastasia Hernandez-Koutoucheva - Myanmar Oxford Clinical Research Unit
Tran Tinh Hien
Catherine A Hill - Centre for Human Genetics
Francis Hombhanje - Centre for Human Genetics
Amanda Hott - Centre for Human Genetics
Ye Htut - Centre for Human Genetics
Mazza Hussein - Centre for Human Genetics
Mallika Imwong - Centre for Human Genetics
Deus Ishengoma - Centre for Human Genetics
Scott A Jackson - Centre for Human Genetics
Chris G Jacob - Myanmar Oxford Clinical Research Unit
Julia Jeans - Myanmar Oxford Clinical Research Unit
Kimberly J Johnson - Myanmar Oxford Clinical Research Unit
Claire Kamaliddin - Centre for Human Genetics
Edwin Kamau - Centre for Human Genetics
Jon Keatley - Myanmar Oxford Clinical Research Unit
Theerarat Kochakarn - Centre for Human Genetics
Drissa S Konate - Centre for Human Genetics
Abibatou Konaté - Centre for Human Genetics
Aminatou Kone - Centre for Human Genetics
Dominic P Kwiatkowski - Myanmar Oxford Clinical Research Unit
Myat P Kyaw - Centre for Human Genetics
Dennis Kyle - Centre for Human Genetics
Mara Lawniczak - Myanmar Oxford Clinical Research Unit
Samuel K Lee - Centre for Human Genetics
Martha Lemnge - University of Oxford
Pharath Lim - Applied Genetic Technologies
Chanthap Lon - Centre for Human Genetics
Kovana M Loua - Centre for Human Genetics
Celine I Mandara - University of Oxford
Jutta Marfurt - University of Oxford
Kevin Marsh - Centre for Human Genetics
Richard James Maude
Mayfong Mayxay
Oumou Maïga-Ascofaré - Centre for Human Genetics
Olivo Miotto - Monash University
Toshihiro Mita - Centre for Human Genetics
Victor Mobegi - Centre for Human Genetics
Abdelrahim Osman Mohamed - Centre for Human Genetics
Olugbenga A Mokuolu - Centre for Human Genetics
Jaqui Montgomery - Centre for Human Genetics
Collins Misita Morang'A
Ivo Mueller - Centre for Human Genetics
Kathryn Murie - Myanmar Oxford Clinical Research Unit
Paul N Newton
Thang Ngo Duc
Thuy Nguyen - Myanmar Oxford Clinical Research Unit
Thuy-Nhien Nguyen - Myanmar Oxford Clinical Research Unit
Tuyen Nguyen Thi Kim
Hong Nguyen Van
Harald Noedl - Centre for Human Genetics
François Nosten
Rintis Noviyanti - Centre for Human Genetics
Vincent Ntui-Njock Ntui - University of Khartoum
Alexis Nzila - University of Oxford
Lynette Isabella Ochola-Oyier
Harold Ocholla - Centre for Human Genetics
Abraham Oduro - Walter Reed Army Institute of Research
Irene Omedo - Myanmar Oxford Clinical Research Unit
Marie A Onyamboko - Centre for Human Genetics
Jean-Bosco Ouedraogo
Kolapo Oyebola - Centre for Human Genetics
Wellington Aghoghovwia Oyibo - Centre for Human Genetics
Richard Pearson - Myanmar Oxford Clinical Research Unit
Norbert Peshu - Centre for Human Genetics
Aung P Phyo - Monash University
Christopher V Plowe - Centre for Human Genetics
Ric N Price - Monash University
Sasithon Pukrittayakamee - University of Oxford
Huynh Hong Quang - Université Félix Houphouët-Boigny
Milijaona Randrianarivelojosia - Université Félix Houphouët-Boigny
Julian C Rayner - Université Félix Houphouët-Boigny
Pascal Ringwald - Université Félix Houphouët-Boigny
Anna Rosanas-Urgell - Université Félix Houphouët-Boigny
Eduard Rovira-Vallbona - Université Félix Houphouët-Boigny
Valentin Ruano-Rubio - Centre for Human Genetics
Lastenia Ruiz
David Saunders - Université Félix Houphouët-Boigny
Alex Shayo - Université Félix Houphouët-Boigny
Peter Siba - Université Félix Houphouët-Boigny
Victoria J Simpson - Myanmar Oxford Clinical Research Unit
Mahamadou S Sissoko - Centre for Human Genetics
Christen Smith - Myanmar Oxford Clinical Research Unit
Xin-Zhuan Su
Colin Sutherland - University of Oxford
Shannon Takala-Harrison - Université Félix Houphouët-Boigny
Arthur M. Talman - Université de Montpellier, Maladies Infectieuses et Vecteurs : Ecologie, Génétique, Evolution et Contrôle - MIVEGEC
Livingstone Tavul - Université Félix Houphouët-Boigny
Ngo Viet Thanh
Vandana Thathy - Genomics
Aung Myint Thu - Myanmar Oxford Clinical Research Unit
Mahamoudou Toure - Centre for Human Genetics
Antoinette Tshefu - Myanmar Oxford Clinical Research Unit
Federica Verra - University of Nairobi
Joseph Vinetz - Myanmar Oxford Clinical Research Unit
Thomas E Wellems - Applied Genetic Technologies
Jason Wendler - Myanmar Oxford Clinical Research Unit
Nicholas J White
Georgia Whitton - Myanmar Oxford Clinical Research Unit
William Yavo - Monash University
Rob W van der Pluijm - Monash University
Publication Details: Wellcome Open Research, Vol.8
Identifiers: 9940094709311
Academic Unit: Maladies Infectieuses et Vecteurs : Ecologie, Génétique, Evolution et Contrôle - MIVEGEC; Laboratory of Pathogens and Host Immunity - LPHI
Language: English
Resource Type: Journal article
Local Fields: hal-04110334