An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples

Malaria Gen; Ambroise Ahouidi; Mozam Ali; Jacob Almagro-Garcia; Alfred Amambua-Ngwa; Chanaki Amaratunga; Roberto Amato; Lucas Amenga-Etego; Ben Andagalu; Tim J.C. Anderson; Voahangy Andrianaranjaka; Tobias Apinjoh; Cristina Ariani; Elizabeth A. Ashley; Sarah Auburn; Gordon A. Awandare; Hampate Ba; Vito Baraka; Alyssa E. Barry; Philip Bejon; Gwladys I. Bertin; Maciej F. Boni; Steffen Borrmann; Teun Bousema; Oralee Branch; Peter C. Bull; George B.J. Busby; Thanat Chookajorn; Kesinee Chotivanich; Antoine Claessens; David Conway; Alister Craig; Umberto D'Alessandro; Souleymane Dama; Nicholas PJ Day; Brigitte Denis; Mahamadou Diakite; Abdoulaye Djimdé; Christiane Dolecek; Arjen M. Dondorp; Chris Drakeley; Eleanor Drury; Patrick Duffy; Diego F. Echeverry; Thomas G. Egwang; Berhanu Erko; Rick M. Fairhurst; Abdul Faiz; Caterina A. Fanello; Mark M. Fukuda; Dionicia Gamboa; Anita Ghansah; Lemu Golassa; Sonia Goncalves; William L. Hamilton; G. L.Abby Harrison; Lee Hart; Christa Henrichs; Tran Tinh Hien; Catherine A. Hill; Abraham Hodgson; Christina Hubbart; Mallika Imwong; Deus S. Ishengoma; Scott A. Jackson; Chris G. Jacob; Ben Jeffery; Anna E. Jeffreys; Kimberly J. Johnson; Dushyanth Jyothi; Claire Kamaliddin; Edwin Kamau; Mihir Kekre; Krzysztof Kluczynski; Theerarat Kochakarn; Abibatou Konaté; Dominic P. Kwiatkowski; Myat Phone Kyaw; Pharath Lim; Chanthap Lon; Kovana M. Loua; Oumou Maïga-Ascofaré; Cinzia Malangone; Magnus Manske; Jutta Marfurt; Kevin Marsh; Mayfong Mayxay; Alistair Miles; Olivo Miotto; Victor Mobegi; Olugbenga A. Mokuolu; Jacqui Montgomery; Ivo Mueller; Paul N. Newton; Thuy Nguyen; Thuy Nhien Nguyen; Harald Noedl; François Nosten; Rintis Noviyanti; Alexis Nzila; Lynette I. Ochola-Oyier; Harold Ocholla; Abraham Oduro; Irene Omedo; Marie A. Onyamboko; Jean Bosco Ouedraogo; Kolapo Oyebola; Richard D. Pearson; Norbert Peshu; Aung Pyae Phyo; Chris V. Plowe; Ric N. Price; Sasithon Pukrittayakamee; Milijaona Randrianarivelojosia; Julian C. Rayner; Pascal Ringwald; Kirk A. Rockett; Katherine Rowlands; Lastenia Ruiz; David Saunders; Alex Shayo; Peter Siba; Victoria J. Simpson; Jim Stalker; Xin zhuan Su; Colin Sutherland; Shannon Takala-Harrison; Livingstone Tavul; Vandana Thathy; Antoinette Tshefu; Federica Verra; Joseph Vinetz; Thomas E. Wellems; Jason Wendler; Nicholas J. White; Ian Wright; William Yavo; Htut Ye

doi:10.12688/wellcomeopenres.16168.2

An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples

Malaria Gen
, Ambroise Ahouidi
, Mozam Ali
, Jacob Almagro-Garcia
, Alfred Amambua-Ngwa
, Chanaki Amaratunga
, Roberto Amato
, Lucas Amenga-Etego
, Ben Andagalu
, Tim J.C. Anderson
, Voahangy Andrianaranjaka
, Tobias Apinjoh
, Cristina Ariani
, Elizabeth A. Ashley
, Sarah Auburn
, Gordon A. Awandare
, Hampate Ba
, Vito Baraka
, Alyssa E. Barry
, Philip Bejon

Gwladys I. Bertin, Maciej F. Boni, Steffen Borrmann, Teun Bousema, Oralee Branch, Peter C. Bull, George B.J. Busby, Thanat Chookajorn, Kesinee Chotivanich, Antoine Claessens, David Conway, Alister Craig, Umberto D'Alessandro, Souleymane Dama, Nicholas PJ Day, Brigitte Denis, Mahamadou Diakite, Abdoulaye Djimdé, Christiane Dolecek, Arjen M. Dondorp, Chris Drakeley, Eleanor Drury, Patrick Duffy, Diego F. Echeverry, Thomas G. Egwang, Berhanu Erko, Rick M. Fairhurst, Abdul Faiz, Caterina A. Fanello, Mark M. Fukuda, Dionicia Gamboa, Anita Ghansah, Lemu Golassa, Sonia Goncalves, William L. Hamilton, G. L.Abby Harrison, Lee Hart, Christa Henrichs, Tran Tinh Hien, Catherine A. Hill, Abraham Hodgson, Christina Hubbart, Mallika Imwong, Deus S. Ishengoma, Scott A. Jackson, Chris G. Jacob, Ben Jeffery, Anna E. Jeffreys, Kimberly J. Johnson, Dushyanth Jyothi, Claire Kamaliddin, Edwin Kamau, Mihir Kekre, Krzysztof Kluczynski, Theerarat Kochakarn, Abibatou Konaté, Dominic P. Kwiatkowski, Myat Phone Kyaw, Pharath Lim, Chanthap Lon, Kovana M. Loua, Oumou Maïga-Ascofaré, Cinzia Malangone, Magnus Manske, Jutta Marfurt, Kevin Marsh, Mayfong Mayxay, Alistair Miles, Olivo Miotto, Victor Mobegi, Olugbenga A. Mokuolu, Jacqui Montgomery, Ivo Mueller, Paul N. Newton, Thuy Nguyen, Thuy Nhien Nguyen, Harald Noedl, François Nosten, Rintis Noviyanti, Alexis Nzila, Lynette I. Ochola-Oyier, Harold Ocholla, Abraham Oduro, Irene Omedo, Marie A. Onyamboko, Jean Bosco Ouedraogo, Kolapo Oyebola, Richard D. Pearson, Norbert Peshu, Aung Pyae Phyo, Chris V. Plowe, Ric N. Price, Sasithon Pukrittayakamee, Milijaona Randrianarivelojosia, Julian C. Rayner, Pascal Ringwald, Kirk A. Rockett, Katherine Rowlands, Lastenia Ruiz, David Saunders, Alex Shayo, Peter Siba, Victoria J. Simpson, Jim Stalker, Xin zhuan Su, Colin Sutherland, Shannon Takala-Harrison, Livingstone Tavul, Vandana Thathy, Antoinette Tshefu, Federica Verra, Joseph Vinetz, Thomas E. Wellems, Jason Wendler, Nicholas J. White, Ian Wright, William Yavo, Htut Ye

West African Center for Cell Biology of Infectious Pathogens

Université Cheikh Anta Diop de Dakar
Wellcome Sanger Institute
Nuffield Department of Medicine
London School of Hygiene & Tropical Medicine
US Department of Health and Human Services
University for Development Studies Ghana
United States Army
Southwest Foundation for Biomedical Research
Université d'Antananarivo
University of Buea
Mahidol-Oxford Tropical Medicine Research Unit
Charles Darwin University
Institut National de Recherche en Santé Publique
National Institute for Medical Research Tanzania
University of Antwerp
Deakin University
Burnet Institute
Walter and Eliza Hall Institute of Medical Research
Wellcome Trust Research Laboratories Nairobi
Université Paris Descartes
University of Oxford
University of Tübingen
Radboud University Nijmegen Medical Centre
New York University
University of Cambridge
Mahidol University
Université Montpellier
Liverpool School of Tropical Medicine
Malawi-Liverpool-Wellcome Trust Clinical Research Programme
University of Science
Centro Internacional de Entrenamiento e Investigaciones Médicas - CIDEIM
Universidad ICESI
Biotech Laboratories
Addis Ababa University
National Institute of Health
Dev Care Foundation
Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS)
Universidad Peruana Cayetano Heredia
University of Ghana
Cambridge University Hospitals NHS Foundation Trust
Purdue University
Ministry of Health, Ghana
East African Consortium for Clinical Research (EACCR)
University of Georgia
Walter Reed Army Institute of Research
UFR Biosciences Université de Cocody
University of Public Health
Medical Care Development International
Institut National de Santé Publique
Bernhard Nocht Insitute for Tropical Medicine
Kwame Nkrumah University of Science and Technology
African Academy of Sciences
Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU)
Ministry of Health Laos
University of Nairobi
University of Ilorin
Monash University
Universitat de Barcelona
MARIB - Malaria Research Initiative Bandarban
Shoklo Malaria Research Unit
Eijkman Institute for Molecular Biology
King Fahd University of Petroleum and Minerals
KEMRI - Centres for Disease Control and Prevention (CDC) Research Program
Université de Kinshasa
Health Sciences Research Institute (IRSS)
Nigerian Institute of Medical Research
University of Lagos
University of Maryland School of Medicine
Institut Pasteur de Madagascar
Universités d'Antananarivo et de Mahajanga
World Health Organization
Universidad Nacional de la Amazonia Peruana
Nelson Mandela Africa Institution of Science and Technology
Papua New Guinea Institute of Medical Research
University of Maryland, Baltimore
Columbia University Medical Center
University of Rome La Sapienza
Yale University
Malaria Research and Control Center of the National Institute of Public Health
Department of Medical Research

Research output: Contribution to journal › Article › peer-review

39 Citations (Scopus)

Abstract

MalariaGEN is a data-sharing network that enables groups around the world to work together on the genomic epidemiology of malaria. Here we describe a new release of curated genome variation data on 7,000 Plasmodium falciparum samples from MalariaGEN partner studies in 28 malaria-endemic countries. High-quality genotype calls on 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using a standardised analysis pipeline. Copy number variants associated with drug resistance and structural variants that cause failure of rapid diagnostic tests were also analysed. Almost all samples showed genetic evidence of resistance to at least one antimalarial drug, and some samples from Southeast Asia carried markers of resistance to six commonly-used drugs. Genes expressed during the mosquito stage of the parasite life-cycle are prominent among loci that show strong geographic differentiation. By continuing to enlarge this open data resource we aim to facilitate research into the evolutionary processes affecting malaria control and to accelerate development of the surveillance toolkit required for malaria elimination.

Original language	English
Pages (from-to)	1-31
Number of pages	31
Journal	Wellcome Open Research
Volume	6
DOIs	https://doi.org/10.12688/wellcomeopenres.16168.2
Publication status	Published - 2021

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

data resource
drug resistance
evolution
genomic epidemiology
genomics
malaria
plasmodium falciparum
population genetics
rapid diagnostic test failure

Access to Document

10.12688/wellcomeopenres.16168.2

Cite this

Gen, M., Ahouidi, A., Ali, M., Almagro-Garcia, J., Amambua-Ngwa, A., Amaratunga, C., Amato, R., Amenga-Etego, L., Andagalu, B., Anderson, T. J. C., Andrianaranjaka, V., Apinjoh, T., Ariani, C., Ashley, E. A., Auburn, S., Awandare, G. A., Ba, H., Baraka, V., Barry, A. E., ... Ye, H. (2021). An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples. Wellcome Open Research, 6, 1-31. https://doi.org/10.12688/wellcomeopenres.16168.2

@article{fd454ce5a3f041ee83a10bced066d872,

title = "An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples",

abstract = "MalariaGEN is a data-sharing network that enables groups around the world to work together on the genomic epidemiology of malaria. Here we describe a new release of curated genome variation data on 7,000 Plasmodium falciparum samples from MalariaGEN partner studies in 28 malaria-endemic countries. High-quality genotype calls on 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using a standardised analysis pipeline. Copy number variants associated with drug resistance and structural variants that cause failure of rapid diagnostic tests were also analysed. Almost all samples showed genetic evidence of resistance to at least one antimalarial drug, and some samples from Southeast Asia carried markers of resistance to six commonly-used drugs. Genes expressed during the mosquito stage of the parasite life-cycle are prominent among loci that show strong geographic differentiation. By continuing to enlarge this open data resource we aim to facilitate research into the evolutionary processes affecting malaria control and to accelerate development of the surveillance toolkit required for malaria elimination.",

keywords = "data resource, drug resistance, evolution, genomic epidemiology, genomics, malaria, plasmodium falciparum, population genetics, rapid diagnostic test failure",

author = "Malaria Gen and Ambroise Ahouidi and Mozam Ali and Jacob Almagro-Garcia and Alfred Amambua-Ngwa and Chanaki Amaratunga and Roberto Amato and Lucas Amenga-Etego and Ben Andagalu and Anderson, \{Tim J.C.\} and Voahangy Andrianaranjaka and Tobias Apinjoh and Cristina Ariani and Ashley, \{Elizabeth A.\} and Sarah Auburn and Awandare, \{Gordon A.\} and Hampate Ba and Vito Baraka and Barry, \{Alyssa E.\} and Philip Bejon and Bertin, \{Gwladys I.\} and Boni, \{Maciej F.\} and Steffen Borrmann and Teun Bousema and Oralee Branch and Bull, \{Peter C.\} and Busby, \{George B.J.\} and Thanat Chookajorn and Kesinee Chotivanich and Antoine Claessens and David Conway and Alister Craig and Umberto D'Alessandro and Souleymane Dama and Day, \{Nicholas PJ\} and Brigitte Denis and Mahamadou Diakite and Abdoulaye Djimd{\'e} and Christiane Dolecek and Dondorp, \{Arjen M.\} and Chris Drakeley and Eleanor Drury and Patrick Duffy and Echeverry, \{Diego F.\} and Egwang, \{Thomas G.\} and Berhanu Erko and Fairhurst, \{Rick M.\} and Abdul Faiz and Fanello, \{Caterina A.\} and Fukuda, \{Mark M.\} and Dionicia Gamboa and Anita Ghansah and Lemu Golassa and Sonia Goncalves and Hamilton, \{William L.\} and Harrison, \{G. L.Abby\} and Lee Hart and Christa Henrichs and Hien, \{Tran Tinh\} and Hill, \{Catherine A.\} and Abraham Hodgson and Christina Hubbart and Mallika Imwong and Ishengoma, \{Deus S.\} and Jackson, \{Scott A.\} and Jacob, \{Chris G.\} and Ben Jeffery and Jeffreys, \{Anna E.\} and Johnson, \{Kimberly J.\} and Dushyanth Jyothi and Claire Kamaliddin and Edwin Kamau and Mihir Kekre and Krzysztof Kluczynski and Theerarat Kochakarn and Abibatou Konat{\'e} and Kwiatkowski, \{Dominic P.\} and Kyaw, \{Myat Phone\} and Pharath Lim and Chanthap Lon and Loua, \{Kovana M.\} and Oumou Ma{\"i}ga-Ascofar{\'e} and Cinzia Malangone and Magnus Manske and Jutta Marfurt and Kevin Marsh and Mayfong Mayxay and Alistair Miles and Olivo Miotto and Victor Mobegi and Mokuolu, \{Olugbenga A.\} and Jacqui Montgomery and Ivo Mueller and Newton, \{Paul N.\} and Thuy Nguyen and Nguyen, \{Thuy Nhien\} and Harald Noedl and Fran{\c c}ois Nosten and Rintis Noviyanti and Alexis Nzila and Ochola-Oyier, \{Lynette I.\} and Harold Ocholla and Abraham Oduro and Irene Omedo and Onyamboko, \{Marie A.\} and Ouedraogo, \{Jean Bosco\} and Kolapo Oyebola and Pearson, \{Richard D.\} and Norbert Peshu and Phyo, \{Aung Pyae\} and Plowe, \{Chris V.\} and Price, \{Ric N.\} and Sasithon Pukrittayakamee and Milijaona Randrianarivelojosia and Rayner, \{Julian C.\} and Pascal Ringwald and Rockett, \{Kirk A.\} and Katherine Rowlands and Lastenia Ruiz and David Saunders and Alex Shayo and Peter Siba and Simpson, \{Victoria J.\} and Jim Stalker and Su, \{Xin zhuan\} and Colin Sutherland and Shannon Takala-Harrison and Livingstone Tavul and Vandana Thathy and Antoinette Tshefu and Federica Verra and Joseph Vinetz and Wellems, \{Thomas E.\} and Jason Wendler and White, \{Nicholas J.\} and Ian Wright and William Yavo and Htut Ye",

note = "Publisher Copyright: {\textcopyright} 2021. MalariaGEN et al.",

year = "2021",

doi = "10.12688/wellcomeopenres.16168.2",

language = "English",

volume = "6",

pages = "1--31",

journal = "Wellcome Open Research",

issn = "2398-502X",

publisher = "F1000 Research Ltd",

}

Gen, M, Ahouidi, A, Ali, M, Almagro-Garcia, J, Amambua-Ngwa, A, Amaratunga, C, Amato, R, Amenga-Etego, L, Andagalu, B, Anderson, TJC, Andrianaranjaka, V, Apinjoh, T, Ariani, C, Ashley, EA, Auburn, S, Awandare, GA, Ba, H, Baraka, V, Barry, AE, Bejon, P, Bertin, GI, Boni, MF, Borrmann, S, Bousema, T, Branch, O, Bull, PC, Busby, GBJ, Chookajorn, T, Chotivanich, K, Claessens, A, Conway, D, Craig, A, D'Alessandro, U, Dama, S, Day, NPJ, Denis, B, Diakite, M, Djimdé, A, Dolecek, C, Dondorp, AM, Drakeley, C, Drury, E, Duffy, P, Echeverry, DF, Egwang, TG, Erko, B, Fairhurst, RM, Faiz, A, Fanello, CA, Fukuda, MM, Gamboa, D, Ghansah, A, Golassa, L, Goncalves, S, Hamilton, WL, Harrison, GLA, Hart, L, Henrichs, C, Hien, TT, Hill, CA, Hodgson, A, Hubbart, C, Imwong, M, Ishengoma, DS, Jackson, SA, Jacob, CG, Jeffery, B, Jeffreys, AE, Johnson, KJ, Jyothi, D, Kamaliddin, C, Kamau, E, Kekre, M, Kluczynski, K, Kochakarn, T, Konaté, A, Kwiatkowski, DP, Kyaw, MP, Lim, P, Lon, C, Loua, KM, Maïga-Ascofaré, O, Malangone, C, Manske, M, Marfurt, J, Marsh, K, Mayxay, M, Miles, A, Miotto, O, Mobegi, V, Mokuolu, OA, Montgomery, J, Mueller, I, Newton, PN, Nguyen, T, Nguyen, TN, Noedl, H, Nosten, F, Noviyanti, R, Nzila, A, Ochola-Oyier, LI, Ocholla, H, Oduro, A, Omedo, I, Onyamboko, MA, Ouedraogo, JB, Oyebola, K, Pearson, RD, Peshu, N, Phyo, AP, Plowe, CV, Price, RN, Pukrittayakamee, S, Randrianarivelojosia, M, Rayner, JC, Ringwald, P, Rockett, KA, Rowlands, K, Ruiz, L, Saunders, D, Shayo, A, Siba, P, Simpson, VJ, Stalker, J, Su, XZ, Sutherland, C, Takala-Harrison, S, Tavul, L, Thathy, V, Tshefu, A, Verra, F, Vinetz, J, Wellems, TE, Wendler, J, White, NJ, Wright, I, Yavo, W & Ye, H 2021, 'An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples', Wellcome Open Research, vol. 6, pp. 1-31. https://doi.org/10.12688/wellcomeopenres.16168.2

TY - JOUR

T1 - An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples

AU - Gen, Malaria

AU - Ahouidi, Ambroise

AU - Ali, Mozam

AU - Almagro-Garcia, Jacob

AU - Amambua-Ngwa, Alfred

AU - Amaratunga, Chanaki

AU - Amato, Roberto

AU - Amenga-Etego, Lucas

AU - Andagalu, Ben

AU - Anderson, Tim J.C.

AU - Andrianaranjaka, Voahangy

AU - Apinjoh, Tobias

AU - Ariani, Cristina

AU - Ashley, Elizabeth A.

AU - Auburn, Sarah

AU - Awandare, Gordon A.

AU - Ba, Hampate

AU - Baraka, Vito

AU - Barry, Alyssa E.

AU - Bejon, Philip

AU - Bertin, Gwladys I.

AU - Boni, Maciej F.

AU - Borrmann, Steffen

AU - Bousema, Teun

AU - Branch, Oralee

AU - Bull, Peter C.

AU - Busby, George B.J.

AU - Chookajorn, Thanat

AU - Chotivanich, Kesinee

AU - Claessens, Antoine

AU - Conway, David

AU - Craig, Alister

AU - D'Alessandro, Umberto

AU - Dama, Souleymane

AU - Day, Nicholas PJ

AU - Denis, Brigitte

AU - Diakite, Mahamadou

AU - Djimdé, Abdoulaye

AU - Dolecek, Christiane

AU - Dondorp, Arjen M.

AU - Drakeley, Chris

AU - Drury, Eleanor

AU - Duffy, Patrick

AU - Echeverry, Diego F.

AU - Egwang, Thomas G.

AU - Erko, Berhanu

AU - Fairhurst, Rick M.

AU - Faiz, Abdul

AU - Fanello, Caterina A.

AU - Fukuda, Mark M.

AU - Gamboa, Dionicia

AU - Ghansah, Anita

AU - Golassa, Lemu

AU - Goncalves, Sonia

AU - Hamilton, William L.

AU - Harrison, G. L.Abby

AU - Hart, Lee

AU - Henrichs, Christa

AU - Hien, Tran Tinh

AU - Hill, Catherine A.

AU - Hodgson, Abraham

AU - Hubbart, Christina

AU - Imwong, Mallika

AU - Ishengoma, Deus S.

AU - Jackson, Scott A.

AU - Jacob, Chris G.

AU - Jeffery, Ben

AU - Jeffreys, Anna E.

AU - Johnson, Kimberly J.

AU - Jyothi, Dushyanth

AU - Kamaliddin, Claire

AU - Kamau, Edwin

AU - Kekre, Mihir

AU - Kluczynski, Krzysztof

AU - Kochakarn, Theerarat

AU - Konaté, Abibatou

AU - Kwiatkowski, Dominic P.

AU - Kyaw, Myat Phone

AU - Lim, Pharath

AU - Lon, Chanthap

AU - Loua, Kovana M.

AU - Maïga-Ascofaré, Oumou

AU - Malangone, Cinzia

AU - Manske, Magnus

AU - Marfurt, Jutta

AU - Marsh, Kevin

AU - Mayxay, Mayfong

AU - Miles, Alistair

AU - Miotto, Olivo

AU - Mobegi, Victor

AU - Mokuolu, Olugbenga A.

AU - Montgomery, Jacqui

AU - Mueller, Ivo

AU - Newton, Paul N.

AU - Nguyen, Thuy

AU - Nguyen, Thuy Nhien

AU - Noedl, Harald

AU - Nosten, François

AU - Noviyanti, Rintis

AU - Nzila, Alexis

AU - Ochola-Oyier, Lynette I.

AU - Ocholla, Harold

AU - Oduro, Abraham

AU - Omedo, Irene

AU - Onyamboko, Marie A.

AU - Ouedraogo, Jean Bosco

AU - Oyebola, Kolapo

AU - Pearson, Richard D.

AU - Peshu, Norbert

AU - Phyo, Aung Pyae

AU - Plowe, Chris V.

AU - Price, Ric N.

AU - Pukrittayakamee, Sasithon

AU - Randrianarivelojosia, Milijaona

AU - Rayner, Julian C.

AU - Ringwald, Pascal

AU - Rockett, Kirk A.

AU - Rowlands, Katherine

AU - Ruiz, Lastenia

AU - Saunders, David

AU - Shayo, Alex

AU - Siba, Peter

AU - Simpson, Victoria J.

AU - Stalker, Jim

AU - Su, Xin zhuan

AU - Sutherland, Colin

AU - Takala-Harrison, Shannon

AU - Tavul, Livingstone

AU - Thathy, Vandana

AU - Tshefu, Antoinette

AU - Verra, Federica

AU - Vinetz, Joseph

AU - Wellems, Thomas E.

AU - Wendler, Jason

AU - White, Nicholas J.

AU - Wright, Ian

AU - Yavo, William

AU - Ye, Htut

PY - 2021

Y1 - 2021

N2 - MalariaGEN is a data-sharing network that enables groups around the world to work together on the genomic epidemiology of malaria. Here we describe a new release of curated genome variation data on 7,000 Plasmodium falciparum samples from MalariaGEN partner studies in 28 malaria-endemic countries. High-quality genotype calls on 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using a standardised analysis pipeline. Copy number variants associated with drug resistance and structural variants that cause failure of rapid diagnostic tests were also analysed. Almost all samples showed genetic evidence of resistance to at least one antimalarial drug, and some samples from Southeast Asia carried markers of resistance to six commonly-used drugs. Genes expressed during the mosquito stage of the parasite life-cycle are prominent among loci that show strong geographic differentiation. By continuing to enlarge this open data resource we aim to facilitate research into the evolutionary processes affecting malaria control and to accelerate development of the surveillance toolkit required for malaria elimination.

AB - MalariaGEN is a data-sharing network that enables groups around the world to work together on the genomic epidemiology of malaria. Here we describe a new release of curated genome variation data on 7,000 Plasmodium falciparum samples from MalariaGEN partner studies in 28 malaria-endemic countries. High-quality genotype calls on 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using a standardised analysis pipeline. Copy number variants associated with drug resistance and structural variants that cause failure of rapid diagnostic tests were also analysed. Almost all samples showed genetic evidence of resistance to at least one antimalarial drug, and some samples from Southeast Asia carried markers of resistance to six commonly-used drugs. Genes expressed during the mosquito stage of the parasite life-cycle are prominent among loci that show strong geographic differentiation. By continuing to enlarge this open data resource we aim to facilitate research into the evolutionary processes affecting malaria control and to accelerate development of the surveillance toolkit required for malaria elimination.

KW - data resource

KW - drug resistance

KW - evolution

KW - genomic epidemiology

KW - genomics

KW - malaria

KW - plasmodium falciparum

KW - population genetics

KW - rapid diagnostic test failure

UR - https://www.scopus.com/pages/publications/85113375527

U2 - 10.12688/wellcomeopenres.16168.2

DO - 10.12688/wellcomeopenres.16168.2

M3 - Article

AN - SCOPUS:85113375527

SN - 2398-502X

VL - 6

SP - 1

EP - 31

JO - Wellcome Open Research

JF - Wellcome Open Research

ER -

An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples

Abstract

UN SDGs

Keywords

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