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

MalariaGEN

doi:10.12688/wellcomeopenres.16168.1

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

MalariaGEN

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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
Article number	42
Pages (from-to)	1-31
Number of pages	31
Journal	Wellcome Open Research
Volume	6
Issue number	42
DOIs	https://doi.org/10.12688/wellcomeopenres.16168.1
Publication status	Published - 24 Feb 2021

Bibliographical note

Publisher Copyright:
© 2021 MalariaGEN et al.

Copyright:
Copyright 2021 Elsevier B.V., All rights reserved.

UN SDGs

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

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10.12688/wellcomeopenres.16168.1

44268209-oaFinal published version, 3.78 MBLicence: CC BY

Cite this

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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 = "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 Gordon Awandare and Hampate Ba and Vito Baraka and Barry, {Alyssa E.} and Philip Bejon and Bertin, {Gwladys I.} and Boni, {Maciej F.} and MalariaGEN 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 P.J.} 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 Nguyen, {Thuy Nhien} and Nguyen, {Thuy Nhien} and Harald Noedl and Francois 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",

year = "2021",

month = feb,

day = "24",

doi = "10.12688/wellcomeopenres.16168.1",

language = "English",

volume = "6",

pages = "1--31",

journal = "Wellcome Open Research",

issn = "2398-502X",

publisher = "F1000 Research Ltd.",

number = "42",

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TY - JOUR

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

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

AU - Ba, Hampate

AU - Baraka, Vito

AU - Barry, Alyssa E.

AU - Bejon, Philip

AU - Bertin, Gwladys I.

AU - Boni, Maciej F.

AU - MalariaGEN

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 P.J.

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 Nhien

AU - Noedl, Harald

AU - Nosten, Francois

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 - 2021/2/24

Y1 - 2021/2/24

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 - http://www.scopus.com/inward/record.url?scp=85103577104&partnerID=8YFLogxK

U2 - 10.12688/wellcomeopenres.16168.1

DO - 10.12688/wellcomeopenres.16168.1

M3 - Article

AN - SCOPUS:85103577104

SN - 2398-502X

VL - 6

SP - 1

EP - 31

JO - Wellcome Open Research

JF - Wellcome Open Research

IS - 42

M1 - 42

ER -

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

Abstract

Bibliographical note

UN SDGs

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