An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples

MalariaGEN

doi:10.12688/wellcomeopenres.17795.1

An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples

MalariaGEN

University of Khartoum Faculty of Medicine
International Centre for Diarrhoeal Disease Research Bangladesh
Armauer Hansen Research Institute
Addis Ababa University
MilliporeSigma
National Institute of Allergy and Infectious Diseases (NIAID)
Wellcome Sanger Institute
University of Antananarivo
Menzies School of Health Research
Wellcome Trust-Mahosot Hospital-Oxford Tropical Medicine Research Collaboration
University of Oxford
Ethiopian Public Health Institute
Mahidol University
QIMR Berghofer Medical Research Institute
Walter and Eliza Hall Institute of Medical Research
Deakin University
Burnet Institute
Centro de Pesquisa em Medicina Tropical de Rondônia
Jiangsu Institute of Parasitic Diseases
Nanjing Medical University
Oxford University Clinical Research Unit
Faculty of Tropical Medicine, Mahidol University
Universidad Del Valle
Research Institute for Tropical Medicine
National Institute of Health
Dev Care Foundation
Centro de Investigaciones Clinicas S.A.S de Cali
Hormozgan University of Medical Sciences
Department of Medical Research
University of Colombo
Harvard T.H. Chan School of Public Health
Fundação de Medicina Tropical Dr. Heitor Vieira Dourado
Fiocruz Amazônia
Parsons Corporation
Universidad de Antioquia
National University of Vanuatu
University of Gondar
Umphang Hospital
Eijkman Institute for Molecular Biology
Centro Internacionale de Entrenamiento e Investigaciones Medicas
Shoklo Malaria Research Unit
Nangarhar University
Institut Pasteur de Madagascar
Universités d'Antananarivo et de Mahajanga
Cambridge Institute for Medical Research
University of São Paulo
NOVA University of Lisbon
Ministry of Health
Queen Elizabeth Hospital
Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit
Universidad de Córdoba, Monteria
Jimma University

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

34 Scopus citations

Abstract

This report describes the MalariaGEN Pv4 dataset, a new release of curated genome variation data on 1,895 samples of Plasmodium vivax collected at 88 worldwide locations between 2001 and 2017. It includes 1,370 new samples contributed by MalariaGEN and VivaxGEN partner studies in addition to previously published samples from these and other sources. We provide genotype calls at over 4.5 million variable positions including over 3 million single nucleotide polymorphisms (SNPs), as well as short indels and tandem duplications. This enlarged dataset highlights major compartments of parasite population structure, with clear differentiation between Africa, Latin America, Oceania, Western Asia and different parts of Southeast Asia. Each sample has been classified for drug resistance to sulfadoxine, pyrimethamine and mefloquine based on known markers at the dhfr, dhps and mdr1 loci. The prevalence of all of these resistance markers was much higher in Southeast Asia and Oceania than elsewhere. This open resource of analysis-ready genome variation data from the MalariaGEN and VivaxGEN networks is driven by our collective goal to advance research into the complex biology of P. vivax and to accelerate genomic surveillance for malaria control and elimination.

Original language	English
Article number	136
Journal	Wellcome Open Research
Volume	7
DOIs	https://doi.org/10.12688/wellcomeopenres.17795.1
State	Published - 2022

UN SDGs

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

SDG 3 Good Health and Well-being

Keywords

Data resource
Genomic epidemiology
Genomics
Malaria
Plasmodium vivax

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10.12688/wellcomeopenres.17795.1

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@article{7b7a7e239f7c4aa79f3e2d51ac7a8428,

title = "An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples",

abstract = "This report describes the MalariaGEN Pv4 dataset, a new release of curated genome variation data on 1,895 samples of Plasmodium vivax collected at 88 worldwide locations between 2001 and 2017. It includes 1,370 new samples contributed by MalariaGEN and VivaxGEN partner studies in addition to previously published samples from these and other sources. We provide genotype calls at over 4.5 million variable positions including over 3 million single nucleotide polymorphisms (SNPs), as well as short indels and tandem duplications. This enlarged dataset highlights major compartments of parasite population structure, with clear differentiation between Africa, Latin America, Oceania, Western Asia and different parts of Southeast Asia. Each sample has been classified for drug resistance to sulfadoxine, pyrimethamine and mefloquine based on known markers at the dhfr, dhps and mdr1 loci. The prevalence of all of these resistance markers was much higher in Southeast Asia and Oceania than elsewhere. This open resource of analysis-ready genome variation data from the MalariaGEN and VivaxGEN networks is driven by our collective goal to advance research into the complex biology of P. vivax and to accelerate genomic surveillance for malaria control and elimination.",

keywords = "Data resource, Genomic epidemiology, Genomics, Malaria, Plasmodium vivax",

author = "MalariaGEN and Ishag Adam and Alam, \{Mohammad Shafiul\} and Sisay Alemu and Chanaki Amaratunga and Roberto Amato and Voahangy Andrianaranjaka and Anstey, \{Nicholas M.\} and Abraham Aseffa and Elizabeth Ashley and Ashenafi Assefa and Sarah Auburn and Barber, \{Bridget E.\} and Alyssa Barry and \{Batista Pereira\}, Dhelio and Jun Cao and Chau, \{Nguyen Hoang\} and Kesinee Chotivanich and Cindy Chu and Dondorp, \{Arjen M.\} and Eleanor Drury and Echeverry, \{Diego F.\} and Berhanu Erko and Fe Espino and Rick Fairhurst and Abdul Faiz and \{Fernanda Villegas\}, Mar{\'i}a and Qi Gao and Lemu Golassa and Sonia Goncalves and Grigg, \{Matthew J.\} and Yaghoob Hamedi and Hien, \{Tran Tinh\} and Ye Htut and Johnson, \{Kimberly J.\} and Nadira Karunaweera and Wasif Khan and Srivicha Krudsood and Kwiatkowski, \{Dominic P.\} and Marcus Lacerda and Benedikt Ley and Pharath Lim and Yaobao Liu and Alejandro Llanos-Cuentas and Chanthap Lon and Tatiana Lopera-Mesa and Jutta Marfurt and Pascal Michon and Olivo Miotto and Rezika Mohammed and Ivo Mueller",

note = "Publisher Copyright: {\textcopyright} 2022 MalariaGEN et al.",

year = "2022",

doi = "10.12688/wellcomeopenres.17795.1",

language = "Ingl{\'e}s",

volume = "7",

journal = "Wellcome Open Research",

issn = "2398-502X",

}

TY - JOUR

T1 - An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples

AU - MalariaGEN

AU - Adam, Ishag

AU - Alam, Mohammad Shafiul

AU - Alemu, Sisay

AU - Amaratunga, Chanaki

AU - Amato, Roberto

AU - Andrianaranjaka, Voahangy

AU - Anstey, Nicholas M.

AU - Aseffa, Abraham

AU - Ashley, Elizabeth

AU - Assefa, Ashenafi

AU - Auburn, Sarah

AU - Barber, Bridget E.

AU - Barry, Alyssa

AU - Batista Pereira, Dhelio

AU - Cao, Jun

AU - Chau, Nguyen Hoang

AU - Chotivanich, Kesinee

AU - Chu, Cindy

AU - Dondorp, Arjen M.

AU - Drury, Eleanor

AU - Echeverry, Diego F.

AU - Erko, Berhanu

AU - Espino, Fe

AU - Fairhurst, Rick

AU - Faiz, Abdul

AU - Fernanda Villegas, María

AU - Gao, Qi

AU - Golassa, Lemu

AU - Goncalves, Sonia

AU - Grigg, Matthew J.

AU - Hamedi, Yaghoob

AU - Hien, Tran Tinh

AU - Htut, Ye

AU - Johnson, Kimberly J.

AU - Karunaweera, Nadira

AU - Khan, Wasif

AU - Krudsood, Srivicha

AU - Kwiatkowski, Dominic P.

AU - Lacerda, Marcus

AU - Ley, Benedikt

AU - Lim, Pharath

AU - Liu, Yaobao

AU - Llanos-Cuentas, Alejandro

AU - Lon, Chanthap

AU - Lopera-Mesa, Tatiana

AU - Marfurt, Jutta

AU - Michon, Pascal

AU - Miotto, Olivo

AU - Mohammed, Rezika

AU - Mueller, Ivo

PY - 2022

Y1 - 2022

N2 - This report describes the MalariaGEN Pv4 dataset, a new release of curated genome variation data on 1,895 samples of Plasmodium vivax collected at 88 worldwide locations between 2001 and 2017. It includes 1,370 new samples contributed by MalariaGEN and VivaxGEN partner studies in addition to previously published samples from these and other sources. We provide genotype calls at over 4.5 million variable positions including over 3 million single nucleotide polymorphisms (SNPs), as well as short indels and tandem duplications. This enlarged dataset highlights major compartments of parasite population structure, with clear differentiation between Africa, Latin America, Oceania, Western Asia and different parts of Southeast Asia. Each sample has been classified for drug resistance to sulfadoxine, pyrimethamine and mefloquine based on known markers at the dhfr, dhps and mdr1 loci. The prevalence of all of these resistance markers was much higher in Southeast Asia and Oceania than elsewhere. This open resource of analysis-ready genome variation data from the MalariaGEN and VivaxGEN networks is driven by our collective goal to advance research into the complex biology of P. vivax and to accelerate genomic surveillance for malaria control and elimination.

AB - This report describes the MalariaGEN Pv4 dataset, a new release of curated genome variation data on 1,895 samples of Plasmodium vivax collected at 88 worldwide locations between 2001 and 2017. It includes 1,370 new samples contributed by MalariaGEN and VivaxGEN partner studies in addition to previously published samples from these and other sources. We provide genotype calls at over 4.5 million variable positions including over 3 million single nucleotide polymorphisms (SNPs), as well as short indels and tandem duplications. This enlarged dataset highlights major compartments of parasite population structure, with clear differentiation between Africa, Latin America, Oceania, Western Asia and different parts of Southeast Asia. Each sample has been classified for drug resistance to sulfadoxine, pyrimethamine and mefloquine based on known markers at the dhfr, dhps and mdr1 loci. The prevalence of all of these resistance markers was much higher in Southeast Asia and Oceania than elsewhere. This open resource of analysis-ready genome variation data from the MalariaGEN and VivaxGEN networks is driven by our collective goal to advance research into the complex biology of P. vivax and to accelerate genomic surveillance for malaria control and elimination.

KW - Data resource

KW - Genomic epidemiology

KW - Genomics

KW - Malaria

KW - Plasmodium vivax

UR - https://www.scopus.com/pages/publications/85131082443

U2 - 10.12688/wellcomeopenres.17795.1

DO - 10.12688/wellcomeopenres.17795.1

M3 - Artículo

AN - SCOPUS:85131082443

SN - 2398-502X

VL - 7

JO - Wellcome Open Research

JF - Wellcome Open Research

M1 - 136

ER -

An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples

Abstract

UN SDGs

Keywords

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