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


Type
Article
Change log
Authors
MalariaGEN 
Adam, Ishag 
Alam, Mohammad Shafiul  ORCID logo  https://orcid.org/0000-0001-8330-5499
Alemu, Sisay 
Amaratunga, Chanaki 
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.

Description
Keywords
data resource, genomic epidemiology, genomics, malaria, plasmodium vivax
Journal Title
Wellcome Open Res
Conference Name
Journal ISSN
2398-502X
2398-502X
Volume Title
7
Publisher