VivaxGEN: An open access platform for comparative analysis of short tandem repeat genotyping data in Plasmodium vivax Populations

Hidayat Trimarsanto, Ernest D. Benavente, Rintis Noviyanti, Retno Ayu Setya Utami, Leily Trianty, Zuleima Pava, Sisay Getachew, Jung-Yeon Kim, Youn-Kyoung Goo, Sonam Wangchuck, Yaobao Liu, Qi Gao, Simone Dowd, Qin Cheng, Taane G. Clark, Ric N. Price, Sarah Auburn

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    Abstract

    Background: The control and elimination of Plasmodium vivax will require a better understanding of its transmission dynamics, through the application of genotyping and population genetics analyses. This paper describes VivaxGEN (http://vivaxgen.menzies.edu.au), a web-based platform that has been developed to support P. vivax short tandem repeat data sharing and comparative analyses. 

    Results: The VivaxGEN platform provides a repository for raw data generated by capillary electrophoresis (FSA files), with fragment analysis and standardized allele calling tools. The query system of the platform enables users to filter, select and differentiate samples and alleles based on their specified criteria. Key population genetic analyses are supported including measures of population differentiation (FST), expected heterozygosity (HE), linkage disequilibrium (IA S), neighbor-joining analysis and Principal Coordinate Analysis. Datasets can also be formatted and exported for application in commonly used population genetic software including GENEPOP, Arlequin and STRUCTURE. To date, data from 10 countries, including 5 publicly available data sets have been shared with VivaxGEN. 

    Conclusions: VivaxGEN is well placed to facilitate regional overviews of P. vivax transmission dynamics in different endemic settings and capable to be adapted for similar genetic studies of P. falciparum and other organisms.

    Original languageEnglish
    Article numbere0005465
    Pages (from-to)1-12
    Number of pages12
    JournalPLoS Neglected Tropical Diseases
    Volume11
    Issue number3
    DOIs
    Publication statusPublished - 31 Mar 2017

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    Trimarsanto, H., Benavente, E. D., Noviyanti, R., Utami, R. A. S., Trianty, L., Pava, Z., Getachew, S., Kim, J-Y., Goo, Y-K., Wangchuck, S., Liu, Y., Gao, Q., Dowd, S., Cheng, Q., Clark, T. G., Price, R. N., & Auburn, S. (2017). VivaxGEN: An open access platform for comparative analysis of short tandem repeat genotyping data in Plasmodium vivax Populations. PLoS Neglected Tropical Diseases, 11(3), 1-12. [e0005465]. https://doi.org/10.1371/journal.pntd.0005465