VivaxGEN: An open access platform for comparative analysis of short tandem repeat genotyping data in <i>Plasmodium vivax</i> populations

다국어 초록 (Multilingual Abstract)

<▼1><P><B>Background</B></P><P>The control and elimination of <I>Plasmodium vivax</I> 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 <I>P</I>. <I>vivax</I> short tandem repeat data sharing and comparative analyses.</P><P><B>Results</B></P><P>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 (<I>F</I><SUB>ST</SUB>), expected heterozygosity (<I>H</I><SUB>E</SUB>), linkage disequilibrium (<I>I</I><SUB>A</SUB><SUP>S</SUP>), neighbor-joining analysis and Principal Coordinate Analysis. Datasets can also be formatted and exported for application in commonly used population genetic software including <I>GENEPOP</I>, <I>Arlequin</I> and <I>STRUCTURE</I>. To date, data from 10 countries, including 5 publicly available data sets have been shared with VivaxGEN.</P><P><B>Conclusions</B></P><P>VivaxGEN is well placed to facilitate regional overviews of <I>P</I>. <I>vivax</I> transmission dynamics in different endemic settings and capable to be adapted for similar genetic studies of <I>P</I>. <I>falciparum</I> and other organisms.</P></▼1><▼2><P><B>Author summary</B></P><P>The <I>Plasmodium vivax</I> malaria parasite inflicts significant morbidity in endemic populations across the globe, but has been overshadowed by the more fatal <I>P</I>. <I>falciparum</I> parasite. In malaria-endemic regions outside of Africa, the declining prevalence of <I>P</I>. <I>falciparum</I> is coupled with a proportionate rise in <I>P</I>. <I>vivax</I>, reflecting the greater refractoriness of <I>P</I>. <I>vivax</I> to transmission interventions. This worrying trend emphasizes the need for a better understanding of the patterns of <I>P</I>. <I>vivax</I> transmission and spread within and across borders. Genotyping parasite population samples at short tandem repeat (STR) markers such as microsatellites informs on diversity, population structure and underlying transmission patterns. We have established vivaxGEN, an online platform providing a repository for <I>P</I>. <I>vivax</I> STR genotyping data, and tools for standard population genetic analyses. The platform currently holds publicly available data from 5 vivax-endemic countries that can be browsed on the website (http://vivaxgen.menzies.edu.au). VivaxGEN will support researchers to conduct local STR-based <I>P</I>. <I>vivax</I> studies with greater autonomy and foster collaborative studies enabling regional overviews of <I>P</I>. <I>vivax</I> diversity in different endemic settings and across borders. The system can be adapted for STR-based analyses in other microorganisms and the open access source code is provided to facilitate these developments.</P></▼2>