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


Trimarsanto, H; Benavente, ED; Noviyanti, R; Utami, RA; Trianty, L; Pava, Z; Getachew, S; Kim, JY; Goo, YK; Wangchuck, S; Liu, Y; Gao, Q; Dowd, S; Cheng, Q; Clark, TG; Price, RN; 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). e0005465. ISSN 1935-2727 DOI: 10.1371/journal.pntd.0005465

[img]
Preview
Text - Published Version
License:

Download (2MB) | Preview

Abstract

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. 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 (IAS), 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. 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.

Item Type: Article
Faculty and Department: Faculty of Epidemiology and Population Health > Dept of Infectious Disease Epidemiology
Faculty of Infectious and Tropical Diseases > Dept of Pathogen Molecular Biology
PubMed ID: 28362818
URI: http://researchonline.lshtm.ac.uk/id/eprint/3716577

Statistics


Download activity - last 12 months
Downloads since deposit
7Downloads
19Hits
Accesses by country - last 12 months
Accesses by referrer - last 12 months
Impact and interest
Additional statistics for this record are available via IRStats2

Actions (login required)

Edit Item Edit Item