TY - JOUR
T1 - VivaxGEN
T2 - An open access platform for comparative analysis of short tandem repeat genotyping data in Plasmodium vivax Populations
AU - Trimarsanto, Hidayat
AU - Benavente, Ernest D.
AU - Noviyanti, Rintis
AU - Utami, Retno Ayu Setya
AU - Trianty, Leily
AU - Pava, Zuleima
AU - Getachew, Sisay
AU - Kim, Jung Yeon
AU - Goo, Youn Kyoung
AU - Wangchuck, Sonam
AU - Liu, Yaobao
AU - Gao, Qi
AU - Dowd, Simone
AU - Cheng, Qin
AU - Clark, Taane G.
AU - Price, Ric N.
AU - Auburn, Sarah
N1 - Publisher Copyright:
© 2017 Trimarsanto et al.
PY - 2017/3/31
Y1 - 2017/3/31
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85016998346&partnerID=8YFLogxK
U2 - 10.1371/journal.pntd.0005465
DO - 10.1371/journal.pntd.0005465
M3 - Article
C2 - 28362818
AN - SCOPUS:85016998346
SN - 1935-2727
VL - 11
JO - PLoS Neglected Tropical Diseases
JF - PLoS Neglected Tropical Diseases
IS - 3
M1 - e0005465
ER -
