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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    Plasmodium vivax
    Population Genetics
    Microsatellite Repeats
    Alleles
    Population
    Information Dissemination
    Linkage Disequilibrium
    Capillary Electrophoresis
    Software
    Datasets

    Cite this

    Trimarsanto, Hidayat ; Benavente, Ernest D. ; Noviyanti, Rintis ; Utami, Retno Ayu Setya ; Trianty, Leily ; Pava, Zuleima ; Getachew, Sisay ; Kim, Jung-Yeon ; Goo, Youn-Kyoung ; Wangchuck, Sonam ; Liu, Yaobao ; Gao, Qi ; Dowd, Simone ; Cheng, Qin ; Clark, Taane G. ; Price, Ric N. ; Auburn, Sarah. / VivaxGEN : An open access platform for comparative analysis of short tandem repeat genotyping data in Plasmodium vivax Populations. In: PLoS Neglected Tropical Diseases. 2017 ; Vol. 11, No. 3. pp. 1-12.
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    title = "VivaxGEN: An open access platform for comparative analysis of short tandem repeat genotyping data in Plasmodium vivax Populations",
    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.",
    author = "Hidayat Trimarsanto and Benavente, {Ernest D.} and Rintis Noviyanti and Utami, {Retno Ayu Setya} and Leily Trianty and Zuleima Pava and Sisay Getachew and Jung-Yeon Kim and Youn-Kyoung Goo and Sonam Wangchuck and Yaobao Liu and Qi Gao and Simone Dowd and Qin Cheng and Clark, {Taane G.} and Price, {Ric N.} and Sarah Auburn",
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    language = "English",
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    Trimarsanto, H, Benavente, ED, Noviyanti, R, Utami, RAS, Trianty, L, Pava, Z, Getachew, S, Kim, J-Y, Goo, Y-K, 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, vol. 11, no. 3, e0005465, pp. 1-12. https://doi.org/10.1371/journal.pntd.0005465

    VivaxGEN : An open access platform for comparative analysis of short tandem repeat genotyping data in Plasmodium vivax Populations. / Trimarsanto, Hidayat; Benavente, Ernest D.; Noviyanti, Rintis; Utami, Retno Ayu Setya; Trianty, Leily; Pava, Zuleima; Getachew, Sisay; Kim, Jung-Yeon; Goo, Youn-Kyoung; Wangchuck, Sonam; Liu, Yaobao; Gao, Qi; Dowd, Simone; Cheng, Qin; Clark, Taane G.; Price, Ric N.; Auburn, Sarah.

    In: PLoS Neglected Tropical Diseases, Vol. 11, No. 3, e0005465, 31.03.2017, p. 1-12.

    Research output: Contribution to journalArticleResearchpeer-review

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    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

    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.

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