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GnpAsso

GnpAsso is an ANR public-private bioinformatics research project, The goal is to develop a complete workbench to manage and explore GWAS (Genome Wide Association Studies) data. This work is done in collaboration with scientists and breeders working on several species (wheat, maize, tomato, pea, grapevine). These experts in genetic associations will express user needs, submit data and test the software tools. New scientists working on other plant species have joined the network. GnpIS-Asso relies on GnpIS URGI informatics system set up in 2003 and improved regularly through various fundings (ANR, INRA, FP7), last reference: D. Steinbach & al. Database, Vol. 2013, Article ID bat058, doi:10.1093/database/bat058. GnpAsso project benefits from INRA URGI platform facities, teams and expertise in software development.

Duration: 01/02/2011 to 28/02/2015

Coordinator: Delphine Steinbach

Laboratories / Institutions :

  • INRA URGI Versailles (Bioinformatics) : Delphine Steinbach (project coordinator), Célia Michotey (CDD hired : software engineer, Raphael Flores CDD hired replaced respectively in 2013 by Guillaume Merceron and Btissam Aissaoui), 72 months hired in total
  • UMR INRA Génétique végétale du Moulon (Bioinformatics, Maize user needs and expertise in GA) : Yannick De Oliveira, Stephane Nicolas, Alain Charcosset, Guy-Ross Ella (CDD hired 6 months)
  • UMR INRA URLEG Dijon (Pea user needs and expertise in GA) : Catherine Delaitre, Mathieu Signol
  • UMR AGAP INRA TGU Montpellier (Bioinformatics, Grape user needs and expertise in GA) : Patrice This
  • IRD RPB Montpellier (Bioinformatics, Coffee user needs) : Alexis Dereeper, Philippe Lashermes, Felix Homa (CDD hired 6 months)

Companies:

  • Biogemma Clermont-Ferrand (Bioinformatics, Maize user needs and expertise in GA) : Frédéric Sapet, Pierre Dubreuil, Clément Buet, Nathalie Rivière

External Collaborators : 

  • INRA GDEC Clermont-Ferrand (Wheat user needs and expertise in GA) : Jacques Legouis
  • INRA GAFL Avignon (Tomato user needs and expertise in GA) : Mathilde Causse, Christopher Sauvage
  • INRA Orléans (Poplar expertise in GA) : Vincent Segura

Deliverables :

  • a complete workbench to manage genetic association studies involving:
    • GnpIS-Asso for data storage and data mining
    • Sniplay for GWAS analysis
    • ThaliaDb for data managed at lab level (before for example submission to GnpIS).
  • It can be used using the 3 components together or not according to needs
  • Several software releases:  3 per year for GnpIS-Asso, with at least one training event per year organized to train users and to get feedbacks for improvement

For information on the project and interest in collaboration please contact: Delphine.Steinbach at versailles.inra.fr

Results in details  :

  • GnpIS-Asso, a new tool to manage genetic association results 
    • a database schema
    • a new query form, available from GnpIS global information system : to explore GWAS data by setting several filters (markers, genetic resources, traits..), that allows the generation of dynamic plots (manhattan plot, QQPlot, BoxPlot), that allows to explore data in files to facilitate their use in external analysis tools and that bridges genetic and genomic data to see associations on genome near genes and all annotations.
    • Automatic software (home made jobs) to load the data into GnpIS based on Talend and a data submission template file to fill by scientists to submit their data to GnpIS-Asso
  • Training sessions, on site or by webinars (virtual class: e-learning on INRA platform)
  • improvement of Sniplay tool to do GWAS analysis and to be compliant with GnpIS-GWAS to store the results
  • improvement of ThaliaDB tool to be compliant with GnpIS-GWAS and Sniplay

What is Sniplay ?

  • Sniplay is an existing tool, developed by Partner INRA AGAP. It is a web-based pipeline and database for SNP analysis and management. It is under GPL License.
  • Results :
    • Sniplay was improved to manage i) short reads processing, ii) to add population stratification analysis and to iii) add specific functionalities for genetic association studies analysis.
    • the Sniplay GWAS analysis workflow is also integrated in Southgreen Galaxy server and available in the Galaxy toolshed: See: the new paper on Sniplay compiling all developments made on this tool independately from funding, that will be in NAR Web Server Issue 2015: Alexis Dereeper et al

What is ThaliaDb ?

  • ThaliaDb is an existing database developped by partner at INRA Moulon.
  • Results : ThaliaDB was improved to generate automatically data in format compliant to Sniplay and GnpIS-GWAS, facilitating data submission to GnpIS-Asso. A new version is planned for 2016.

Funding :

  • ANR (Research french National Agency)

References :

  • Christopher Sauvage and al. : tomato GWAS data: Plant Physiology 2014
  • Bouchet et al: maize GWAS data : PlosOne 2013
  • All the public data of these 2 papers were submitted to GnpIS-Asso and used to show demos on tool.
  • Steinbach D et al: GnpIS Database Journal 2013
  • Steinbach D et al: GnpIS-Asso: in prep 2015

Communication:

  • GnpIS-Asso was presented at Plant and Animal meeting in San Diego in January 2015 : software demo and poster
  • GnpIS-Asso was presented at Jobim french bioinformatics conference in July 2015: software demo and poster
  • ThaliaDB: was presented at Jobim french bioinformatics conference in July 2015: poster and at ECCB 2014

Perspectives: After the end of the project

  • The tool GnpIS-Asso is used for the data management of GWAS data of these investment for the future national projects: 
    • BreedWheat project (Wheat species)
    • Amaizing project (Maize), 
    • Aker project (sugarbeet)
    • PeaMUST (pea)
    • RapsoDyn (rapeseed)
  • Software improvements for dealing with genomic selection data was done in the frame of a new project coordinated by D. Steinbach (INRA Metaprogramme SELGEN 2014). Data are in prep in lab and will be made available.
  • New developments are currently planned to continue the development of GnpIS-Asso tool in the following months. User needs are coming from the investment for the future projects that are currently using the tool. 
  • GnpIS-Asso software can also be transfer to labs or compagnies that want to use it for their own use. It is under license conditions. Please contact D. Steinbach for information. The tool is for example today installed in Biogemma and in Florimont Desprez compagnies.
  • GnpIS-Asso code is included into GnpIS software and a global deposit is done to the APP (Agence de protection des programmes).

Update: 29 May 2016
Creation date: 02 Nov 2011