title: easyGWAS: A Cloud-Based Platform for Comparing the Results of Genome-Wide Association Studies.
abstract: The ever-growing availability of high-quality genotypes for a multitude of species has enabled researchers to explore the underlying genetic architecture of complex phenotypes at an unprecedented level of detail using genome-wide association studies (GWAS). The systematic comparison of results obtained from GWAS of different traits opens up new possibilities, including the analysis of pleiotropic effects. Other advantages that result from the integration of multiple GWAS are the ability to replicate GWAS signals and to increase statistical power to detect such signals through meta-analyses. In order to facilitate the simple comparison of GWAS results, we present easyGWAS, a powerful, species-independent online resource for computing, storing, sharing, annotating, and comparing GWAS. The easyGWAS tool supports multiple species, the uploading of private genotype data and summary statistics of existing GWAS, as well as advanced methods for comparing GWAS results across different experiments and data sets in an interactive and user-friendly interface. easyGWAS is also a public data repository for GWAS data and summary statistics and already includes published data and results from several major GWAS. We demonstrate the potential of easyGWAS with a case study of the model organismArabidopsis thaliana, using flowering and growth-related traits.
authors.affiliation: Machine Learning and Computational Biology Research Group, Max Planck Institute for Intelligent Systems and Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany dominik.grimm@bsse.ethz.ch karsten.borgwardt@bsse.ethz.ch.|Zentrum für Bioinformatik, Eberhard Karls Universität, 72074 Tübingen, Germany.|Department for Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland.|Swiss Institute of Bioinformatics, 4058 Basel, Switzerland.
authors.forename: Dominik G
authors.identifier: 0000-0003-2085-4591
authors.initials: DG
authors.lastname: Grimm
authors.affiliation: Department for Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland.|Swiss Institute of Bioinformatics, 4058 Basel, Switzerland.
authors.forename: Damian
authors.initials: D
authors.lastname: Roqueiro
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
authors.forename: Patrice A
authors.initials: PA
authors.lastname: Salomé
authors.affiliation: Machine Learning and Computational Biology Research Group, Max Planck Institute for Intelligent Systems and Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Kleeberger
authors.affiliation: Machine Learning and Computational Biology Research Group, Max Planck Institute for Intelligent Systems and Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
authors.forename: Bastian
authors.identifier: 0000-0002-9925-9623
authors.initials: B
authors.lastname: Greshake
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
authors.forename: Wangsheng
authors.initials: W
authors.lastname: Zhu
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
authors.forename: Chang
authors.identifier: 0000-0001-6363-2556
authors.initials: C
authors.lastname: Liu
authors.affiliation: Machine Learning and Computational Biology Research Group, Max Planck Institute for Intelligent Systems and Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
authors.forename: Christoph
authors.initials: C
authors.lastname: Lippert
authors.affiliation: Machine Learning and Computational Biology Research Group, Max Planck Institute for Intelligent Systems and Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
authors.forename: Oliver
authors.initials: O
authors.lastname: Stegle
authors.affiliation: Department of Empirical Inference, Max Planck Institute for Intelligent Systems, 72076 Tübingen, Germany.
authors.forename: Bernhard
authors.initials: B
authors.lastname: Schölkopf
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
authors.forename: Detlef
authors.identifier: 0000-0002-2114-7963
authors.initials: D
authors.lastname: Weigel
authors.affiliation: Machine Learning and Computational Biology Research Group, Max Planck Institute for Intelligent Systems and Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany dominik.grimm@bsse.ethz.ch karsten.borgwardt@bsse.ethz.ch.|Zentrum für Bioinformatik, Eberhard Karls Universität, 72074 Tübingen, Germany.|Department for Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland.|Swiss Institute of Bioinformatics, 4058 Basel, Switzerland.
authors.forename: Karsten M
authors.identifier: 0000-0001-7221-2393
authors.initials: KM
authors.lastname: Borgwardt
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000254:growth & development; D019295:Computational Biology / Q000379:methods*; D035264:Flowers / Q000235:genetics / Q000254:growth & development; D018745:Genome, Plant / Q000235:genetics*; D055106:Genome-Wide Association Study / Q000379:methods*; D005838:Genotype; D006801:Humans; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D012984:Software; D014584:User-Computer Interface