title: High-Performance Mixed Models Based Genome-Wide Association Analysis with omicABEL software.
abstract: To raise the power of genome-wide association studies (GWAS) and avoid false-positive results in structured populations, one can rely on mixed model based tests. When large samples are used, and when multiple traits are to be studied in the 'omics' context, this approach becomes computationally challenging. Here we consider the problem of mixed-model based GWAS for arbitrary number of traits, and demonstrate that for the analysis of single-trait and multiple-trait scenarios different computational algorithms are optimal. We implement these optimal algorithms in a high-performance computing framework that uses state-of-the-art linear algebra kernels, incorporates optimizations, and avoids redundant computations, increasing throughput while reducing memory usage and energy consumption. We show that, compared to existing libraries, our algorithms and software achieve considerable speed-ups. The OmicABEL software described in this manuscript is available under the GNU GPL v. 3 license as part of the GenABEL project for statistical genomics at http: //www.genabel.org/packages/OmicABEL.
authors.affiliation: Aachen Institute for Advanced Study in Computational Engineering Science, Aachen, 52062, Germany.
authors.forename: Diego
authors.initials: D
authors.lastname: Fabregat-Traver
authors.affiliation: Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, 630090, Russian Federation ; Novosibirsk State University, Novosibirsk, 630090, Russian Federation.
authors.forename: Sodbo Zh
authors.initials: SZh
authors.lastname: Sharapov
authors.affiliation: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK.
authors.forename: Caroline
authors.initials: C
authors.lastname: Hayward
authors.affiliation: Centre for Population Health Sciences, University of Edinburgh, Edinburgh, EH8 9AG, UK ; Split University, Split, 21000, Croatia.
authors.forename: Igor
authors.initials: I
authors.lastname: Rudan
authors.affiliation: Centre for Population Health Sciences, University of Edinburgh, Edinburgh, EH8 9AG, UK.
authors.forename: Harry
authors.initials: H
authors.lastname: Campbell
authors.affiliation: Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, 630090, Russian Federation ; Novosibirsk State University, Novosibirsk, 630090, Russian Federation ; Centre for Population Health Sciences, University of Edinburgh, Edinburgh, EH8 9AG, UK.
authors.forename: Yurii
authors.initials: Y
authors.lastname: Aulchenko
authors.affiliation: Aachen Institute for Advanced Study in Computational Engineering Science, Aachen, 52062, Germany.
authors.forename: Paolo
authors.initials: P
authors.lastname: Bientinesi