title: GLIDE: GPU-based linear regression for detection of epistasis.
abstract: Due to recent advances in genotyping technologies, mapping phenotypes to single loci in the genome has become a standard technique in statistical genetics. However, one-locus mapping fails to explain much of the phenotypic variance in complex traits. Here, we present GLIDE, which maps phenotypes to pairs of genetic loci and systematically searches for the epistatic interactions expected to reveal part of this missing heritability. GLIDE makes use of the computational power of consumer-grade graphics cards to detect such interactions via linear regression. This enabled us to conduct a systematic two-locus mapping study on seven disease data sets from the Wellcome Trust Case Control Consortium and on in-house hippocampal volume data in 6 h per data set, while current single CPU-based approaches require more than a year's time to complete the same task.
authors.affiliation: Machine Learning and Computational Biology Research Group, Max Planck Institutes Tübingen,  Tübingen, Germany.
authors.forename: Tony
authors.initials: T
authors.lastname: Kam-Thong
authors.forename: Chloé-Agathe
authors.initials: CA
authors.lastname: Azencott
authors.forename: Lawrence
authors.initials: L
authors.lastname: Cayton
authors.forename: Benno
authors.initials: B
authors.lastname: Pütz
authors.forename: André
authors.initials: A
authors.lastname: Altmann
authors.forename: Nazanin
authors.initials: N
authors.lastname: Karbalai
authors.forename: Philipp G
authors.initials: PG
authors.lastname: Sämann
authors.forename: Bernhard
authors.initials: B
authors.lastname: Schölkopf
authors.forename: Bertram
authors.initials: B
authors.lastname: Müller-Myhsok
authors.forename: Karsten M
authors.initials: KM
authors.lastname: Borgwardt
mesh_terms: D001714:Bipolar Disorder / Q000175:diagnosis / Q000453:epidemiology / Q000235:genetics; D002874:Chromosome Mapping / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D016208:Databases, Factual; D004843:Epistasis, Genetic; D056426:Genetic Loci; D020022:Genetic Predisposition to Disease; D005828:Genetics, Population / Q000379:methods; D055106:Genome-Wide Association Study; D006624:Hippocampus / Q000033:anatomy & histology; D006801:Humans; D016014:Linear Models; D009929:Organ Size; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D013997:Time Factors