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          Institute: MPI für Entwicklungsbiologie     Collection: Abteilung 6 - Molecular Biology (D. Weigel)     Display Documents



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ID: 636048.0, MPI für Entwicklungsbiologie / Abteilung 6 - Molecular Biology (D. Weigel)
GLIDE: GPU-based linear regression for detection of epistasis
Authors:Kam-Thong, T.; Azencott, C. A.; Cayton, L.; Putz, B.; Altmann, A.; Karbalai, N.; Samann, P. G.; Scholkopf, B.; Muller-Myhsok, B.; Borgwardt, K. M.
Date of Publication (YYYY-MM-DD):2012
Title of Journal:Hum Hered
Volume:73
Issue / Number:4
Start Page:220
End Page:236
Review Status:not specified
Audience:Not Specified
Abstract / Description: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.
Free Keywords:Bipolar Disorder/diagnosis/epidemiology/genetics; Chromosome Mapping/*methods; Computational Biology/*methods; Databases, Factual; *Epistasis, Genetic; Genetic Loci; *Genetic Predisposition to Disease; Genetics, Population/methods; Genome-Wide Association Study; Hippocampus/anatomy & histology; Humans; Linear Models; Organ Size; Phenotype; Polymorphism, Single Nucleotide; Reproducibility of Results; Time Factors
External Publication Status:published
Document Type:Article
Affiliations:MPI für Entwicklungsbiologie/Abteilung 6 - Molekulare Biologie (Detlef Weigel)
MPI für Intelligente Systeme/Abt. Schölkopf
External Affiliations:%G eng
Identifiers:ISSN:1423-0062 (Electronic) 0001-5652 (Linking) %R 10.1... [ID No:1]
URL:http://www.ncbi.nlm.nih.gov/pubmed/22965145 [ID No:2]
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