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.
© 2012 S. Karger AG, Basel
- Genome-wide interaction analysis
- Computational biology
- Graphics processing units
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Statistical Genetics Group, Max Planck Institute of Psychiatry
DE–80804 Munich (Germany)
Tel. +49 893 062 2246, E-Mail firstname.lastname@example.org
Tony Kam-Thong and Chloé-Agathe Azencott are equal first authors. Bertram Müller-Myhsok and Karsten M. Borgwardt are equal last authors.
Received: January 14, 2012
Accepted after revision: July 13, 2012
Published online: September 4, 2012
Number of Print Pages : 17
Number of Figures : 8, Number of Tables : 13, Number of References : 46
Human Heredity (International Journal of Human and Medical Genetics)
Vol. 73, No. 4, Year 2012 (Cover Date: September 2012)
Journal Editor: Devoto M. (Philadelphia, Pa./Rome)
ISSN: 0001-5652 (Print), eISSN: 1423-0062 (Online)
For additional information: http://www.karger.com/HHE
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