GPU-accelerated exhaustive search for third-order epistatic interactions in case–control studies
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GPU-accelerated exhaustive search for third-order epistatic interactions in case–control studiesDate
2015Citation
Jorge González-Domínguez, Bertil Schmidt, GPU-accelerated exhaustive search for third-order epistatic interactions in case–control studies, Journal of Computational Science, Volume 8, 2015, Pages 93-100, ISSN 1877-7503, https://doi.org/10.1016/j.jocs.2015.04.001.
Abstract
[Abstract] Interest in discovering combinations of genetic markers from case–control studies, such as Genome Wide Association Studies (GWAS), that are strongly associated to diseases has increased in recent years. Detecting epistasis, i.e. interactions among k markers (k ≥ 2), is an important but time consuming operation since statistical computations have to be performed for each k-tuple of measured markers. Efficient exhaustive methods have been proposed for k = 2, but exhaustive third-order analyses are thought to be impractical due to the cubic number of triples to be computed. Thus, most previous approaches apply heuristics to accelerate the analysis by discarding certain triples in advance. Unfortunately, these tools can fail to detect interesting interactions. We present GPU3SNP, a fast GPU-accelerated tool to exhaustively search for interactions among all marker-triples of a given case–control dataset. Our tool is able to analyze an input dataset with tens of thousands of markers in reasonable time thanks to two efficient CUDA kernels and efficient workload distribution techniques. For instance, a dataset consisting of 50,000 markers measured from 1000 individuals can be analyzed in less than 22 h on a single compute node with 4 NVIDIA GTX Titan boards. Source code is available at: http://sourceforge.net/projects/gpu3snp/.
Keywords
GPU
CUDA
Epistasis
GWAS
Mutual information
CUDA
Epistasis
GWAS
Mutual information
Description
This is a post-peer-review, pre-copyedit version of an article published in Journal of Computational Science. The final authenticated version is available online at: https://doi.org/10.1016/j.jocs.2015.04.001
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Atribución-NoComercial-SinDerivadas 3.0 España
ISSN
1877-7503
1877-7511
1877-7511