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High-speed exhaustive 3-locus interaction epistasis analysis on FPGAs

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URI: http://hdl.handle.net/2183/34790
DOI: 10.1016/j.jocs.2015.04.030

Publication date

2015-07

Authors

Kässens, Jan Christian
Wienbrandt, Lars
Schmidt, Bertil
Schimmler, Manfred

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Journal Title

Bibliographic citation

J. Christian Kässens, L. Wienbrandt, J. González-Domínguez, B. Schmidt, and M. Schimmler, "High-speed exhaustive 3-locus interaction epistasis analysis on FPGAs", Journal of Computational Science, Vol. 9, Pp 131-136, July 2015, doi: 10.1016/j.jocs.2015.04.030

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Academic degree

Abstract

[Abstract]: Epistasis, the interaction between genes, has become a major topic in molecular and quantitative genetics. It is believed that these interactions play a significant role in genetic variations causing complex diseases. Several algorithms have been employed to detect pairwise interactions in genome-wide association studies (GWAS) but revealing higher order interactions remains a computationally challenging task. State of the art tools are not able to perform exhaustive search for all three-locus interactions in reasonable time even for relatively small input datasets. In this paper we present how a hardware-assisted design can solve this problem and provide fast, efficient and exhaustive third-order epistasis analysis with up-to-date FPGA technology.

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Keywords

Epistasis GWAS FPGA High performance computing Gene–gene interactions Mutual information Entropy Bioinformatics

Editor version

https://doi.org/10.1016/j.jocs.2015.04.030

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©2015 Elsevier B.V. All rights reserved.

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Investigación (FIC)