NDLI: An evolutionary optimization strategy using graphics processing units to efficiently investigate gene-gene interactions in genetic association studies

Content Provider	IEEE Xplore Digital Library
Author	Fontanarosa, J.B. Yang Dai
Copyright Year	2011
Description	Author affiliation: Bioinformatics Program in the Department of Bioengineering at The University of Illinois at Chicago, Chicago, IL 60607 USA (Fontanarosa, J.B.; Yang Dai)
Abstract	The analysis of gene-gene interactions related to common complex human diseases is complicated by the increasing scale of genetic association analysis. Concurrent with the advances in genetic technology that led to these large data sets, improvements have been made in parallel computing with graphics processing units (GPUs). The data-intensive nature of genetic association analysis makes this problem particularly suitable for improved computation with the powerful computing resources available in GPUs. In this study, we present a GPU-accelerated discrete optimization strategy to improve the computational efficiency of multi-locus association analysis. We implemented an adaptive evolutionary algorithm that takes advantage of linkage disequilibrium to reduce the need for exhaustive search for combinations of genetic markers. The proposed GPU algorithm was shown to have improved efficiency and equivalent power relative to the CPU version.
Starting Page	5547
Ending Page	5550
File Size	677110
Page Count	4
File Format	PDF
ISBN	9781424441211
ISSN	1557170X
e-ISBN	9781457715891
e-ISBN	9781424441228
DOI	10.1109/IEMBS.2011.6091415
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2011-08-30
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Graphics processing unit Optimization Diseases Bioinformatics Couplings Genomics
Content Type	Text
Resource Type	Article
Subject	Signal Processing Biomedical Engineering Health Informatics Computer Vision and Pattern Recognition

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4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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