Cloud4SNP: Distributed Analysis of SNP Microarray Data on the Cloud

Authors:
Giuseppe Agapito;Mario Cannataro;Pietro Hiram Guzzi;Fabrizio Marozzo;Domenico Talia;Paolo Trunfio
Affiliations:
DSMC, University of Catanzaro, Italy;DSMC, University of Catanzaro, ICAR-CNR, Italy;DSMC, University of Catanzaro, Italy;DIMES, University of Calabria, Italy;DIMES, University of Calabria, ICAR-CNR, Italy;DIMES, University of Calabria, Italy
Venue:
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
Year:
2013

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Abstract

Pharmacogenomics studies the impact of genetic variation of patients on drug responses and searches for correlations between gene expression or Single Nucleotide Polymorphisms (SNPs) of patient's genome and the toxicity or efficacy of a drug. SNPs data, produced by microarray platforms, need to be preprocessed and analyzed in order to find correlation between the presence/absence of SNPs and the toxicity or efficacy of a drug. Due to the large number of samples and the high resolution of instruments, the data to be analyzed can be very huge, requiring high performance computing. The paper presents the design and experimentation of Cloud4SNP, a novel Cloud-based bioinformatics tool for the parallel preprocessing and statistical analysis of pharmacogenomics SNP microarray data. Experimental evaluation shows good speed-up and scalability. Moreover, the availability on the Cloud platform allows to face in an elastic way the requirements of small as well as very large pharmacogenomics studies.