Supercomputing enabling exhaustive statistical analysis of genome wide association study data: Preliminary results

Most published GWAS do not examine SNP interactions due to the high computational complexity of computing p-values for the interaction terms. Our aim is to utilize supercomputing resources to apply complex statistical techniques to the world's accumulating GWAS, epidemiology, survival and patho...

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Published in:2012 Annual International Conference of the IEEE Engineering in Medicine and Biology Society Vol. 2012; pp. 1258 - 1261
Main Authors: Reumann, M., Makalic, E., Goudey, B. W., Inouye, M., Bickerstaffe, A., Bui, M., Park, D. J., Kapuscinski, M. K., Schmidt, D. F., Zhou, Z., Qian, G., Zobel, J., Wagner, J., Hopper, J. L.
Format: Conference Proceeding Journal Article
Language:English
Published: United States IEEE 01.01.2012
Subjects:
Bayes Theorem
Bayesian methods
Bioinformatics
Computational Biology - methods
Computer Simulation
Genome-Wide Association Study - methods
Genomics
Humans
Monte Carlo Method
Neoplasms - genetics
Phenotype
Polymorphism, Single Nucleotide
Runtime
ISBN:1424441196, 9781424441198
ISSN:1094-687X, 1557-170X, 2694-0604, 2694-0604
Online Access:Get full text
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Summary:Most published GWAS do not examine SNP interactions due to the high computational complexity of computing p-values for the interaction terms. Our aim is to utilize supercomputing resources to apply complex statistical techniques to the world's accumulating GWAS, epidemiology, survival and pathology data to uncover more information about genetic and environmental risk, biology and aetiology. We performed the Bayesian Posterior Probability test on a pseudo data set with 500,000 single nucleotide polymorphism and 100 samples as proof of principle. We carried out strong scaling simulations on 2 to 4,096 processing cores with factor 2 increments in partition size. On two processing cores, the run time is 317h, i.e. almost two weeks, compared to less than 10 minutes on 4,096 processing cores. The speedup factor is 2,020 that is very close to the theoretical value of 2,048. This work demonstrates the feasibility of performing exhaustive higher order analysis of GWAS studies using independence testing for contingency tables. We are now in a position to employ supercomputers with hundreds of thousands of threads for higher order analysis of GWAS data using complex statistics.
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ISBN:1424441196
9781424441198
ISSN:1094-687X
1557-170X
2694-0604
2694-0604
DOI:10.1109/EMBC.2012.6346166