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KMID : 1132720220200010014
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Genomics & Informatics
2022 Volume.20 No. 1 p.14 ~ p.14
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MPI-GWAS: a supercomputing-aided permutation approach for genome-wide association studies
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Paik Hyo-Jung
Cho Yong-Seong
Cho Seong-Beom
Kwon Oh-Kyoung
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Abstract
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Permutation testing is a robust and popular approach for significance testing in genomic research that has the advantage of reducing inflated type 1 error rates; however, its computational cost is notorious in genome-wide association studies (GWAS). Here, we developed a supercomputing-aided approach to accelerate the permutation testing for GWAS, based on the message-passing interface (MPI) on parallel computing architecture. Our application, called MPI-GWAS, conducts MPI-based permutation testing using a parallel computing approach with our supercomputing system, Nurion (8,305 compute nodes, and 563,740 central processing units [CPUs]). For 107 permutations of one locus in MPI-GWAS, it was calculated in 600 s using 2,720 CPU cores. For 107 permutations of ~30,000?50,000 loci in over 7,000 subjects, the total elapsed time was ~4 days in the Nurion supercomputer. Thus, MPI-GWAS enables us to feasibly compute the permutation-based GWAS within a reason-able time by harnessing the power of parallel computing resources.
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KEYWORD
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genome-wide association study, message-passing interface, parallel computing, supercomputing
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