MPI-GWAS: a
supercomputing-aided permutation approach for genomewide association studies.
Genomics Inform 2022;
20:e14. [PMID:
35399013 PMCID:
PMC9001997 DOI:
10.5808/gi.22001]
[Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 02/10/2022] [Indexed: 11/21/2022] Open
Abstract
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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