Epistatic SNP network analysis (ESNA): A scalable framework for genome-wide detection of higher-order genetic interactions
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Le résumé fourni par la source
Abstract Although genome-wide association studies (GWASs) have been widely applied to investigate the genetic basis of common traits and diseases in human populations, the associated loci do not fully account for the estimated heritability. The missing heritability may be explained, in part, by epistasis or gene-gene interactions. Existing methods for detecting epistasis, however, are limited to pair-wise interactions and/or targeted genomic regions. Here, we present a novel model, termed the Epistatic SNP Network Analysis ( ESNA ), which detects higher-order epistatic interactions using genome-wide SNP data. ESNA employs a scale-free network algorithm within a parallel computing framework that identifies modules of correlated SNPs, potentially interacting variants that converge on common biological pathways, while enhancing computational efficiency. We applied ESNA to investigate epistatic interactions contributing to respiratory outcomes such as recurrent wheeze and asthma among preschool-aged children in the CHILD Cohort Study. Using genome-wide data comprising 775,569 SNPs from 1,899 children, ESNA identified 914 SNP network modules, 9 of which were significantly associated with recurrent wheeze between ages 2 and 5 years (P<5.47×10 -5 ). Furthermore, 7 of these wheeze-associated modules were also associated with asthma by age 5 years (P<5.47×10 -5 ). Pathway enrichment analysis revealed that the associated modules consist of SNPs located in genes previously implicated in asthma and related biological processes, such as cellular response to stimuli and nervous system development. Compared to existing network-based methods for epistasis, ESNA demonstrated substantial improvements in computational efficiency, reducing memory usage by 50% and processing genome-wide SNP data 48 times faster. The code implementation and documentation are available at https://github.com/ComputationalGenomicsLaboratory/ESNA .
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Le contrôle bibliographique ouvert
DOI retrouvé dans Crossref DOI retrouvé ; titre concordant.
- Titre Crossref
- Epistatic SNP network analysis (ESNA): A scalable framework for genome-wide detection of higher-order genetic interactions
- Date Crossref
- 13/05/2026
- Éditeur
- openRxiv
- Type
- posted-content
Ce recoupement confirme des métadonnées liées au DOI. Il ne confirme ni la méthode ni les conclusions de l’étude, et il ne compte pas comme une seconde source scientifique indépendante.
Où se fait cette recherche
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Queen's University Dept. of Biomedical and Molecular Sciences pays non établi dans la noticeUniversité ou école supérieure
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University of British Columbia Division of Allergy and Immunology pays non établi dans la noticeUniversité ou école supérieure
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University of Alberta Dept. of Pediatrics pays non établi dans la noticeUniversité ou école supérieure
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Manitoba Health pays non établi dans la noticeÉtablissement de santé
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Children's Hospital Research Institute of Manitoba pays non établi dans la noticeÉtablissement de santé
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University of Manitoba Dept. of Pediatrics and Child Health pays non établi dans la noticeUniversité ou école supérieure
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Hospital for Sick Children Dept. of Pediatrics pays non établi dans la noticeÉtablissement de santé
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McMaster University Dept. of Medicine pays non établi dans la noticeUniversité ou école supérieure
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School of Computing pays non établi dans la noticeUniversité ou école supérieure
Dept. of Biomedical and Molecular Sciences — Queen's University, Division of Allergy and Immunology — University of British Columbia et Dept. of Pediatrics — University of Alberta, avec 6 autres affiliations.
Une affiliation ne permet pas de déduire la nationalité d’un auteur.