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25 May 2020 : Clinical Research  

Functional Annotations of Single-Nucleotide Polymorphism (SNP)-Based and Gene-Based Genome-Wide Association Studies Show Genes Affecting Keratitis Susceptibility

Yue Xu1BCDEF, Xiao-Lin Yang2BCDEF, Xiao-Long Yang1BCD, Ya-Ru Ren1BC, Xin-Yu Zhuang1BC, Lei Zhang2ADE*, Xiao-Feng Zhang1ADE

DOI: 10.12659/MSM.922710

Med Sci Monit 2020; 26:e922710

Abstract

BACKGROUND: Keratitis is a complex condition in humans and is the second most common cause of legal blindness worldwide.

MATERIAL AND METHODS: To reveal the genomic loci underlying keratitis, we performed functional annotations of SNP-based and gene-based genome-wide association studies of keratitis in the UK Biobank (UKB) cohort with 337 199 subjects of European ancestry.

RESULTS: The publicly available SNP-based association results showed a total of 34 SNPs, from 14 distinct loci, associated with keratitis in the UKB. Gene-based association analysis identified 2 significant genes: IQCF3 (p=2.0×10⁻⁶) and SOD3 (p=2.0×10⁻⁶). Thirty-two candidate genes were then prioritized using information from multiple sources. The overlap of IQCF3 in these 2 analyses resulted in a total of 33 hub genes. Functional annotation of hub genes was performed and transcriptional factors of IQCF3 and SOD3 were predicted.

CONCLUSIONS: A total of 34 SNPs from 14 distinct loci were identified as being associated with keratitis, and 32 candidate genes were then prioritized. In addition, IQCF3 and SOD3 were identified by their p values through gene-based tests on the basis of individual SNP-based tests. The functional relationship between these suspect genes and keratitis suggest that IQCF3 and SOD3 are candidate genes underlying keratitis.

Keywords: Genes, vif, Genome-Wide Association Study, Keratitis, Polymorphism, Single Nucleotide, Superoxide Dismutase, Adaptor Proteins, Signal Transducing, Biological Specimen Banks, Cohort Studies, Disease Susceptibility, Genetic Predisposition to Disease, genetic testing, Genomics, Whites

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Medical Science Monitor eISSN: 1643-3750
Medical Science Monitor eISSN: 1643-3750