title: Identifying CpG sites associated with eczema via random forest screening of epigenome-scale DNA methylation.
abstract: BACKGROUND
  The prevalence of eczema is increasing in industrialized nations. Limited evidence has shown the association of DNA methylation (DNA-M) with eczema. We explored this association at the epigenome-scale to better understand the role of DNA-M. Data from the first generation (F1) of the Isle of Wight (IoW) birth cohort participants and the second generation (F2) were examined in our study. Epigenome-scale DNA methylation of F1 at age 18 years and F2 in cord blood was measured using the Illumina Infinium HumanMethylation450 Beadchip. A total of 307,357 cytosine-phosphate-guanine sites (CpGs) in the F1 generation were screened via recursive random forest (RF) for their potential association with eczema at age 18. Functional enrichment and pathway analysis of resulting genes were carried out using DAVID gene functional classification tool. Log-linear models were performed in F1 to corroborate the identified CpGs. Findings in F1 were further replicated in F2.
  
  
  RESULTS
  The recursive RF yielded 140 CpGs, 88 of which showed statistically significant associations with eczema at age 18, corroborated by log-linear models after controlling for false discovery rate (FDR) of 0.05. These CpGs were enriched among many biological pathways, including pathways related to creating transcriptional variety and pathways mechanistically linked to eczema such as cadherins, cell adhesion, gap junctions, tight junctions, melanogenesis, and apoptosis. In the F2 generation, about half of the 83 CpGs identified in F1 showed the same direction of association with eczema risk as in F1, of which two CpGs were significantly associated with eczema risk, cg04850479 of the PROZ gene (risk ratio (RR) = 15.1 in F1, 95 % confidence interval (CI) 1.71, 79.5; RR = 6.82 in F2, 95 % CI 1.52, 30.62) and cg01427769 of the NEU1 gene (RR = 0.13 in F1, 95 % CI 0.03, 0.46; RR = 0.09 in F2, 95 % CI 0.03, 0.36).
  
  
  CONCLUSIONS
  Via epigenome-scaled analyses using recursive RF followed by log-linear models, we identified 88 CpGs associated with eczema in F1, of which 41 were replicated in F2. Several identified CpGs are located within genes in biological pathways relating to skin barrier integrity, which is central to the pathogenesis of eczema. Novel genes associated with eczema risk were identified (e.g., the PROZ and NEU1 genes).
authors.affiliation: Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, 236A Robison Hall, Memphis, TN 38152 USA.
authors.forename: B M
authors.initials: BM
authors.lastname: Quraishi
authors.affiliation: Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, 236A Robison Hall, Memphis, TN 38152 USA.
authors.forename: H
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Department of Epidemiology, and Biostatistics, Arnold School of Public Health, University of South Carolina, 800 Sumter Street, Columbia, SC 29208 USA.
authors.forename: T M
authors.initials: TM
authors.lastname: Everson
authors.affiliation: Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, 236A Robison Hall, Memphis, TN 38152 USA.
authors.forename: M
authors.initials: M
authors.lastname: Ray
authors.affiliation: Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, SO16 6YD UK.
authors.forename: G A
authors.initials: GA
authors.lastname: Lockett
authors.affiliation: Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, SO16 6YD UK ; Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, SO16 6YD UK.
authors.forename: J W
authors.initials: JW
authors.lastname: Holloway
authors.affiliation: Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, 236A Robison Hall, Memphis, TN 38152 USA.
authors.forename: S R
authors.initials: SR
authors.lastname: Tetali
authors.affiliation: Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, SO16 6YD UK ; The David Hide Asthma and Allergy Research Centre, St Mary's Hospital, Parkhurst Road, Newport, Isle of Wight, PO30 5TG UK.
authors.forename: S H
authors.initials: SH
authors.lastname: Arshad
authors.affiliation: Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, 236A Robison Hall, Memphis, TN 38152 USA.
authors.forename: A
authors.initials: A
authors.lastname: Kaushal
authors.affiliation: Human Development and Health, Faculty of Medicine, University of Southampton, University Road, Southampton, SO17 1BJ UK.
authors.forename: F I
authors.initials: FI
authors.lastname: Rezwan
authors.affiliation: Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, 236A Robison Hall, Memphis, TN 38152 USA.
authors.forename: W
authors.initials: W
authors.lastname: Karmaus
keywords: Allergic disease; CpG; DNA methylation; Eczema; Epigenetics; Epigenome-scale; F1 and F2 generations; Random forest