A Functional Genomics Pipeline to Identify High-Value CpG Dinucleotides Related to Allergy or Asthma in the Human Methylome

DNA methylation of cytosines at CpG dinucleotides is a widespread epigenetic mark that is responsive to environmental exposures and associated with a wide range of human pathologies. However, compared to genetic variation, genome wide epigenetic variation has been relatively unexplored due to the limited representation of variable CpGs on commercial high throughput platforms. To address this gap, we developed a pipeline to identify high value asthma and allergy associated CpGs among the >28 million CpG sites in the human genome. We focused on epithelial cells: sentinels in the airway that respond to inhaled microbes, pollution and allergens and mediate their downstream effects on asthma and allergic disease risk. We combined whole genome bisulfite sequencing in these cells from children with and without allergic asthma and in silico evidence of functionality to identify high value CpGs for a custom DNA methylation array. Compared to commercial arrays, the Asthma&Allergy Custom array was enriched for CpGs with intermediate methylation levels, which are more likely to be correlated with the expression of their nearest or target genes and associated with allergic sensitization in children of diverse ancestries compared to CpGs on the commercial array. Our study revealed signature features of functional CpGs and unveiled a wealth of DNA methylation variation at functional CpG sites that are missed by existing high throughput arrays, indicating that inter individual variation in DNA methylation may contribute more to disease risk than previously appreciated.

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