High-resolution targeted bisulfite sequencing reveals blood cell type-specific DNA methylation patterns in IL13 and ORMDL3

Abstract

Background Methylation of DNA at CpG sites is an epigenetic modification and a potential modifier of disease risk, possibly mediating environmental effects. Currently, DNA methylation is commonly assessed using specific microarrays that sample methylation at a few % of all methylated sites. Methods To understand if significant information on methylation can be added by a more comprehensive analysis of methylation, we set up a quantitative method, bisulfite oligonucleotide-selective sequencing (Bs-OS-seq), and compared the data with microarray-derived methylation data. We assessed methylation at two asthma-associated genes, IL13 and ORMDL3, in blood samples collected from children with and without asthma and fractionated white blood cell types from healthy adult controls. Results Our results show that Bs-OS-seq can uncover vast amounts of methylation variation not detected by commonly used array methods. We found that high-density methylation information from even one gene can delineate the main white blood cell lineages. Conclusions We conclude that high-resolution methylation studies can yield clinically important information at selected specific loci missed by array-based methods, with potential implications for future studies of methylation-disease associations.

Current Challenges of Methylation-Based Liquid Biopsies in Cancer Diagnostics

“…A targeted bisulfite sequencing of precise loci is deemed more effective [ 56 ], offering a reliable tool for validating data obtained, for example, by array-based methods. Array-based methods enable the screening of methylation on a genome-wide scale, but similar to whole-genome sequencing, this method also has a relatively high error rate, and targeted bisulfite sequencing could serve as one of its validation options in clinical practice [ 56 , 57 ].…”