Genetic influences on DNA methylation (mQTL) in pediatric Crohn's disease patients

Previously, we conducted an epigenome-wide study of DNA methylation (~850K sites) in peripheral blood at diagnosis and during follow-up from the RISK pediatric Crohn’s disease inception cohort and data are deposited in GEO with an access number GSE112611. We further followed up this study and identified here the genetic influence on ~850K DNAm sites (mQTL) in peripheral blood as well as newly added 41 ileal biopsies. All the ileal biopsies DNAm data are collected from the subset of primary 238 pediatric CD cohort that contains the peripheral blood DNAm data in GSE112611. Comparing the mQTL effect sizes among 164 CD cases at baseline, 164 CD cases at 3 years follow-up, 74 healthy controls and 41 ileal biopsies confirms that genetic influence on DNAm sites are strongly consistent among these groups. This study further concludes that the mQTLs are largely not disease-specific or inflammation-specific or tissue-specific. DNA methylation was assessed in Ileal biopsies from pediatric non-IBD controls and patients with Crohn's disease at diagnosis. Ileal biopsy DNA was extracted, bisulfite converted and genome-wide DNA methylation was interrogated using the HumanMethylationEPIC BeadChip (Illumina).