This EWAS was undertaken in an incident T2DM case-cohort study nested within the EPIC-Norfolk study, a prospective cohort study that recruited 25,639 individuals aged between 40-79 years at baseline in 1993-1997. Incident T2DM cases were ascertained from multiple sources: two follow-up health and lifestyle questionnaires providing self-reported information on doctor-diagnosed diabetes or medications; medications brought to the second clinical exam; and medical record linkage.

DNAm intensity was measured using the Illumina HumanMethylation450 array. Bisulfite conversion of DNA was performed using the EZ DNA methylation kit (Zymo Research, Orange, CA, USA). Diabetes DNAm was measured in DNA extracted from whole blood samples collected at baseline. Converted DNA was assayed by PCR (Polymerase Chain Reaction) and gel electrophoresis. Each 96 well DNA sample plate contained two duplicate samples. The average correlation between the duplicate samples was 98%.

To identify MVPs associated with incident T2DM, we performed a logistic regression model for each methylation marker with incident T2DM status, adjusted for age, sex, estimated cell counts, and sample plate.