Table 4.

Checklist of key components that should be described in DNA methylation studies

Justify sample size:	• If previous literature has been published: estimate sample size102 • If no previous literature has been published: perform a pilot study in a small number of patients as an exploration. Report as explorative study design, a stepping-stone for future research
Limit confounding:	• Include detailed cohort description: ◦ Age, sex, smoking behaviour ◦ Disease duration, Montreal classification, surgical history ◦ Inflammatory status at time of sampling [CRP, faecal calprotectin, clinical and or endoscopy scores] ◦ Current and previous IBD-related medication, concomitant medication • If mixed tissue [whole blood, mucosal biopsy]: explore cellular heterogeneity • Describe sample quality control and describe actions taken to limit batch effects
Increase reproducibility:	•Report sample type [tube], sampling protocol, storage and isolation of DNA [kits] • When reporting differences in methylation, specify where the differences are found using genomic coordinates • Publish raw data in .idat or .fastq format in publicly available databases [Gene Expression Omnibus, ArrayExpress, European Genome-phenome Archive]
Increase interpretability:	• Include technical and/or independent validation in your design • Perform functional analysis of observed markers

CRP, C-reactive protein; IBD, inflammatory bowel disease.