DNA methylation plays a crucial role in gene regulation and disease pathogenesis. This project aims to perform comprehensive differential methylation analysis using Illumina Infinium MethylationEPIC (850K) microarray data to identify autoimmune disease-associated epigenetic patterns at prenatal/ birth. The dataset consists of 96 samples with approximately 750,000 CpG sites per sample. The analysis will follow best-practice workflows, including quality control, normalization, transformation of beta values to M-values, and differential methylation testing using the limma framework while adjusting for relevant covariates. Downstream analyses will include identification of differentially methylated CpG sites (DMCs), detection of differentially methylated regions (DMRs), and functional enrichment analysis to interpret biological significance. Association of environmental factors (parental questionnaires) in the epigenetic landscape for each disease group – CpG level insights and at population level will be investigated.