The strongest enrichment signals were in the antigen processing and presentation categories, involving various HLA variants (e.g. HLA-DRA) as well as the genes TAP1, TAP2, TAPBP, MICA, MICB and PSMB8. Additionally, excluding MHC regions showed no pathways linking LADA to Crohn’s disease, ulcerative colitis or Graves’ disease, with only a limited number identified for hypothyroidism and vitiligo (ESM Figs 9 and 10), suggesting that these pathways are mostly driven by the MHC. Here, HLA-C is linked to hypothyroidism.