BackgroundEpidemiological studies have shown increased comorbidity between depression and autoimmune diseases. The mechanisms driving the comorbidity are poorly understood, and a highly powered investigation is needed to understand the relative importance of shared genetic influences. We investigated the evidence for pleiotropy from shared genetic risk alleles between these traits in the UK Biobank (UKB).MethodsWe defined autoimmune and depression cases using information from hospital episode statistics, self-reported conditions and medications, and mental health questionnaires. Pairwise comparisons of depression prevalence between autoimmune cases and controls, and vice-versa, were performed. Cross-trait polygenic risk score (PRS) analyses were performed to test for pleiotropy, i.e. testing whether PRS for depression could predict autoimmune disease status, and vice-versa.ResultsWe identified 28k cases of autoimmune diseases (pooling across 14 traits), and 65k cases of depression. The prevalence of depression was significantly higher in autoimmune cases compared to controls, and vice-versa. PRS for myasthenia gravis and psoriasis were significantly associated with depression case-status (p < 5.2×10−5, R2 <= 0.04%). PRS for depression were significantly associated with case-status for coeliac disease, inflammatory bowel disease, psoriasis, psoriatic arthritis, rheumatoid arthritis and type 1 diabetes (p < 5.8×10−5, R2 range 0.06% to 0.27%).ConclusionsConsistent with the literature, depression was more common in individuals with autoimmune diseases compared to controls, and vice-versa, in the UKB. PRS showed some evidence for involvement of shared genetic factors, but the modest R2 values suggest that shared genetic architecture accounts for only a small proportion of the increased risk across traits.