Genetic confounding in the associations between maternal health and autism

The etiology of autism is influenced by genetic and non-genetic factors, with observational studies suggesting associations between early maternal health diagnoses and offspring autism. However, these associations may partly reflect shared familial genetic liability rather than direct causal effects. Using comprehensive national health registers and individual-level genetic data from the iPSYCH cohort (N=117,542), we examined whether maternal health diagnoses are associated with offspring polygenic scores (PGS) for autism. Such associations between maternal health and offspring autism would indicate shared genetic factors and the possibility of genetic confounding in the observational associations. We also tested such associations with PGSs for other neuropsychiatric and neurodevelopmental conditions that are genetically correlated with autism, but with better-powered PGS (due to larger GWAS sample sizes and likely more polygenic genetic architecture), as well as height, a negative control. Several maternal diagnoses were nominally associated with autism PGS in the child, including, e.g., certain obstetric complications, asthma, and obesity. After adjustment for multiple testing, the only statistically significant results included those between maternal diagnoses, predominantly psychiatric, and other neuropsychiatric and neurodevelopmental PGSs in the child. Sensitivity analyses confirmed the robustness of our results across exposure windows, diagnostic settings, and socioeconomic adjustments. These findings indicate that maternal diagnoses associated with autism partially reflect shared genetic liabilities between mothers and their children. However, such genetic effects, as captured by child PGS do not fully explain the observed associations, suggesting additional factors, including e.g., non-genetic familial factors, rare variants, and indirect effects.