Evaluating the performance of polygenic indices of neuropsychiatric conditions and brain endophenotypes in four UK population samples

Neuropsychiatric polygenic indices (NPGIs) are used as genetic predictors of poor mental health. However, NPGIs are also associated with environmental factors which could affect mental health in adulthood, including the rearing environment. Hence, their “genetic” effects are both direct and environmentally mediated. There is a need to identify alternative genetic predictors without environmental signal. Endophenotype-based polygenic indices (EPGIs) trained on brain structure and function are under-studied alternatives which, due to their relative biological proximity, may exhibit associations with mental health outcomes which are less environmentally mediated than those of NPGIs. Using four representative UK samples ( Understanding Society ; UKHLS, NCDS, BCS70 and MCS) we employ sex-stratified path models to estimate the direct and environmentally mediated effects of eleven NPGIs and 30 EPGIs on adult mental health, focussing on the rearing environment. The depression NPGI is consistently associated with mental health symptoms across most sex-stratified sub-samples (best meta-analysis β = 0.091, p 0.001) but demonstrates 1.6 - 24.5% environmental mediation. Seven other NPGIs and three EPGIs show sample- and sex-specific associations with mental health symptoms. NPGIs for attention deficit hyperactivity disorder, depression and substance use disorder are robustly associated with measures of the rearing environment, which in turn are frequently associated with mental health symptoms. Sensitivity analyses find that NPGI associations vary substantially depending on who is included in the sample. In conclusion, the rearing environment likely mediates a substantial portion of NPGIs’ so-called “genetic” effects on mental health symptoms, but EPGIs are not currently powerful enough to replace them.