Neuroimaging-AI Endophenotypes of Brain Diseases in the General Population: Towards a Dimensional System of Vulnerability

Disease heterogeneity poses a significant challenge for precision diagnostics in both clinical and sub-clinical stages. Recent work leveraging artificial intelligence (AI) has offered promise to dissect this heterogeneity by identifying complex intermediate phenotypes – herein called dimensional neuroimaging endophenotypes (DNEs) – which subtype various neurologic and neuropsychiatric diseases. We investigate the presence of nine such DNEs derived from independent yet harmonized studies on Alzheimer’s disease (AD1-2)(1), autism spectrum disorder (ASD1-3)(2), late-life depression (LLD1-2)(3), and schizophrenia (SCZ1-2)(4), in the general population of 39,178 participants in the UK Biobank study. Phenome-wide associations revealed prominent associations between the nine DNEs and phenotypes related to the brain and other human organ systems. This phenotypic landscape aligns with the SNP-phenotype genome-wide associations, revealing 31 genomic loci associated with the nine DNEs (Bonferroni corrected P-value < 5×10(−8)/9). The DNEs exhibited significant genetic correlations, colocalization, and causal relationships with multiple human organ systems and chronic diseases. A causal effect (odds ratio=1.25 [1.11, 1.40], P-value=8.72×1(−4)) was established from AD2, characterized by focal medial temporal lobe atrophy, to AD. The nine DNEs and their polygenic risk scores significantly improved the prediction accuracy for 14 systemic disease categories and mortality. These findings underscore the potential of the nine DNEs to identify individuals at a high risk of developing the four brain diseases during preclinical stages for precision diagnostics. All results are publicly available at: http://labs.loni.usc.edu/medicine/.