Liver Enzyme Genetics and Health Conditions in East Asians: Genetic Architecture and Causal Insights

Elevated serum levels of alanine aminotransferase (ALT) and aspartate aminotransferase (AST) are biomarkers of liver dysfunction and predictors of cirrhosis and liver cancer. While European-ancestry GWAS have identified hundreds of loci influencing these enzymes and driven drug discovery and personalized interventions, comparable genetic studies in Han Taiwanese and other East Asian populations remain lacking.

We performed GWAS of ALT (n = 137,312) and AST (n = 111,527) in Han Taiwanese to characterize liver enzyme genetics. To assess broader East Asian relevance, we performed cross-trait genetic correlation analyses across five East Asian biobanks. We then conducted phenome-wide association studies (PheWAS) using polygenic risk scores (PRSs) to identify disease associations and applied bidirectional Mendelian randomization (MR) to assess causality.

We identified 16 genome-wide significant loci-including novel East Asian variants-linking enzyme liability to metabolic, hematologic, and malignancy traits. PheWAS revealed strong links to endocrine-metabolic disorders, especially type 2 diabetes (T2D), and to circulatory, genitourinary, digestive, and infectious diseases. MR showed a causal effect of genetically elevated ALT on increased T2D risk; AST's effect was evident only after BMI adjustment. Neither enzyme showed a causal influence on malignancy, though genetic predisposition to malignancy was associated with lower ALT levels. PRSs for ALT and AST robustly predicted higher T2D risk and earlier onset.

These findings elucidated the genetic architecture of liver enzymes in Han Taiwanese and highlight their relevance across East Asian populations. ALT and AST PRSs show promise as genomic markers for diabetes risk and precision prevention.