Perspectives on genetic studies of type 2 diabetes from the genome-wide association studies era to precision medicine

Abstract

Genome-wide association studies (GWAS) have facilitated a substantial and rapid increase in the number of confirmed genetic susceptibility variants for complex diseases. Approximately 700 variants predisposing individuals to the risk for type 2 diabetes have been identified through GWAS until 2023. From 2018 to 2022, hundreds of type 2 diabetes susceptibility loci with smaller effect sizes were identified through large-scale GWAS with sample sizes of 200,000 to >1 million. The clinical translation of genetic information for type 2 diabetes includes the development of novel therapeutics and risk predictions. Although drug discovery based on loci identified in GWAS remains challenging owing to the difficulty of functional annotation, global efforts have been made to identify novel biological mechanisms and therapeutic targets by applying multi-omics approaches or searching for disease-associated coding variants in isolated founder populations. Polygenic risk scores (PRSs), comprising up to millions of associated variants, can identify individuals with higher disease risk than those in the general population. In populations of European descent, PRSs constructed from base GWAS data with a sample size of approximately 450,000 have predicted the onset of diseases well. However, European GWAS-derived PRSs have limited predictive performance in non-European populations. The predictive accuracy of a PRS largely depends on the sample size of the base GWAS data. The results of GWAS meta-analyses for multi-ethnic groups as base GWAS data and cross-population polygenic prediction methodology have been applied to establish a universal PRS applicable to small isolated ethnic populations.

Keywords: Genome‐wide association studies; Polygenic risk scores; Type 2 diabetes.

Figure 1

Clinical implications of type 2 diabetes genome‐wide association studies.

Figure 2

Discovery of potential drug targets for the treatment of type 2 diabetes (T2D). Upper half shows the strategy of drug targets search based on the genome‐wide association studies‐derived genetic information. Biological type 2 diabetes risk genes were selected from among the type 2 diabetes potential risk genes located in any of the established type 2 diabetes risk loci, using a scoring system by summing up the number of prioritization criteria: (1)–(6) satisfied. Novel type 2 diabetes therapeutic targets were discovered by searching overlapping genes between the biological type 2 diabetes risk genes plus genes which products are in direct protein–protein interaction (PPI) with the biological type 2 diabetes risk gene products and the drug target genes. The lower half shows representative connections between type 2 diabetes risk single‐nucleotide polymorphisms (SNPs; blue), type 2 diabetes biological genes (gray), drug target genes (yellow) and targeted drugs. *Approved compounds for type 2 diabetes treatment. **Compounds for treatment against diseases other than type 2 diabetes under clinical trial. Modified citation from reference Imamura M et al, 2016.