Fig. 3: Model evaluation and comparison.

A bar chart displays AUC. The two-sided DeLong test examined the difference between AUCs. Bonferroni’s correction was applied to control for a family-wise error rate in multiple comparisons. Symbols *, **, and *** indicate p-values < 0.05, 0.01, and 0.001, respectively. A SNP selection. Model predictors were SNPs selected from published studies or our GWAS under different p-value thresholds, where our GWAS association test is a two-sided Wald test for the slope coefficient in a logistic regression. The average AUCs of prediction models for four phenotype definitions were compared. B T2D Phenotype Definition. In addition to including the selected variables in Fig. 3A, the AUCs of four phenotype definitions were compared. C Family history of T2D. In addition to including the selected variables in Fig. 3A, B, the AUCs of the four types of T2D family history (i.e., (i): parents (binary factor), (ii) sibs (binary factor), (iii) either parents or sibs (binary factors), and (iv) both parents and sibs (ordinal factor)) were compared. D Demographic variables. In addition to including the selected variables in Fig. 3A–C, the AUCs of different combinations of demographic factors, including age, sex, and family history of T2D, are compared. E PRS and demographic variables. In addition to including the selected variables in Fig. 3A–D, the AUCs of different combinations of genetic variables, including SNPs, PRS-CS, and PRS-CSx, and demographic variables, including age, sex, and family history of T2D, are compared. F Impact of including PRS after SNPs. The AUCs of the models that consider SNPs, SNPs+PRS-CS, and SNPs+PRS-CSx as predictors are compared. G Impact of including additional SNPs after PRS. The additional 137 SNPs were collected from published studies (Supplemental Text 2). The AUCs of the models that consider additional SNPs given PRS in the model are compared. Source data are provided as a Source Data file.