Fig. 3.

Comparisons of the predictive performance for HGT by the aid of BMI among LDpred, MTAG, STGBLUP, MTGBLUP, and CTPR using UK Biobank data (N = 30K or 437K) as a training set and either UK Biobank (N = 20K) or NHS/HPFS/PHS cohort (N = 20K) as a validation set. We considered human height (HGT) as the primary trait and body mass index (BMI) as the secondary trait. Prediction R² were computed with two different validation sets (UK Biobank, NHS/HPFS/PHS data) and two different training sample sizes (30K, 437K) using summary-based prediction methods (LDpred, MTAG), GBLUP (STGBLUP, MTGBLUP), and the proposed prediction methods (MCP/MCP + CTPR, Lasso/Lasso + CTPR). Clearly, our multi-trait methods (Lasso + CTPR, MCP + CTPR) generated better predictive performance than our single-trait methods and the existing prediction methods with different training sample sizes and different validation sets. All error bars represent standard errors of prediction R². a Real GWAS analysis results with 30K training samples for prediction R² of HGT by the aid of BMI. b Real GWAS analysis results with 437K training samples for prediction R² of HGT by the aid of BMI