Comparison of polygenic risk prediction methods for 13 complex diseases.

<p>For all figures, the y-coordinate is the prediction R² in the observational scale. “1D” denotes 1D PRS; “2D, blood eSNPs” denotes 2D PRS using blood eSNPs as high-prior SNP set. In the x-axis, “NO” denotes PRS without winner’s curse correction; “LASSO” and “MLE” denote lasso-type and MLE winner’s curse correction, respectively. (A) Prediction R² values for six diseases in WTCCC data, estimated based on five-fold cross-validation. (B) Prediction R² values for three GWAS of cancers, estimated based on ten-fold cross-validation. (C) Prediction R² values for four complex diseases estimated based on independent validation samples.