Table 4.
Prediction accuracy in simulation studies in which the phenotype is associated with SNPs only (heritability = 0.10).
| Distribution of the true SNP effects | Prediction models | Number of true susceptibility variants | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| 100 | 200 | 500 | 2000 | 5000 | |||||||
| Mean (SE) PCC | Powera | Mean (SE) PCC | Powera | Mean (SE) PCC | Powera | Mean (SE) PCC | Powera | Mean (SE) PCC | Powera | ||
| Laplace distribution | STMGP | 0.1520 (0.0293) | 1.00 | 0.1029 (0.0408) | 1.00 | 0.0521 (0.0252) | 0.80 | 0.0241 (0.0193) | 0.35 | 0.0217 (0.0171) | 0.25 |
| PRS | 0.0454 (0.0434) | 0.75 | 0.0421 (0.0247) | 0.85 | –0.0018 (0.0283) | 0.10 | 0.0128 (0.0203) | 0.15 | 0.0004 (0.0203) | 0.10 | |
| GBLUP | 0.0137 (0.0134) | 0.05 | 0.0201 (0.0143) | 0.15 | 0.0163 (0.0190) | 0.20 | 0.0198 (0.0133) | 0.25 | 0.0199 (0.0201) | 0.15 | |
| SBLUP | 0.0140 (0.0148) | 0.05 | 0.0186 (0.0143) | 0.10 | 0.0150 (0.0200) | 0.20 | 0.0189 (0.0159) | 0.25 | 0.0186 (0.0189) | 0.15 | |
| BayesR | 0.1217 (0.0680) | 0.90 | 0.0782 (0.0475) | 0.85 | 0.0345 (0.0337) | 0.35 | 0.0202 (0.0195) | 0.25 | 0.0172 (0.0222) | 0.15 | |
| Ridge | 0.0183 (0.0158) | 0.20 | 0.0188 (0.0138) | 0.20 | 0.0215 (0.0212) | 0.30 | 0.0184 (0.0111) | 0.10 | 0.0171 (0.0192) | 0.15 | |
| Normal distribution | STMGP | 0.1045 (0.0281) | 1.00 | 0.0638 (0.0205) | 0.95 | 0.0236 (0.0122) | 0.30 | 0.0208 (0.0156) | 0.25 | 0.0195 (0.0186) | 0.15 |
| PRS | 0.0258 (0.0305) | 0.50 | 0.0177 (0.0220) | 0.30 | 0.0079 (0.0224) | 0.15 | 0.0053 (0.0216) | 0.10 | 0.0015 (0.0233) | 0.00 | |
| GBLUP | 0.0220 (0.0168) | 0.30 | 0.0202 (0.0172) | 0.15 | 0.0161 (0.0147) | 0.15 | 0.0172 (0.0191) | 0.15 | 0.0204 (0.0132) | 0.15 | |
| SBLUP | 0.0215 (0.0173) | 0.30 | 0.0195 (0.0174) | 0.15 | 0.0173 (0.0150) | 0.15 | 0.0185 (0.0198) | 0.20 | 0.0206 (0.0129) | 0.15 | |
| BayesR | 0.0943 (0.0489) | 0.90 | 0.0444 (0.0224) | 0.70 | 0.0210 (0.0171) | 0.15 | 0.0189 (0.0135) | 0.20 | 0.0130 (0.0127) | 0.05 | |
| Ridge | 0.0251 (0.0156) | 0.40 | 0.0269 (0.0180) | 0.40 | 0.0187 (0.0184) | 0.15 | 0.0170 (0.0162) | 0.15 | 0.0154 (0.0179) | 0.10 | |
PCC predictive correlation coefficient, SE standardized error, STMGP Smooth-Threshold Multivariate Genetic Prediction, PRS polygenic risk scores, GBLUP genomic best linear-unbiased prediction, SBLUP summary-data-based best linear-unbiased prediction, NEG normal–exponential–gamma.
aPower is the proportion of replicates achieving a significant prediction at P value < 0.05.