TABLE 1.
The median and standard deviation of R-squared for each method in different simulation settings. We only show the outcomes of simulated settings that benefit from sex-specific PRSs. Because the prediction performances on females and males are consistent when sample sizes and heritability are both balanced across sexes, we only report the prediction accuracy on females in these cases. Bold and italics indicate the best results in each simulation setting, and the second-best results are presented only in bold.
| Sample Sizes (females/males) | 25,000/25,000 | 100,000/100,000 | 10,000/50,000 | 25,000/25,000 | ||||
|---|---|---|---|---|---|---|---|---|
| Heritability (females/males) | 0.3/0.3 | 0.1/0.5 | ||||||
| Proportion of shared causal SNPs | 0.8 | 1 | 1 | 1 | 1 | |||
| Genetic correlation | 0.5 | 0.8 | 0.5 | 0.5 | 0.5 | |||
| Testing samples | Females | Females | Females | Males | Males | |||
| Combined sex | LDpred2-mult | 0.132 (0.030) | 0.141 (0.004) | 0.223 (0.011) | 0.224 (0.013) | 0.078 (0.005) | 0.191 (0.010) | 0.282 (0.008) |
| PRScs-mult | 0.102 (0.010) | 0.106 (0.007) | 0.224 (0.014) | 0.219 (0.012) | 0.062 (0.008) | 0.162 (0.008) | 0.246 (0.010) | |
| PRScsx-mult | 0.121 (0.010) | 0.128 (0.007) | 0.235 (0.014) | 0.239 (0.013) | 0.094 (0.005) | 0.172 (0.009) | 0.256 (0.013) | |
| Female-specific | LDpred2-f | 0.130 (0.010) | 0.132 (0.005) | 0.217 (0.011) | 0.225 (0.013) | 0.049 (0.007) | 0.012 (0.003) | 0.016 (0.004) |
| PRScs-f | 0.094 (0.009) | 0.099 (0.007) | 0.219 (0.013) | 0.217 (0.012) | 0.031 (0.005) | 0.007 (0.003) | 0.010 (0.003) | |
| PRScsx-f | 0.121 (0.010) | 0.128 (0.007) | 0.234 (0.014) | 0.238 (0.013) | 0.091 (0.005) | 0.058 (0.008) | 0.085 (0.014) | |
| Male-specific | LDpred2-m | 0.030 (0.010) | 0.029 (0.007) | 0.133 (0.010) | 0.052 (0.008) | 0.045 (0.005) | 0.191 (0.010) | 0.280 (0.008) |
| PRScs-m | 0.025 (0.006) | 0.026 (0.006) | 0.130 (0.011) | 0.050 (0.006) | 0.040 (0.006) | 0.162 (0.009) | 0.244 (0.010) | |
| PRScsx-m | 0.049 (0.009) | 0.052 (0.007) | 0.168 (0.012) | 0.071 (0.011) | 0.052 (0.007) | 0.171 (0.009) | 0.256 (0.013) | |
| Sex-agnostic | LDpred2-all | 2 0.116 (0.009) | 0.122 (0.009) | 0.197 (0.009) | 0.172 (0.015) | 0.073 (0.006) | 0.187 (0.010) | 0.234 (0.015) |
| PRScs-all | 0.093 (0.010) | 0.103 (0.009) | 0.210 (0.014) | 0.173 (0.011) | 0.067 (0.010) | 0.163 (0.007) | 0.189 (0.013) | |