Table 5.
Comparison between prediction R2 of PRSunadj, PRSadj, and PRSadj + ancestry in simulations with different training sample sizes
The fluctuations in R2 of PRSunadj are not statistically significant based on the number of simulations performed.
| R2 | |||
|---|---|---|---|
| Training sample size (N) | PRSunadj (SE) | PRSadj (SE) | PRSadj + ancestry (SE) |
| 1,000 | 0.041 (0.0016) | 0.003 (0.0002) | 0.042 (0.0016) |
| 5,000 | 0.041 (0.0020) | 0.014 (0.0004) | 0.051 (0.0019) |
| 10,000 | 0.043 (0.0019) | 0.027 (0.0005) | 0.064 (0.0018) |
| 50,000 | 0.045 (0.0020) | 0.111 (0.011) | 0.139 (0.0019) |
| 100,000 | 0.044 (0.0020) | 0.182 (0.0011) | 0.201 (0.0017) |
| 500,000 | 0.042 (0.0020) | 0.380 (0.0015) | 0.384 (0.0016) |
| 1,000,000 | 0.042 (0.0018) | 0.439 (0.0012) | 0.440 (0.0013) |
SE: standard error