Table 2.
Comparisons of GRM Methods when the Genetic Architecture of the Simulated Trait Varies and the True Simulated h2 Is 0.5
|
Var(Allele Effect Size) ∼ [piqi]−1 |
Var(Allele Effect Size) ∼ [piqi]0 |
|||
|---|---|---|---|---|
| (SD) | ΔAICa(SD) | (SD) | ΔAICa(SD) | |
| Causal Variants Randomly Assigned | ||||
| ArchitecturebA | ArchitecturebB | |||
| Standard GRM with s = −1 | 0.51 (0.04) | 117 (20) | 0.57 (0.04) | 149 (24) |
| Standard GRM with s = 0 | 0.39 (0.04) | 102 (19) | 0.49 (0.03) | 168 (24) |
| Speed et al. weighted GRM | 0.56 (0.12) | 31 (13) | 0.59 (0.09) | 35 (11) |
| MAF-stratified approach | 0.51 (0.04) | 113 (20) | 0.51 (0.05) | 164 (24) |
| Causal Variants Randomly Assigned in 7:3 Ratio for MAF < 0.1: MAF > 0.1 | ||||
| ArchitecturebC | ArchitecturebD | |||
| Standard GRM with s = −1 | 0.45 (0.05) | 93 (23) | 0.53 (0.05) | 128 (26) |
| Standard GRM with s = 0 | 0.29 (0.04) | 58 (21) | 0.42 (0.04) | 123 (25) |
| Speed et al. weighted GRM | 0.55 (0.10) | 33 (18) | 0.57 (0.10) | 32 (11) |
| MAF-stratified approach | 0.51 (0.05) | 104 (19) | 0.51 (0.05) | 126 (26) |
| Causal Variants Randomly Assigned to MAF < 0.1 | ||||
| ArchitecturebE | ArchitecturebF | |||
| Standard GRM with s = −1 | 0.38 (0.05) | 65 (19) | 0.44 (0.04) | 86 (18) |
| Standard GRM with s = 0 | 0.18 (0.05) | 21 (11) | 0.23 (0.04) | 36 (12) |
| Speed et al. weighted GRM | 0.53 (0.09) | 28 (10) | 0.58 (0.12) | 34 (14) |
| MAF-stratified approach | 0.49 (0.06) | 130 (42) | 0.56 (0.05) | 154 (28) |
a
Average ΔAIC between the null model (no GRM fitted) and the full model. A high ΔAIC indicates a better fit.
b
The architecture letters match those in Table 1. The SD is over 50 replicates.