Table 3.
Comparison between observed and estimated case probabilities across polygenic score quantiles for binary phenotypes.
| Phenotype | Mean Abs. Diff. | Mean Abs. Diff. of SD | N | Ncas | Ncon | Skewness |
|---|---|---|---|---|---|---|
| Binary | ||||||
| Depression | 1.6% | NA | 49,999 | 24,999 | 25,000 | NA |
| T2D | 3.4% | NA | 49,999 | 14,888 | 35,111 | NA |
| CAD | 4.3% | NA | 49,999 | 25,000 | 24,999 | NA |
| IBD | 38.6% | NA | 49,999 | 3461 | 46,538 | NA |
| MultiScler | 43.7% | NA | 49,999 | 1137 | 48,862 | NA |
| RheuArth | 40% | NA | 49,999 | 3408 | 46,591 | NA |
| Breast_Cancer | 12.5% | NA | 49,999 | 8512 | 41,487 | NA |
| Prostate_Cancer | 11.1% | NA | 50,000 | 2927 | 47,073 | NA |
| Continuous | ||||||
| Intelligence | 1.9% | 1.5% | 50,000 | NA | NA | 0.144 |
| Height | 0.2% | 2.5% | 49,999 | NA | NA | 0.117 |
| BMI | 0.3% | 6% | 49,999 | NA | NA | 0.592 |
Estimated values are based on the lassosum estimated AUC/R2 of the polygenic score.
Mean Abs. Diff. mean absolute difference between expected and observed case probability (binary) or trait mean (continuous), Mean Abs. Diff. of SD mean absolute difference between expected and observed trait standard deviation, N sample size, Ncas number of cases, Ncon number of controls.