Table 3.
Comparison of estimated odds ratio (OR) for pre-defined disease SNPs under moderate population stratification in GWAS simulation
| PS | Chr | rsID | True OR | Estimated Odds Ratio (95% CI) |
Absolute % Change from True OR |
|||
|---|---|---|---|---|---|---|---|---|
| PCA | PCAPS | PCA | PCAPS | Less-biased Method | ||||
| Moderate | ||||||||
| 2 | rs13027563 | 1.5 | 1.419 (1.244 – 1.619) | 1.430 (1.246 – 1.641) | 5.4% | 4.7% | PCAPS | |
| 6 | rs214445 | 1.5 | 1.517 (1.338 – 1.719) | 1.495 (1.311 – 1.704) | 1.1% | 0.3% | PCAPS | |
| 19 | rs919276 | 1.5 | 1.466 (1.239 – 1.736) | 1.486 (1.239 – 1.783) | 2.3% | 0.9% | PCAPS | |
| 1 | rs1334997 | 2 | 2.070 (1.757 – 2.445) | 1.965 (1.653 – 2.331) | 3.5% | 1.8% | PCAPS | |
| 8 | rs12680139 | 2 | 1.965 (1.689 – 2.283) | 1.908 (1.634 – 2.227) | 1.8% | 4.6% | PCA | |
| 17 | rs2598435 | 2 | 2.119 (1.842 – 2.439) | 2.066 (1.776 – 2.410) | 6.0% | 3.3% | PCAPS | |
PS, population stratification; Chr, chromosome; rsID, dbSNP rs number; OR, odds ratio; PCA, principal components analysis; PCAPS, principal components and propensity score.