Table 1.
Power of the Cochran-Armitage trend test for 1- and 2-stage study designs across a range of sample sizes, SNPs in stage 1, and disease prevalences. Study controls are assumed to be screened and disease free.
| Number of Public Controls
|
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| 2,000 | 5,000 | 10,000 | ||||||||
| Ka | Study Controls Only | Public Controls Only | Study + Public Controls | Two-Stageb | Public Controls Only | Study + Public Controls | Two-Stageb | Public Controls Only | Study + Public Controls | Two-Stageb |
| 2,000 Cases and 2,000 Screened Study Controls/500,000 SNPs
| ||||||||||
| 0.0001 | 0.57 | 0.56 | 0.85 | 0.71 | 0.90 | 0.94 | 0.82 | 0.97 | 0.97 | 0.84 |
| 0.01 | 0.59 | 0.56 | 0.86 | 0.72 | 0.90 | 0.94 | 0.82 | 0.97 | 0.97 | 0.85 |
| 0.05 | 0.68 | 0.56 | 0.89 | 0.76 | 0.90 | 0.96 | 0.86 | 0.97 | 0.98 | 0.88 |
| 0.1 | 0.79 | 0.56 | 0.92 | 0.82 | 0.90 | 0.96 | 0.89 | 0.97 | 0.98 | 0.91 |
| 0.25 | 0.98 | 0.56 | 0.99 | 0.95 | 0.90 | 0.99 | 0.97 | 0.97 | 0.99 | 0.97 |
| 0.5 | 1.00 | 0.56 | 1.00 | 1.00 | 0.90 | 1.00 | 1.00 | 0.97 | 1.00 | 1.00 |
a
Population prevalence of disease
b
Optimal replication-based two-stage design using all public controls in stage 1 and all screened controls in stage 2, 2-sided test in stage 1 and 1-sided test in stage 2
Risk allele frequency in general population (fD) = 0.3, genetic relative risk (GRR) = 1.3 assuming a multiplicative model, overall type I error (α) = 0.05
fD = 0.3 corresponds to fD = 0.358 in cases for all K and fD = 0.300, 0.299, 0.297, 0.293, 0.278, 0.228 in screened controls for K = 0.0001, 0.01, 0.05, 0.1, 0.25, and 0.5, respectively