Table 3. The power comparison (at P-value threshold of 10−8) between our LHS method (with a single EM run) and three other haplotype methods—Beagle in Browning and Browning (2007), FZ in Feng and Zhu (2010), and Whait in Li et al. (2010a)—under different simulation conditions.
Conditions | Power | |||||
---|---|---|---|---|---|---|
Case/control | Sporadic ratea | Causal haplotypes | LHS | Beagle | FZ | Whait |
1000/1000 | 0.01 | 2 | 1.00 | 0.99 | 0.99 | 0.97 |
4 | 0.95 | 0.93 | 0.92 | 0.95 | ||
8 | 0.71 | 0.60 | 0.64 | 0.64 | ||
0.02 | 2 | 0.98 | 0.95 | 0.95 | 0.93 | |
4 | 0.93 | 0.74 | 0.89 | 0.87 | ||
8 | 0.53 | 0.33 | 0.32 | 0.41 | ||
2000/2000 | 0.01 | 2 | 1.00 | 0.99 | 1.00 | 1.00 |
4 | 0.98 | 0.98 | 0.98 | 0.99 | ||
8 | 0.83 | 0.71 | 0.81 | 0.73 | ||
0.02 | 2 | 0.98 | 0.96 | 0.98 | 0.98 | |
4 | 0.97 | 0.92 | 0.97 | 0.95 | ||
8 | 0.71 | 0.56 | 0.68 | 0.63 |
Note that Beagle, FZ, and Whait require phased haplotypes for association and we supplied them with the true haplotypes; our LHS method used diplotypes.
The penetrance is assumed to be fixed at 0.10, so that a higher sporadic rate results in a lower power.