Table 5 Sensitivity results of MB-MDR to detect two locus model of pure epistatic interaction in 1200 simulated datasets with real human genome LD patterns, for 3 effect sizes and after 5 LD pruning levels
LD block setting | LD pruning | Effect Size | Exact | Signal Sensitivity | |
|---|---|---|---|---|---|
|  |  |  | Sensitivity | −−−−−−−−−−−−−−−−−− | |
| Â | Â | Â | Â | tag-SNP condition | tag-SNP condition |
|  |  |  |  | LD r2≥0.45 | LD r2≥0.20 |
A | unpruned | β3=0.90 | 0.61 | 0.67 | 0.73 |
Two SNPs |  | β3=0.75 | 0.55 | 0.65 | 0.77 |
in same |  | β3=0.50 | 0.70 | 0.85 | 0.89 |
LD block | LD r2≤0.75 | β3=0.90 | 0.01 | 0.90 | 0.91 |
|  |  | β3=0.75 | 0.04 | 0.92 | 0.94 |
|  |  | β3=0.50 | 0.03 | 0.93 | 0.93 |
|  | LD r2≤0.60 | β3=0.90 | 0.01 | 0.93 | 0.94 |
|  |  | β3=0.75 | 0.00 | 0.94 | 0.94 |
|  |  | β3=0.50 | 0.01 | 0.92 | 0.94 |
|  | LD r2≤0.50 | β3=0.90 | 0.00 | 0.91 | 0.92 |
|  |  | β3=0.75 | 0.00 | 0.90 | 0.91 |
|  |  | β3=0.50 | 0.01 | 0.91 | 0.95 |
|  | LD r2≤0.20 | β3=0.90 | 0.00 | 0.61 | 0.74 |
|  |  | β3=0.75 | 0.00 | 0.69 | 0.80 |
|  |  | β3=0.50 | 0.01 | 0.66 | 0.84 |
B | unpruned | β3=0.90 | 0.54 | 0.75 | 0.75 |
Two SNPs |  | β3=0.75 | 0.46 | 0.70 | 0.71 |
in middle |  | β3=0.50 | 0.41 | 0.75 | 0.76 |
of two | LD r2≤0.75 | β3=0.90 | 0.64 | 0.91 | 0.91 |
separate |  | β3=0.75 | 0.58 | 0.91 | 0.91 |
LD blocks |  | β3=0.50 | 0.44 | 0.93 | 0.94 |
|  | LD r2≤0.60 | β3=0.90 | 0.49 | 0.92 | 0.92 |
|  |  | β3=0.75 | 0.41 | 0.93 | 0.93 |
|  |  | β3=0.50 | 0.27 | 0.94 | 0.95 |
|  | LD r2≤0.50 | β3=0.90 | 0.39 | 0.92 | 0.92 |
|  |  | β3=0.75 | 0.32 | 0.93 | 0.93 |
|  |  | β3=0.50 | 0.23 | 0.94 | 0.95 |
|  | LD r2≤0.20 | β3=0.90 | 0.19 | 0.57 | 0.81 |
|  |  | β3=0.75 | 0.16 | 0.69 | 0.91 |
|  |  | β3=0.50 | 0.21 | 0.83 | 0.92 |
C | unpruned | β3=0.90 | 0.18 | 0.33 | 0.43 |
One SNP |  | β3=0.75 | 0.23 | 0.36 | 0.49 |
in a block |  | β3=0.50 | 0.18 | 0.36 | 0.51 |
and one | LD r2≤0.75 | β3=0.90 | 0.0 | 0.65 | 0.74 |
in the edge |  | β3=0.75 | 0.0 | 0.72 | 0.83 |
of a separate |  | β3=0.50 | 0.0 | 0.57 | 0.76 |
LD block | LD r2≤0.60 | β3=0.90 | 0.0 | 0.56 | 0.74 |
|  |  | β3=0.75 | 0.0 | 0.59 | 0.81 |
|  |  | β3=0.50 | 0.0 | 0.47 | 0.74 |
|  | LD r2≤0.50 | β3=0.90 | 0.0 | 0.48 | 0.71 |
|  |  | β3=0.75 | 0.0 | 0.50 | 0.81 |
|  |  | β3=0.50 | 0.0 | 0.36 | 0.70 |
|  | LD r2≤0.20 | β3=0.90 | 0.0 | 0.07 | 0.60 |
|  |  | β3=0.75 | 0.0 | 0.05 | 0.62 |
|  |  | β3=0.50 | 0.0 | 0.04 | 0.57 |
D | unpruned | β3=0.90 | 0.39 | 0.68 | 0.82 |
Two SNPs |  | β3=0.75 | 0.40 | 0.69 | 0.81 |
on LD blocks |  | β3=0.50 | 0.58 | 0.76 | 0.84 |
of separate | LD r2≤0.75 | β3=0.90 | 0.18 | 0.86 | 0.94 |
chromosomes |  | β3=0.75 | 0.18 | 0.93 | 0.99 |
|  |  | β3=0.50 | 0.23 | 0.84 | 0.90 |
|  | LD r2≤0.60 | β3=0.90 | 0.14 | 0.87 | 0.94 |
|  |  | β3=0.75 | 0.13 | 0.93 | 0.98 |
|  |  | β3=0.50 | 0.17 | 0.85 | 0.90 |
|  | LD r2≤0.50 | β3=0.90 | 0.13 | 0.85 | 0.92 |
|  |  | β3=0.75 | 0.13 | 0.93 | 0.97 |
|  |  | β3=0.50 | 0.16 | 0.83 | 0.89 |
|  | LD r2≤0.20 | β3=0.90 | NA | NA | NA |
|  |  | β3=0.75 | 0.10 | 0.67 | 0.86 |
|  |  | β3=0.50 | 0.17 | 0.75 | 0.84 |