Table 4 Prediction of Sampling Scheme III
From: Inferring linkage disequilibrium from non-random samples†
p | q | (D min , D max ) | D | q was from population survey | q was from sample estimation | ||
|---|---|---|---|---|---|---|---|
|
|
|
| ||||
0.6 | 0.005 | (-0.003,0.002) | -0.002 | -0.011 ± 0.149 | -0.002 ± 0.000 | -0.113 ± 0.015 | -0.071 ± 0.011 |
0.5 | 0.01 | (-0.005,0.005) | 0.004 | 0.280 ± 0.011 | 0.004 ± 0.001 | 0.108 ± 0.013 | 0.080 ± 0.013 |
0.5 | 0.02 | (-0.010, 0.010) | 0.008 | 0.273 ± 0.010 | 0.008 ± 0.001 | 0.110 ± 0.014 | 0.081 ± 0.013 |
0.3 | 0.03 | (-0.009, 0.021) | 0.010 | 0.191 ± 0.026 | 0.011 ± 0.002 | 0.104 ± 0.019 | 0.057 ± 0.018 |
0.7 | 0.04 | (-0.028, 0.012) | 0.010 | 0.309 ± 0.016 | 0.011 ± 0.002 | 0.071 ± 0.012 | 0.061 ± 0.017 |
0.3 | 0.05 | (-0.015, 0.035) | 0.020 | 0.192 ± 0.044 | 0.021 ± 0.004 | 0.122 ± 0.017 | 0.066 ± 0.017 |
0.5 | 0.10 | (-0.050, 0.050) | 0.040 | 0.227 ± 0.008 | 0.045 ± 0.006 | 0.124 ± 0.014 | 0.088 ± 0.012 |
± s.d.
± s.d.- Simulation parameters for the case-control sampling scheme and means and standard deviation of estimates of the disequilibrium coefficients,
and 
, from Methods H and L respectively. p, q and D are simulated values of population allele frequencies at the marker and disease loci and linkage disequilibrium respectively. (D
min
, D
max
) are the theoretical minimum and maximum values of D. The disequilibrium coefficients were calculated when the marker allele frequency, p was calculated directly from the control sub-samples while the disease allele frequency q was either from population survey or directly estimated from the case-control samples.