Inferring linkage disequilibrium from non-random samples†

BMC Genomics

Table 6 LD estimation from case and control samples with varying proportions

p	q	D	c:c= 3/4:1/4	c:c= 2/3:1/3	c:c= 1/3:2/3	c:c= 1/4:3/4
± s.d.
0.6	0.005	-0.002	0.002 ± 0.000	-0.002 ± 0.000	-0.002 ± 0.000	-0.002 ± 0.000
0.5	0.010	0.004	0.004 ± 0.001	0.004 ± 0.001	0.004 ± 0.001	0.004 ± 0.001
0.5	0.020	0.008	0.008 ± 0.001	0.008 ± 0.001	0.008 ± 0.001	0.008 ± 0.002
0.3	0.030	0.010	0.010 ± 0.003	0.010 ± 0.003	0.010 ± 0.002	0.010 ± 0.003
0.7	0.040	0.010	0.010 ± 0.003	0.011 ± 0.002	0.010 ± 0.002	0.010 ± 0.003
0.3	0.050	0.020	0.021 ± 0.004	0.021 ± 0.004	0.021 ± 0.004	0.021 ± 0.004
0.5	0.100	0.040	0.043 ± 0.007	0.044 ± 0.006	0.045 ± 0.006	0.045 ± 0.007
LOD ± s.d.
0.6	0.005	-0.002	1.814 ± 0.855	2.420 ± 1.063	4.707 ± 2.172	5.362 ± 2.695
0.5	0.010	0.004	1.906 ± 0.832	2.493 ± 0.997	4.915 ± 1.994	5.715 ± 2.502
0.5	0.020	0.008	1.969 ± 0.812	2.579 ± 1.029	5.112 ± 2.160	5.916 ± 2.653
0.3	0.030	0.010	1.481 ± 0.812	1.950 ± 1.025	3.888 ± 2.011	4.463 ± 2.519
0.7	0.040	0.010	1.063 ± 0.580	1.453 ± 0.724	2.714 ± 1.368	3.130 ± 1.783
0.3	0.050	0.020	2.162 ± 0.966	2.982 ± 1.161	5.876 ± 2.446	6.695 ± 3.029
0.5	0.100	0.040	2.275 ± 0.816	3.152 ± 1.071	6.657 ± 2.241	7.616 ± 2.772

Means and standard deviations of the estimates of the disequilibrium coefficients and the corresponding LOD score from use of case-control samples of a constant size of 200 individuals but with varying proportions between the 'case and control' individuals, c:c.

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