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. Author manuscript; available in PMC: 2009 Nov 25.
Published in final edited form as: Ann Hum Genet. 2009 Mar 25;73(Pt 3):346–359. doi: 10.1111/j.1469-1809.2009.00515.x

Table II.

Performance of the log-linear model that enforced both the random mating assumption and R2=R12 for estimating offspring genetic effects (N =400). Genotypes were simulated mimicking RFC1 haplotypes under Hardy-Weinberg Disequilibrium and R2=R12 with 5,000 simulations per scenario

Log-linear
model
assumption		 HWD
coefficient
(D11)		 Simulated
R1 		Pattern of
missingness1 		Mean total
number of
transmission
tetratypes		 Mean number
of triads with
multiple
transmission
tetratypes		 Power
(1df)		 Empirical
coverage of
nominal
95%
confidence
interval		 Frequency of carriers
of the risk haplotype2
 Geometric mean of
estimated R1
(95% CI)3
HWE -0.1 1 None 419.4 19.1 0.071 0.929 0.36 0.48 0.16 1.00(0.99,1.00)
20% g 917.4 205.0 0.073 0.927 0.36 0.48 0.16 1.00 (1.00,1.00)
-0.1 1.414 None 419.3 19.0 0.988 0.876 0.39 0.47 0.14 1.51(1.5,1.51)
20% g 921.1 205.0 0.983 0.873 0.39 0.47 0.14 1.51(1.5,1.51)
0.1 1 None 407.7 7.6 0.021 0.979 0.36 0.48 0.16 1.00 (1.00,1.01)
20% g 863.1 191.9 0.021 0.979 0.36 0.48 0.16 1.00 (1.00,1.00)
0.1 1.414 None 407.1 7.0 0.618 0.916 0.33 0.49 0.18 1.29(1.29,1.29)
20% g 854.0 189.7 0.570 0.912 0.32 0.49 0.19 1.28(1.28,1.29)
Random
Mating		 -0.1 1 None same as above 0.049 0.951 0.26 0.68 0.06 1.00 (1.00,1.00)
20% g 0.053 0.947 0.26 0.68 0.06 1.00 (1.00,1.00)
-0.1 1.414 None 0.982 0.946 0.26 0.68 0.06 1.41(1.41,1.42)
20% g 0.977 0.949 0.26 0.68 0.06 1.41(1.41,1.42)
0.1 1 None 0.050 0.950 0.46 0.28 0.26 1.00 (1.00,1.01)
20% g 0.048 0.952 0.46 0.28 0.26 1.00 (1.00,1.01)
0.1 1.414 None 0.744 0.952 0.46 0.28 0.26 1.42(1.41,1.42)
20% g 0.702 0.953 0.46 0.28 0.26 1.42(1.41,1.42)
1

None: no missing data; 20% g: 20% of SNP genotypes are missing randomly.

2

Expected frequencies of diplotypes with 0, 1, 2 copies of the risk haplotype are 0.26, 0.68, and 0.06, respectively, when D11 =-0.1 and 0.46, 0.28, and 0.26, respectively, when D11 = 0.1.

3

The 95% CI is based on the empirical standard error calculated using the estimates from 5000 independent simulation.