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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 I.

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

Number of
triads		 Risk
haplotype
frequency		 Pattern of
missingness1 		Mean total
number of TT		 Mean number
of triads with
multiple TT		 Empirical
coverage of
nominal 95%
CI		 Geometric mean of
estimated R1 (95% CI)2
True R1=2≈1.414
400 0.05 None 408.5 8.5 0.950 1.43(1.42,1.43)
20% g 901.4 199.5 0.945 1.43(1.42,1.44)
20% g & 20% f 4104.1 241.2 0.946 1.43(1.42,1.44)
0.142 None 411.1 11.0 0.950 1.42(1.41,1.42)
20% g 905.9 200.8 0.951 1.42(1.41,1.42)
20% g & 20% f 4141.3 242.2 0.951 1.42(1.41,1.43)
0.25 None 412.8 12.7 0.948 1.42(1.41,1.42)
20% g 904.6 200.8 0.947 1.42(1.41,1.42)
20% g & 20% f 4196.8 241.9 0.948 1.42(1.41,1.42)
0.4 None 412.4 12.2 0.949 1.41(1.41,1.42)
20% g 885.6 197.1 0.948 1.41(1.41,1.42)
20% g & 20% f 4212.6 238.4 0.947 1.41(1.41,1.42)
1000 0.02 None 1018.6 18.5 0.942 1.43(1.42,1.43)
20% g 2226.7 491.9 0.945 1.43(1.42,1.44)
20% g & 20% f 10057.1 597.0 0.942 1.44(1.42,1.45)
0.05 None 1021.3 21.2 0.944 1.42(1.41,1.43)
20% g 2228.5 493.1 0.948 1.42(1.41,1.43)
20% g & 20% f 10074.4 597.8 0.948 1.42(1.42,1.43)
0.142 None 1027.9 27.7 0.949 1.42(1.41,1.42)
20% g 2240.0 497.4 0.945 1.42(1.41,1.42)
20% g & 20% f 10198.4 601.0 0.945 1.42(1.41,1.42)
0.25 None 1032.0 31.7 0.952 1.41(1.41,1.42)
20% g 2236.9 497.8 0.954 1.42(1.41,1.42)
20% g & 20% f 10333.8 601.2 0.953 1.42(1.41,1.42)
0.4 None 1031.0 30.6 0.954 1.41(1.41,1.42)
20% g 2193.7 489.2 0.957 1.41(1.41,1.42)
20% g & 20% f 10357.3 593.2 0.958 1.41(1.41,1.42)

Abbreviations: TT, transmission tetratype; CI, confidence interval

1

None: no missing data; 20% g: 20% of SNP genotypes are missing randomly; 20%g & 20% f: 20% of SNP genotypes are missing randomly and 20% of triads have missing father.

2

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