TABLE 2

Estimated penetrances and empirical type I error rates in the dominant mode

qcSample size N+aaType I
 error rateb
0.210000.20025 ± 0.020850.20000 ± 0.016250.05060
0.110000.09996 ± 0.015700.10008 ± 0.012410.05580
0.2 2000.19929 ± 0.047190.19973 ± 0.036540.05040
0.2 1000.19987 ± 0.066440.20118 ± 0.052380.05640
0.4 1000.39986 ± 0.082450.40040 ± 0.064000.05980
0.5 1000.50117 ± 0.084710.49938 ± 0.064180.05280
  • a Mean ± SD of the estimates for two penetrances obtained by analysis under the alternative hypothesis.

  • b The proportion of attempts that yielded values of the statistic over 3.841 (the value that yields the cumulative density function of 0.95 for the χ2 distribution with 1 d.f.).

  • Each simulation was performed with a given penetrance (qc) and a sample size (N) under the null hypothesis in the dominant mode as stated in simulation (under methods). After removing the phase information, PENHAPLO was used to estimate + and under the alternative hypothesis. The same software also calculates Lmax by analysis under the alternative hypothesis and L0max by analysis under the null hypothesis. The statistic −2 log(L0max/Lmax) was then calculated. This simulation was repeated 10,000 times for each parameter set.