Simulation study on covariance component estimation for two binary traits in an underlying continuous scale.

The usefulness of the variance and covariance component estimation methods based on a threshold model was studied in a multiple-trait situation with two binary traits. Estimation equations that yield marginal maximum likelihood estimates of variance components on the underlying continuous variable scale and point estimates of location parameters with empirical Bayesian properties are described. Methods were tested on simulated data sets that were generated to exhibit three different incidences, 25, 15, and 5%. Results were compared with analyses of the same data sets with a REML method based on normal distribution and a linear model. Heritabilities and residual correlations calculated from discrete observations were transformed to underlying parameters. In estimation of heritabilities, all methods performed equally well at all incidence levels and with no detectable bias. As suggested by threshold theory, the genetic correlation was accurately estimated directly from the observations without any need of correction for incidence. Marginal maximum likelihood estimates of genetic correlations were similar to linear model estimates; discrepancies from the true parameters were consistent with both methods. In estimation of residual correlations, the method with the linear model approach yielded satisfactory estimates only at the highest incidence level, 25%. For 5% incidence, the uncorrected estimate of residual correlation was 50% less than the true value, and after correction for incidence, the parameter was overestimated by 90%. The estimates of residual correlation from the threshold model were regarded fair, except at the lowest level of incidence, where the estimate was 27% higher than the true value. Results indicated that when an accurate estimate of residual correlation is needed, the marginal maximum likelihood estimates are superior to the estimates calculated with the linear model. Using correction for the incidence level for residual correlation did not work well except at the highest incidence level.