Estimation of segregation and linkage parameters in simulated data. I. Segregation analyses with different ascertainment schemes

We report the results of a simulation study designed to assess the capability of segregation analysis to detect Mendelian transmission and to estimate genetic model parameters for complex qualitative traits, characterized by heritability in the range 0.20-0.45 and low heterozygote penetrance. The pedigree analysis package, PAP, was used to perform the analyses. For all data sets, models of no transmission could be rejected. In most cases, models of Mendelian transmission could not be rejected; however, several samples approached significance levels. When Mendelian transmission was assumed, reasonably good parameter estimates were obtained, although heterozygote penetrances were often overestimated. Different sampling schemes were imposed on the simulated data in order to examine the extent of information loss with the reduction in sample size. One of these strategies (a sequential sampling scheme) appears to have resulted in critical loss of information in some cases.