Conclusions of segregation analysis for family data generated under two-locus models

Susceptibility to a disease may involve the interactive effect of two genes. What conclusions will be drawn by segregation analysis in such a case? To answer this question, we considered a set of two-locus models and the corresponding exact distribution for 300 families. We investigated the conclusions and parameter estimations obtained for this sample, by comparing the likelihood expectations of the unified model and of more restricted models. In many cases, segregation analysis leads to the conclusion of a major gene effect, with or without a polygenic component--usually without a polygenic component in multiplicative models (i.e., where two genes have a multiplicative effect) and with such a component in nonmultiplicative models. For all the models considered, existence of a major gene effect is supported by transmission probability tests; there is evidence for transmission and agreement with the hypothesis of Mendelian transmission. Accordingly, there is no means of detecting that the effect of a major gene, with or without a polygenic component, does not correspond to the correct model. In addition, the parameter estimates for the major gene do not correspond to the characteristics of either of the two genes of the true model. This may substantially affect further linkage analysis.