It is of interest to compare measures of association of binary traits among
samples of bivariate data. One example is the comparison of association wi
thin a sample of monozygotic (MZ) twins to that within a sample of dizygoti
c (DZ) twins. A larger association in the MZ twins suggests that the trait
of interest may have a genetic component. The Bivariate data in this exampl
e are binary traits for the twins in each pair. Another example is the comp
arison of a measure of Hardy-Weinberg disequilibrium across several populat
ions. The bivariate data in this example are the two alleles comprising the
genotype of interest. We propose using derived logistic regression equatio
ns from the full exponential model for the bivariate outcomes to test for h
omogeneity. We adjust for correlation among outcomes via generalized estima
ting equations. This modeling approach allows for adjustment for individual
-level and pair-level covariates and thereby allows for testing for gene x
environment interactions. Further, we extend the model to allow for simulta
neous analysis of two diseases, which allows for testing for a genetic comp
onent to the coaggregation of two diseases. In contrast to approaches propo
sed by previous authors, no special software is required; our approach can
be easily implemented in standard software packages. We compare our results
to those of other methods proposed in the literature for data from the Vie
tnam Era Twins Study. We apply our methods also to the Anqing Twin Study an
d to data on major depression and generalized anxiety disorder from the Vir
ginia Twin Register. (C) 2001 Wiley-Liss, Inc.