Correlation among sibling marker genotypes may invalidate the results of fa
mily-based tests of association in the presence of linkage. We apply an emp
irical variance estimation method, which is implemented in the program pack
age FBAT, on Caucasian families with asthma in the presence and absence of
linkage and compare the results with those obtained using the TDT (TDTEX-PA
IRS) on the same data sets. Our results indicate that both tests generally
perform comparably in either setting. ((C))2001 Wiley-Liss, Inc.