Advances in marker technology have made a dense marker map a reality. If ea
ch marker is considered separately and separate tests for association with
a disease gene are performed, then multiple testing becomes an issue. A com
mon solution uses a Bonferroni correction to account for multiple tests per
formed. However, with dense marker maps, neighboring markers are tightly li
nked and may have associated alleles; thus tests at nearby marker loci may
not be independent. When alleles at different marker loci are associated, t
he Bonferroni correction may lead to a conservative test, and hence a power
loss. As an alternative, for tests of association that use family data, we
propose a Monte Carlo procedure that provides a global assessment of signi
ficance. We examine the case of tightly linked markers with varying amounts
of association between them. Using computer simulations, we study a family
-based test for association (the transmission/disequilibrium test), and com
pare its power when either the Bonferroni or Monte Carlo procedure is used
to determine significance. Our results show that when the alleles at differ
ent marker loci are not associated, using either procedure results in tests
with similar power. However, when alleles at linked markers are associated
, the test using the Monte Carlo procedure is more powerful than the test u
sing the Bonferroni procedure. This proposed Monte Carlo procedure can be a
pplied whenever it is suspected that markers examined have high amounts of
association, or as a general approach to ensure appropriate significance le
vels and optimal power. Genet. Epidemiol. 19:18-29, 2000. (C) 2000 Wiley-Li
ss, Inc.