STEPC stands for STatistical Explanation for Positional
Cloning. It implements the methods proposed in
Sun L, Cox NJ, McPeek MS (2002).
A Statistical Method for Identification of Polymorphisms That Explain a
Result. American Journal of Human Genetics 70:399-411.
Suppose that many polymorphic sites
have been identified and genotyped in a region
showing strong linkage with a trait.
A key question of interest is
which site (or combination of sites) in the region
influences susceptibility to the trait.
STEPC uses linkage data to
identify the polymorphic sites whose genotypes could
fully explain the observed linkage to the region.
It performs hypothesis tests and derives a confidence set
for the true causal polymorphic site,
under the assumption that there
is only one site in the region influencing the trait.
The information provided by this analysis is different from
that provided by tests of either linkage or association.
This method is appropriate under a very general
model for how the site influences the trait, including
epistasis with unlinked loci, correlated environmental effects within
and gene-environment interaction.
Currently, William Wen in Dr. Nancy Cox lab at the University of Chicago
is developing and testing the