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 Linkage 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 families, and gene-environment interaction.

Currently, William Wen in Dr. Nancy Cox lab at the University of Chicago is developing and testing the software package.