Whole Genome Scans: The Significance Level

Abstract

The task of mapping loci related to a trait is carried out in a number of steps. The aim of the first step is the identification of the chromosome carrying the trait-related polymorphism. Within that chromosome, one finds a wide region which is likely to contain the genetic factor. The second step involves the narrowing down of the region. Finally, once the functional polymorphism has been barricaded within a small enough chromosomal region, the direct examination of polymorphic loci is carried out. An experimental design, which is efficient for one step, may be less efficient for a subsequent step. Therefore, it is useful to apply different experimental resources for each step. Likewise, the statistical tools and the analytic theory may vary from one step to the next. In this and the next chapters we will concentrate on the statistical considerations that are important for the first step: a whole genome scan aimed at the identification of a (relatively wide) chromosomal region containing the functional polymorphism.