As a first step we estimate the genetic background of unrelated individuals (cases, controls, and trio probands) using a dimension reduction technique. Here as an illustration we consider genotypic data from the International HapMap Project (30 CEU trios) and from the POPRES database [29]. Trio probands are matched to one or more controls that are genetically similar based on the eigenmap (Figure 1) [17]. The Euclidean distance between individuals in this eigenspace are representative of their genetic differences. When data consist of family-based samples as trios of parents and their affected offspring, as well as additional controls, we will prefer one case:many control matching.
