Family-based designs are robust to population stratification. For simplicity, we will only consider the trio design, in which both parents are genotyped along with the affected offspring. Analysis involves designation of a case (the affected offspring) and matched ‘pseudo-controls’ inferred on the basis of the transmitted and untransmitted alleles of the parents [19-22]. The structure of the data is equivalent to a matched case–control sample and hence can be analyzed via CLR [23, 24]. An extension to more general types of family data can be found in the discussion.
