Combining evidence for association from transmission disequilibrium and case-control studies using single-nucleotide polymorphisms

The aim of the present analysis is to combine evidence for association from the two most commonly used designs in genetic association analysis, the case-control design and the transmission disequilibrium test (TDT) design. The cases here are affected offspring from nuclear families and are used in both the case-control and TDT designs. As a result, inference from these designs is not independent. We applied a simple logistic regression method for combining evidence for association from case-control and TDT designs to single-nucleotide polymorphism data purchased on a region on chromosome 3, replicate 1 of the Aipotu population. Combining the evidence from the case-control and TDT designs yielded a 5–10% reduction in the standard errors of the relative risk estimates. The authors did not know the results before the analyses were conducted.