Modeling the LLS data needs to account for (1) ascertainment, that is, cases were long-lived sibling pairs (ASPs), and (2) the fact that one of the sibs in each pair had most markers imputed because it belonged to the Affy500 data. On the basis of the argument that the ascertainment event depends on the phenotype but is conditionally independent of the genotype given a phenotype, we use the score statistic corresponding to the retrospective likelihood for testing.
