A Likelihood Ratio Approach to Family‐based Association Studies with Covariates

Summary We introduce a procedure for association based analysis of nuclear families that allows for dichotomous and more general measurements of phenotype and inclusion of covariate information. Standard generalized linear models are used to relate phenotype and its predictors. Our test procedure, based on the likelihood ratio, unifies the estimation of all parameters through the likelihood itself and yields maximum likelihood estimates of the genetic relative risk and interaction parameters. Our method has advantages in modelling the covariate and gene‐covariate interaction terms over recently proposed conditional score tests that include covariate information via a two‐stage modelling approach. We apply our method in a study of human systemic lupus erythematosus and the C‐reactive protein that includes sex as a covariate.