Incorporating parental information into family-based association tests

Assumptions regarding the true underlying genetic model, or mode of inheritance, are necessary when quantifying genetic associations with disease phenotypes.Here we propose new methods to ascertain the underlying genetic model from parental data in family-based association studies.Specifically, for parental mating-type data, we propose a novel statistic to test whether the underlying genetic model is additive, dominant, or recessive; for parental genotype.phenotype data, we propose three strategies to determine the true mode of inheritance.We illustrate how to incorporate the information gleaned from these strategies into family-based association tests.Because family-based association tests are conducted conditional on parental genotypes, the type I error rate of these procedures is not inflated by the information learned from parental data.This result holds even if such information is weak or when the assumption of Hardy.Weinberg equilibrium is violated.Our simulations demonstrate that incorporating parental data into family-based association tests can improve power under common inheritance models.The application of our proposed methods to a candidate-gene study of type 1 diabetes successfully detects a recessive effect in MGAT5 that would otherwise be missed by conventional family-based association tests.