Correlated frailty model for analysis of genetic association in family studies

Abstract

Family-based study designs allow the investigation of gene mutation effects on a disease risk by considering related family members. Some methods have been developed for testing sets of genetic variants in family studies but only very few can handle right-censored time-to-event data. We propose here a correlated frailty model for the analysis of a survival outcome related to cancer in presence of familial correlations. These familial correlations are explained by a residual familial component specified by a kinship matrix and a region- or gene-based specific correlation structure modeled via identical-by-descent (IBD) probability matrix. The proposed approach is used to quantify and evaluate the association between a set of common single nucleotide polymorphism (SNPs) or rare variants (or both) from the same genomic region and a survival outcome, e.g. time to disease onset. The model's marginal likelihood is maximized using the Marquardt algorithm. We evaluated the method by simulations under various scenarios where we varied the family size, the strength of genetic associations from multiple rare variants and the presence or not of residual familial correlation. The results indicate that the correlated frailty model can be valuable in family cancer studies, for example to identify genomic regions significantly associated with the time to cancer onset.