UGMDR: A unified conceptual framework for detection of multifactor interactions underlying complex traits

Abstract

Biological outcomes are governed by multiple genetic and environmental factors that act in concert. Determining multifactor interactions is the primary topic of interest in recent genetics studies but presents enormous statistical and mathematical challenges. The computationally efficient multifactor dimensionality reduction (MDR) approach has emerged as a promising tool for meeting these challenges. On the other hand, complex traits are expressed in various forms and have different data generation mechanisms that cannot be appropriately modeled by a dichotomous model; the subjects in a study may be recruited according to its own analytical goals, research strategies and resources available, not only consisting of homogeneous unrelated individuals. Although several modifications and extensions of MDR have in part addressed the practical problems, they are still limited in statistical analyses of diverse phenotypes, multivariate phenotypes and correlated observations, correcting for potential population stratification and unifying both unrelated and family samples into a more powerful analysis. I propose a comprehensive statistical framework, referred as to unified generalized MDR (UGMDR), for systematic extension of MDR. The proposed approach is quite versatile, not only allowing for covariate adjustment, being suitable for analyzing almost any trait type, for example, binary, count, continuous, polytomous, ordinal, time-to-onset, multivariate and others, as well as combinations of those, but also being applicable to various study designs, including homogeneous and admixed unrelated-subject and family as well as mixtures of them. The proposed UGMDR offers an important addition to the arsenal of analytical tools for identifying nonlinear multifactor interactions and unraveling the genetic architecture of complex traits.