A hierarchical clustering method for dimension reduction in joint analysis of multiple phenotypes

Genome-wide association studies (GWAS) have become a very effective research tool to identify genetic variants of underlying various complex diseases. In spite of the success of GWAS in identifying thousands of reproducible associations between genetic variants and complex disease, in general, the association between genetic variants and a single phenotype is usually weak. It is increasingly recognized that joint analysis of multiple phenotypes can be potentially more powerful than the univariate analysis, and can shed new light on underlying biological mechanisms of complex diseases. In this paper, we develop a novel variable reduction method using hierarchical clustering method (HCM) for joint analysis of multiple phenotypes in association studies. The proposed method involves two steps. The first step applies a dimension reduction technique by using a representative phenotype for each cluster of phenotypes. Then, existing methods are used in the second step to test the association between genetic variants and the representative phenotypes rather than the individual phenotypes. We perform extensive simulation studies to compare the powers of multivariate analysis of variance (MANOVA), joint model of multiple phenotypes (MultiPhen), and trait-based association test that uses extended simes procedure (TATES) using HCM with those of without using HCM. Our simulation studies show that using HCM is more powerful than without using HCM in most scenarios. We also illustrate the usefulness of using HCM by analyzing a whole-genome genotyping data from a lung function study