title: Identifying Pleiotropic Genes in Genome-Wide Association Studies for Multivariate Phenotypes with Mixed Measurement Scales.
abstract: We propose a multivariate genome-wide association test for mixed continuous, binary, and ordinal phenotypes. A latent response model is used to estimate the correlation between phenotypes with different measurement scales so that the empirical distribution of the Fisher's combination statistic under the null hypothesis is estimated efficiently. The simulation study shows that our proposed correlation estimation methods have high levels of accuracy. More importantly, our approach conservatively estimates the variance of the test statistic so that the type I error rate is controlled. The simulation also shows that the proposed test maintains the power at the level very close to that of the ideal analysis based on known latent phenotypes while controlling the type I error. In contrast, conventional approaches-dichotomizing all observed phenotypes or treating them as continuous variables-could either reduce the power or employ a linear regression model unfit for the data. Furthermore, the statistical analysis on the database of the Study of Addiction: Genetics and Environment (SAGE) demonstrates that conducting a multivariate test on multiple phenotypes can increase the power of identifying markers that may not be, otherwise, chosen using marginal tests. The proposed method also offers a new approach to analyzing the Fagerström Test for Nicotine Dependence as multivariate phenotypes in genome-wide association studies.
authors.affiliation: School of Nursing, University of Michigan, Ann Arbor, Michigan, United States of America.
authors.forename: James J
authors.identifier: http://orcid.org/0000-0003-0331-9706
authors.initials: JJ
authors.lastname: Yang
authors.affiliation: Department of Internal Medicine, Henry Ford Health System, Detroit, Michigan, United States of America.|The Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, Michigan, United States of America.
authors.forename: L Keoki
authors.initials: LK
authors.lastname: Williams
authors.affiliation: Department of Health Behavior and Biological Sciences, University of Michigan, Ann Arbor, Michigan, United States of America.
authors.forename: Anne
authors.initials: A
authors.lastname: Buu
mesh_terms: D005796:Genes; D055106:Genome-Wide Association Study; D008957:Models, Genetic; D010641:Phenotype