MOTIVATION: The Sequence Kernel Association Test (SKAT) and its extensions are the most popular methods for studying the association between phenotypes and a set of single nucleotide polymorphisms. Their practical application is very wide, but most of these methods are designed for continuous and binary phenotypes. Ordered categorical phenotypes are also very common in practice, so there is an urgent need to develop SKAT-type tests for proportional odds model. RESULTS: To accommodate ordered categorical phenotypes, we propose a test named the Sequence Kernel Association Test for the Proportional Odds Model (POM-SKAT). It constructs a score test for the variance of the coefficients of interest using a quasi-likelihood and the P-value is evaluated by approximating the asymptotic distribution of the test statistic with the Pearson Type III distribution. Simulation studies demonstrate that our method performs well and achieves high power in detecting gene-phenotype associations. We apply POM-SKAT to rheumatoid arthritis data provided by Genetic Analysis Workshop 16, identifying multiple relevant gene variants. AVAILABILITY AND IMPLEMENTATION: Code is available at GitHub (https://github.com/amss-stat/POM-SKAT).

Herein, we propose a Spearman rank correlation-based screening procedure for ultrahigh-dimensional data with censored response cases. The proposed method is model-free without specifying any regression forms of predictors or response variables and is robust under the unknown monotone transformations of these response variable and predictors. The sure-screening and rank-consistency properties are established under some mild regularity conditions. Simulation studies demonstrate that the new screening method performs well in the presence of a heavy-tailed distribution, strongly dependent predictors or outliers, and offers superior performance over the existing nonparametric screening procedures. In particular, the new screening method still works well when a response variable is observed under a high censoring rate. An illustrative example is provided.