Data-adaptive gene and pathway-based tests forrare-variant associations with survival outcomes

Abstract

Statistical methods for testing aggregate rare-variant genetic associations are typically based on either burden or dispersion tests (or a combination of the two). These methods lack statistical power in the presence of diverse genetic architectures. Moreover, few aggregate rare-variant association methods have been developed specifically for survival data. To address these issues, we propose data-adaptive gene- and pathway-based association tests based on Schoenfeld residuals in Cox proportional hazards models for association studies between an aggregate of rare-variants and survival outcomes. Our methods improve statistical power while maintaining flexibility across various genetic effect sizes and directions. We develop an efficient R package that enables fast computation and supports data simulation as well as gene- and pathway-level testing. Applying our approach to late bladder toxicity following radiotherapy for non-metastatic prostate cancer, we identify biologically relevant genes and pathways, replicate known signals, and capture additional associations. Our method provides a powerful, adaptive framework for survival-based genetic association studies of rare-variants. Keywords: aSPU, time-to-event outcomes, rare-variant associations, Cox regression, Schoenfeld residuals