Genetic interactions play an important role in the progression of complex diseases, providing explanation of variations in disease phenotype missed by main genetic effects. Comparatively, there are fewer investigations on prognostic survival time, given its challenging characteristics such as censoring. In recent biomedical research, two-level analysis of both genes and their involved pathways has received much attention and been demonstrated to be more effective than single-level analysis, however such analysis is limited to main effects. Pathways are not isolated and their interactions have also been suggested to have important contributions to the prognosis of complex diseases. In this article, we develop a novel two-level Bayesian interaction analysis approach for survival data. This approach is the first to conduct the analysis of lower-level gene-gene interactions and higher-level pathway-pathway interactions simultaneously. Significantly advancing from existing Bayesian studies based on the Markov Chain Monte Carlo (MCMC) technique, we propose a variational inference framework based on the accelerated failure time model with favourable priors to account for two-level selection as well as censoring. The computational efficiency is much desirable for high dimensional interaction analysis. We examine performance of the proposed approach using extensive simulation. Application to TCGA melanoma and lung adenocarcinoma data leads to biologically sensible findings with satisfactory prediction accuracy and selection stability.
翻译:遗传互动在复杂疾病的演变中起着重要作用,解释了因主要遗传效应而错失的疾病细胞型的变异性。比较而言,鉴于诸如审查等具有挑战性的特点,对预测性存活时间的调查较少。在最近的生物医学研究中,对两种基因及其参与途径的两级分析都受到极大关注,并证明比单一分析更有效,但这种分析仅限于主要影响。途径并非孤立,它们的互动也被认为对复杂疾病的预测有重要贡献。在本篇文章中,我们为生存数据开发了新型的双级巴耶西亚互动分析方法。这是首次同时分析较低层次基因-基因互动和更高层次路径-路径互动的方法。从现有的巴伊西亚研究中大大推进了以马尔科夫链蒙特卡洛(MC)技术为基础的显著进展,我们提议基于加速失败时间模型的变异推论框架,在进行两级选择和审查之前,考虑得益。计算效率对于高层面的贝耶斯互动分析非常可取。这是首次对较低层次的基因-基因-基因互动和更高层次-路径-路径互动进行分析。我们用高清晰度-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-空气-