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arXiv 2006.05455stat.ME
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基因-环境交互作用的稳健贝叶斯变量选择

Robust Bayesian variable selection for gene-environment interactions

Jie Ren, Fei Zhou, Xiaoxi Li, Shuangge Ma, Yu Jiang, Cen Wu

摘要:

基因-环境(G $\times$ E)相互作用对阐明主要遗传和环境效应之外的复杂疾病的病因具有重要意义。在G $\times$ E研究的疾病表型中经常遇到异常值和数据污染,这导致了广泛的鲁棒正则化方法的发展。然而,在贝叶斯框架内,这个问题还没有得到照顾,在现有的研究。我们开发了一个完全贝叶斯稳健的变量选择方法G $\times$ E相互作用的研究。所提出的贝叶斯方法可以有效地容纳重尾误差和离群值的响应变量,同时进行变量选择,占结构稀疏。特别是,对于强大的稀疏组选择,穗和板先验已被施加在个人和组的水平,以确定重要的主要和相互作用的影响。一个有效的吉布斯采样器已被开发,以促进快速计算。对来自护士健康研究的具有SNP测量的糖尿病数据和具有基因表达测量的TCGA黑色素瘤数据的广泛模拟研究和分析表明,所提出的方法优于多个竞争替代方案。

英文摘要:

Gene-environment (G$\times$E) interactions have important implications to elucidate the etiology of complex diseases beyond the main genetic and environmental effects. Outliers and data contamination in disease phenotypes of G$\times$E studies have been commonly encountered, leading to the development of a broad spectrum of robust regularization methods. Nevertheless, within the Bayesian framework, the issue has not been taken care of in existing studies. We develop a fully Bayesian robust variable selection method for G$\times$E interaction studies. The proposed Bayesian method can effectively accommodate heavy-tailed errors and outliers in the response variable while conducting variable selection by accounting for structural sparsity. In particular, for the robust sparse group selection, the spike-and-slab priors have been imposed on both individual and group levels to identify important main and interaction effects robustly. An efficient Gibbs sampler has been developed to facilitate fast computation. Extensive simulation studies and analysis of both the diabetes data with SNP measurements from the Nurses' Health Study and TCGA melanoma data with gene expression measurements demonstrate the superior performance of the proposed method over multiple competing alternatives.

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