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Integration of Multiple Genomic Data Sources in a Bayesian Cox Model for Variable Selection and Prediction

机译:贝叶斯考克斯模型中多个基因组数据源的集成用于变量选择和预测

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摘要

Bayesian variable selection becomes more and more important in statistical analyses, in particular when performing variable selection in high dimensions. For survival time models and in the presence of genomic data, the state of the art is still quite unexploited. One of the more recent approaches suggests a Bayesian semiparametric proportional hazards model for right censored time-to-event data. We extend this model to directly include variable selection, based on a stochastic search procedure within a Markov chain Monte Carlo sampler for inference. This equips us with an intuitive and flexible approach and provides a way for integrating additional data sources and further extensions. We make use of the possibility of implementing parallel tempering to help improve the mixing of the Markov chains. In our examples, we use this Bayesian approach to integrate copy number variation data into a gene-expression-based survival prediction model. This is achieved by formulating an informed prior based on copy number variation. We perform a simulation study to investigate the model's behavior and prediction performance in different situations before applying it to a dataset of glioblastoma patients and evaluating the biological relevance of the findings.
机译:在统计分析中,尤其是在高维中执行变量选择时,贝叶斯变量选择变得越来越重要。对于生存时间模型和基因组数据的存在,目前还没有充分利用现有技术。一种较新的方法提出了针对右删失的事件时间数据的贝叶斯半参数比例风险模型。我们基于马尔可夫链蒙特卡洛采样器中的随机搜索过程,将该模型扩展为直接包括变量选择,以进行推理。这为我们提供了一种直观而灵活的方法,并提供了一种集成其他数据源和进一步扩展的方法。我们利用实施平行回火的可能性来帮助改善马尔可夫链的混合。在我们的示例中,我们使用这种贝叶斯方法将拷贝数变异数据整合到基于基因表达的生存预测模型中。这是通过根据副本数量变化制定知情先验来实现的。我们进行了模拟研究,以研究模型在不同情况下的行为和预测性能,然后将其应用于胶质母细胞瘤患者数据集并评估发现的生物学相关性。

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