论文标题
贝叶斯的方法,用于估算全转录组关联框架下的基因级多基因研究
A Bayesian method for estimating gene-level polygenicity under the framework of transcriptome-wide association study
论文作者
论文摘要
多核心是指多种遗传变异对复杂性状具有非零影响的现象。它被定义为对性状具有非零影响的遗传变异的比例。多基因的评估可以为特征的遗传结构提供宝贵的见解。最近的几项著作试图在SNP级别估计多基因。但是,在生物学上评估基因水平的多基因可以更有意义。我们提出了基因级多基因的概念,该概念定义为在整个转录组关联研究框架下对特征的基因比例。我们引入了一种贝叶斯方法聚苯烯,以估计特征的这一数量。该方法基于尖峰和平板先验,同时提供了非无效基因的最佳子集。我们的仿真研究表明,多月有效估计基因级多基因。该方法由于非无效基因而导致的特质遗传性少量产生向下偏置,该基因随着GWAS样本量的增加而迅速减少。在识别非无效基因的最佳子集的同时,聚乙烯提供了高水平的特异性和整体良好的灵敏度水平 - 灵敏度随着参考面板表达式的样本量和GWAS数据的增加而增加。我们将该方法应用于英国生物库中的七个表型,并集成了表达数据。我们发现高度最多的多基因和哮喘是最少的多基因。我们的分析表明,HDL和甘油三酸酯都比LDL更多基因。
Polygnicity refers to the phenomenon that multiple genetic variants have a non-zero effect on a complex trait. It is defined as the proportion of genetic variants that have a nonzero effect on the trait. Evaluation of polygenicity can provide valuable insights into the genetic architecture of the trait. Several recent works have attempted to estimate polygenicity at the SNP level. However, evaluating polygenicity at the gene level can be biologically more meaningful. We propose the notion of gene-level polygenicity, defined as the proportion of genes having a non-zero effect on the trait under the framework of transcriptome-wide association study. We introduce a Bayesian approach polygene to estimate this quantity for a trait. The method is based on spike and slab prior and simultaneously provides an optimal subset of non-null genes. Our simulation study shows that polygene efficiently estimates gene-level polygenicity. The method produces downward bias for small choices of trait heritability due to a non-null gene, which diminishes rapidly with an increase in the GWAS sample size. While identifying the optimal subset of non-null genes, polygene offers a high level of specificity and an overall good level of sensitivity -- the sensitivity increases as the sample size of the reference panel expression and GWAS data increase. We applied the method to seven phenotypes in the UK Biobank, integrating expression data. We find height to be most polygenic and asthma to be the least polygenic. Our analysis suggests that both HDL and triglycerides are more polygenic than LDL.