A Review of Statistical Methods for Identifying Trait-Relevant Tissues and Cell Types.
A Review of Statistical Methods for Identifying Trait-Relevant Tissues and Cell Types.
复制标题
DOI：
10.3389/fgene.2020.587887
复制
发表时间：
2020
影响因子：
3.7
通讯作者：
Zhou X
中科院分区：
文献类型：
--
作者：
Zhu H;Shang L;Zhou X
全基因组关联研究（GWASs）已经发现并复制了许多与疾病和疾病相关的复杂性状相关的遗传变异。然而，这些已确定的关联背后的生物学机制在很大程度上仍然难以捉摸。探索这些关联背后的生物学机制需要识别与性状相关的组织和细胞类型，因为遗传变异可能以组织和细胞类型特异性的方式影响复杂的性状。最近，已经开发了几种统计方法来整合基因组数据与GWAS，用于识别性状相关的组织和细胞类型。这些方法通常依赖于不同的基因组信息，并使用不同的统计模型进行性状-组织相关性推断。在这里，我们提出了一个全面的技术审查，总结现有的10种方法的性状组织相关性推断。这些方法利用不同的基因组信息，包括功能注释信息、表达数量性状位点信息、遗传调控基因表达信息以及基因共表达网络信息。这些方法还使用不同的统计模型，从线性混合模型到协方差网络模型。我们希望这篇评论可以作为一个有用的参考方法学家谁开发的方法和应用分析师谁应用这些方法来识别性状相关的组织和细胞类型。
Genome-wide association studies (GWASs) have identified and replicated many genetic variants that are associated with diseases and disease-related complex traits. However, the biological mechanisms underlying these identified associations remain largely elusive. Exploring the biological mechanisms underlying these associations requires identifying trait-relevant tissues and cell types, as genetic variants likely influence complex traits in a tissue- and cell type-specific manner. Recently, several statistical methods have been developed to integrate genomic data with GWASs for identifying trait-relevant tissues and cell types. These methods often rely on different genomic information and use different statistical models for trait-tissue relevance inference. Here, we present a comprehensive technical review to summarize ten existing methods for trait-tissue relevance inference. These methods make use of different genomic information that include functional annotation information, expression quantitative trait loci information, genetically regulated gene expression information, as well as gene co-expression network information. These methods also use different statistical models that range from linear mixed models to covariance network models. We hope that this review can serve as a useful reference both for methodologists who develop methods and for applied analysts who apply these methods for identifying trait relevant tissues and cell types.