CNVRanger：CNV 与基因表达和定量表型的关联分析。
CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes.
机构信息
Department of Animal Breeding and Genomics, Wageningen University and Research, 6708 PB Wageningen, The Netherlands.
Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala 75007, Sweden.
出版信息
Bioinformatics. 2020 Feb 1;36(3):972-973. doi: 10.1093/bioinformatics/btz632.
SUMMARY
Copy number variation (CNV) is a major type of structural genomic variation that is increasingly studied across different species for association with diseases and production traits. Established protocols for experimental detection and computational inference of CNVs from SNP array and next-generation sequencing data are available. We present the CNVRanger R/Bioconductor package which implements a comprehensive toolbox for structured downstream analysis of CNVs. This includes functionality for summarizing individual CNV calls across a population, assessing overlap with functional genomic regions, and genome-wide association analysis with gene expression and quantitative phenotypes.
AVAILABILITY AND IMPLEMENTATION
摘要
拷贝数变异（CNV）是一种主要的结构性基因组变异，目前在不同物种中越来越多地被研究，以与疾病和生产性状相关联。已经有用于从 SNP 芯片和下一代测序数据中实验检测和计算推断 CNV 的既定方案。我们提出了 CNVRanger R/Bioconductor 包，它实现了一个全面的工具框，用于对 CNV 进行结构化的下游分析。这包括功能，用于总结人群中个体 CNV 调用，评估与功能基因组区域的重叠，以及与基因表达和定量表型的全基因组关联分析。
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