CNVRanger: association analysis of CNVs with geneexpression and quantitative phenotypes.

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Author(s): SILVA, V. da; RAMOS, M.; GROENEN, M.; CROOIJMANS, R.; JOHANSSON, A.; REGITANO, L. C. de A.; COUTINHO, L.; ZIMMER, R.; WALDRON, L.; GEISTLINGER, L.

Summary: Copy number variation (CNV) is a major type of structural genomic variation that is increasingly studied acrossdifferent species for association with diseases and production traits. Established protocols for experimental detection andcomputational inference of CNVs from SNP array and next-generation sequencing data are available. We present theCNVRangerR/Bioconductor package which implements a comprehensive toolbox for structured downstream analysis ofCNVs. This includes functionality for summarizing individual CNV calls across a population, assessing overlap with func-tional genomic regions, and genome-wide association analysis with gene expression and quantitative phenotypes.

Publication year: 2020

Types of publication: Journal article

Unit: Embrapa Southeastern Livestock

Keywords: Expressão gênica, Fenótipos quantitativos, Genomic hybridization, Quantitative phenotypes, Structural genomic

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