CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes

Vinicius da Silva; Marcel Ramos; Martien Groenen; Richard Crooijmans; Anna Johansson; Luciana Regitano; Luiz Coutinho; Ralf Zimmer; Levi Waldron; Ludwig Geistlinger

doi:10.1093/bioinformatics/btz632

CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes

Bioinformatics. 2020 Feb 1;36(3):972-973. doi: 10.1093/bioinformatics/btz632.

Authors

Affiliations

¹ Department of Animal Breeding and Genomics, Wageningen University and Research, 6708 PB Wageningen, The Netherlands.
² Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala 75007, Sweden.
³ Department of Epidemiology and Biostatistics, Graduate School of Public Health and Health Policy, City University of New York, New York, NY 10027, USA.
⁴ Embrapa Pecuaria Sudeste, 13560-970 São Carlos, Brazil.
⁵ Department of Animal Science, University of São Paulo, 13418-900 Piracicaba, Brazil.
⁶ Department of Bioinformatics, Ludwig-Maximilians-Universität München, 80333 München, Germany.

Abstract

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: http://bioconductor.org/packages/CNVRanger.

MeSH terms

Computational Biology
DNA Copy Number Variations*
Genome-Wide Association Study*
Phenotype
Polymorphism, Single Nucleotide