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Other publication in scientific journal - Peer-reviewed, 2020

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

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

Abstract

A 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.

Keywords

Copy number variation (CNV); structural genomic variation; SNP-arrays; next-generation sequencing data

Published in

Bioinformatics
2020, Volume: 36, number: 3, pages: 972-973

      SLU Authors

    • UKÄ Subject classification

      Bioinformatics (Computational Biology)

      Publication identifier

      DOI: https://doi.org/10.1093/bioinformatics/btz632

      Permanent link to this page (URI)

      https://res.slu.se/id/publ/101819