CNVRanger

CNVRanger provides structured downstream analysis of copy number variations (CNVs) from SNP array and next-generation sequencing (NGS) data to summarize CNV calls across populations, assess overlap with functional genomic regions, and perform association analyses linking CNVs to gene expression and quantitative phenotypes.

Key Features:

• R/Bioconductor implementation: Implemented as an R/Bioconductor package for integration into R-based analysis workflows.
• Input data support: Processes CNV calls derived from SNP array data and next-generation sequencing (NGS) technologies.
• CNV summarization: Summarizes individual CNV calls across populations to characterize population-level CNV patterns.
• Functional overlap analysis: Assesses overlap between CNVs and functional genomic regions to link structural variation with genomic features.
• Association analysis: Conducts genome-wide association analyses linking CNVs with gene expression levels and quantitative phenotypes.

Scientific Applications:

• Population-level CNV profiling: Characterizes CNV distribution and diversity across populations and species.
• CNV-functional genomics integration: Identifies CNVs that intersect genes and other functional regions to study potential regulatory impacts.
• CNV-expression and phenotype associations: Links CNVs to gene expression changes and quantitative traits to investigate genetic bases of phenotypic variation.
• Disease and production-trait studies: Applies to investigations of diseases and production traits across various species.

Methodology:

Implemented in R/Bioconductor; accepts CNV calls from SNP array and NGS data; summarizes individual CNV calls across populations; computes overlaps between CNVs and functional genomic regions; and performs genome-wide association analyses linking CNVs with gene expression levels and quantitative phenotypes.