CNVScope

CNVScope visualizes copy number variation (CNV) data to reveal and analyze interchromosomal relationships and interaction domains in cancer genomes.

Key Features:

• Interchromosomal Heatmaps: Generates interchromosomal heatmaps to represent CN interactions across different chromosomes.
• CNV Interaction Maps: Constructs CNV interaction maps to identify interaction domains within CN data analogous to Hi-C domains and to highlight amplifications and deletions.
• Gene Annotation and Interaction Visualization: Annotates CN interactions with gene information to provide functional context on interaction maps.
• Integration with Multiple Data Types: Integrates RNASeq data, sample information, Cancer Gene Census data, and structural variants for combined interpretation of CN events.
• Color-Coded Relationship Visualization: Depicts relationships between chromosomal regions using blue for negative associations and red for positive associations.

Scientific Applications:

• Cancer genomics analysis: Enables exploration of CN interaction patterns relevant to basic and translational cancer research, including identification of regions with coordinated copy-number changes.
• Neuroblastoma MYCN investigation: Has been applied to publicly available neuroblastoma CN data to reveal distinct CN interactions involving the MYCN amplicon.

Methodology:

Generates interchromosomal heatmaps and CNV interaction maps, annotates interactions with gene information, integrates RNASeq, sample metadata, Cancer Gene Census entries, and structural variant data, applies color coding for positive/negative associations, and supports multinode/multiprocessor analysis of large CN variant datasets.