copy number variation
Definition
Copy number variation (CNV) refers to structural genomic alterations where segments of DNA, typically ranging from 1 kilobase to several megabases, are duplicated or deleted, resulting in an abnormal number of copies compared to a reference genome. CNVs represent a significant source of genetic diversity and can encompass entire genes or regulatory regions, affecting gene dosage and expression levels. These variations occur in approximately 12% of the human genome and play crucial roles in evolution, disease susceptibility, and phenotypic variation. CNVs are particularly important in cancer biology, where amplifications of oncogenes or deletions of tumor suppressors drive malignant transformation, and in neurodevelopmental disorders where dosage imbalances affect brain development and function.
Visualize copy number variation in Nodes Bio
Researchers can map CNV-affected genes onto protein-protein interaction networks to identify functional modules disrupted by dosage imbalances. Network visualization reveals how amplified or deleted genes propagate effects through signaling cascades and regulatory pathways. Users can overlay CNV data with gene expression profiles to distinguish direct dosage effects from downstream compensatory mechanisms, enabling identification of therapeutic targets in CNV-driven diseases.
Visualization Ideas:
- Gene-disease association networks showing CNV hotspots across cancer types
- Protein interaction networks highlighting dosage-sensitive complexes affected by CNVs
- Multi-omics integration networks connecting CNV regions to transcriptional and phenotypic changes
Example Use Case
A cancer genomics team investigating glioblastoma identifies recurrent amplification of chromosome 7 and deletion of chromosome 10 in patient samples. By mapping these CNVs onto molecular interaction networks in Nodes Bio, they discover that EGFR amplification (chromosome 7) and PTEN deletion (chromosome 10) converge on PI3K/AKT signaling. Network analysis reveals synthetic lethal partners and compensatory pathways activated in response to these CNVs, guiding combination therapy strategies targeting both the amplified oncogenic driver and its network dependencies.