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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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CNVScope: Visually Exploring Copy Number Aberrations in Cancer Genomes.

James Lt Dalgleish1, Yonghong Wang1, Jack Zhu1

  • 1Genetics Branch, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA.

Cancer Informatics
|December 14, 2019
PubMed
Summary

This study introduces CNVScope, a toolkit for visualizing DNA copy number interactions in cancer research. It helps identify relationships between chromosomal regions, aiding in the discovery of novel cancer-related events.

Keywords:
CNACNVRcancercopy numbercopy number variationshinyvisualization

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Area of Science:

  • Genomics
  • Bioinformatics
  • Cancer Research

Background:

  • DNA copy number (CN) data are crucial for cancer research but often lack context regarding chromosomal region relationships.
  • Existing CN segmentation data do not fully capture the complex interactions between chromosomal regions.

Purpose of the Study:

  • To develop a toolkit for visually exploring the copy number interactome.
  • To enable scientists without programming experience to analyze CN data.
  • To construct CN interactomes from publicly available datasets.

Main Methods:

  • Development of the CNVScope toolkit, including a shiny application and an R package.
  • Utilizing publicly available neuroblastoma CN data for demonstration.
  • Visual exploration of CN interactome to identify cis and trans events.

Main Results:

  • CNVScope visualization clearly shows CN interactions around the MYCN amplicon in neuroblastoma.
  • Identified cis and trans events, including a significant anticorrelation between 11q loss and 17q gain.
  • The 11q loss region was found to be bounded by the cell cycle regulator CCND1.

Conclusions:

  • CNVScope provides a valuable tool for exploring complex CN interactions in cancer research.
  • The toolkit facilitates the discovery of novel genomic alterations and their relationships.
  • CNVScope is accessible to researchers without extensive programming experience.