Copy number variation is large-scale change in many locations in the genome, including insertions, deletions, inversions and duplications. A CNV can be defined as a DNA segment that is 1 kb or larger and present at variable copy number in comparison with a reference genome (Redon, R., et al. 2006) . CNV has been linked to many human diseases and has been found in all human populations. It also plays an important role in evolution. Array Studio provides comprehensive functions to manage, visualize, analyze and integrate CNV data. In this article, we will introduce the basic functions of CNV analysis.
- 1 Getting Started with CNV Analysis
- 2 Segment Probe-Level SNP Intensity Data to Copy Number Predictions
- 3 Visualize Segmented CNV Data to identify Gains, Losses, and Loss of Heterozygosity
- 4 Integrate CNV chip and DNA-seq Visualizations in the Omicsoft Genome Browser
Array Studio can import SNP and Copy Number Variation (CNV) intensity data, to analyze your samples for chromosome-wide and local amplifications, deletions, and Loss-of-Heterozygosity (LOH) events. The users can easily view, sort and filter data.
Array Studio can merge probe-level SNP intensity data to genomic regions, or segments, with predicted copy numbers for each segment. The CNV Segmentation command will generate segmentation results for Log2Ratio CNV Data, using a variety of criteria, to identify copy number segments, and any Loss of Heterozygosity segments.
After segmenting CNV data, Array Studio has multiple interactive Views to help quickly identify meaningful amplifications and deletions. As with all Array Studio Views, users can sort, filter, and customize the Views to maximize the ability to identify these changes. These data can also be viewed in the Omicsoft Genome Browser.
Omicsoft Genome Browse also allows user to integrate CNV data with DNA-seq data.
For more details on how to use Genome Browser, please refer to blog:
Redon, R., et al. Global variation in copy number in the human genome. Nature 444, 444–454 (2006) doi:10.1038/nature05329