Getting Started with Copy Number Variation Analysis

From Array Suite Wiki

Getting Started with CNV Analysis

Array Studio can import SNP and Copy Number Variation (CNV) intensity data, to analyze your samples for chromosome-wide and focal amplifications, deletions, and Loss-of-Heterozygosity (LOH) events.

For details of Array Studio's approach to identifying CNV in microarray data, see the following White Paper.

  • Import a SNP dataset [00:45]
  • Update your Project to view your new -Omic Dataset[01:55]
  • Add additional sample metadata to your Design table [02:25]
  • View, Sort, and Filter log2ratio intensity data [03:25]

Segment Probe-Level SNP Intensity Data to Copy Number Predictions

Array Studio merges probe-level SNP intensity data to genomic regions, or segments, with predicted copy numbers for each segment.

You can also incorporate B-allele frequency into calls for copy number and Loss-of-Heterozygosity events.

  • Customize CNV Sample IDs by combining Metadata Columns [00:14]
  • Segment CNV SNP-level intensity data with the Segmentation Module [01:45]
  • Output results from Segmentation [02:55]

Visualize Segmented CNV Data to identify Gains, Losses, and Loss of Heterozygosity

After segmenting your CNV data, Array Studio has multiple interactive Views to help you quickly identify meaningful amplifications and deletions. As with all Array Studio Views, you can sort, filter, and customize the Views to maximize your ability to identify these changes. These data can also be viewed in the Omicsoft Genome Browser.

  • Genome View displays Probe-level signal and B-allele frequency [00:20]
  • Segmentation output Table View displays segmented intensities and Copy Number predictions [01:41]
  • Scatter View plots Log2Ratio of segment intensity vs B-allele frequency deviation [02:06]
  • Segment View plots Segmented signal intensity along each chromosome's length[04:30]
  • Segment Chromosome View plots Copy Number predictions along chromosome schematics [05:50]
  • Basic visualization in the Genome Browser [07:25]

Integrate CNV chip and DNA-seq Visualizations in the Omicsoft Genome Browser

After importing and segmenting your SNP chip and DNAseq (WXS/WGS) data into Array Studio, you can quickly visualize them in the Genome Browser. Array Studio Views can take you to a region of interest, or you can just explore.

  • Source Data: DNA-seq pipeline .bam and segmented CNV calls, SNP chip intensity and segmented CNV calls [00:19]
  • Open Genome Browser session on region of interest [01:18]
  • Set .bam display track properties to compare coverage [02:17]
  • Add SNP Array probe-level intensity data [02:50]
  • Set SNP display track properties to compare intensities [03:29]
  • Add Copy number predictions [04:15]
  • Customize Copy number tracks [04:55]
  • Choose a new region from Analysis to view with custom Genome Browser tracks [05:45]

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