CNV visualization

 
CNV Browser

The CNV Browser can be found under the variant table. It provides an interactive graph to visualize the CNV call region in all samples of the cohort.

The position of the CNV call in the reference genome is represented in the top of the CNV Browser.

The position field can be filled with other genomic positions. Click "Go" to visualize a different genomic region in the test sample.

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The region of the CNV call is highlighted in red. The grey area shows the 95% confidence interval of the read ratio (observed/expected reads). Each colored rectangle represents a read ratio measure for the selected sample. The read ratio measures falling within the confidence interval will be colored in blue while the ones not falling within the expected range will be shown in red.

Below the CNV call there is a graph representing the coverage in the selected genomic range where the coverage of the test sample is shown as a red line. The user can choose to view the coverage in logarithmic or linear scale.

On the right side of the CNV Browser, the user can find the following information:

  • Hovered position: this represents the position in the reference genome when the user hovers over the browser with the mouse. It also shows the coverage, the read ratio and the expected read ratio for the hovered position.

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  • Selected call: information about the selected CNV call in the variant table: copy number (assuming a diploid state), call type, start and end of the call, length and number of exons involving the CNV call.
  • Analyses: this allows the user to visualize the CNV call region in the rest of the samples of the CNV analysis. This contains the names of all samples of the cohort, no matter if they have been used for building the reference set for the given test sample or not. The test sample name is highlighted in bold. When hovering over a sample name different than the test sample, the line coverage is highlighted in blue. 

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When hovering over the 👁️ icon next to the sample name, the user can visualize the observed/expected read ratio for the given position in other samples of the cohort. 

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The different exons conforming the genes overlapping the CNV call are represented below. Click on the graph and zoom out to visualize the whole gene in the CNV browser.

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CNV Plot

For CNV cohort analyses, VarSome Clinical provides a CNV plot, showing how the observed read depth in the area of the CNV differs from the expected. The plot can be found on its own tab, under the Variant Table.

The CNV plots are generated using a modified version of the ExomeDepth tool.  

  • The grey area indicates the 95% confidence interval of the observed/expected read ratio and the red crosses are specific read depth values at those positions. The genomic location of the CNV is given by the vertical dotted lines.
  • The left Y-axis shows the "Observed vs expected read ratio" and the right Y-axis represents the "Copy number". The X-axis shows the chromosome coordinates.
  • For short CNVs that encompass a few exons, the plot is displayed in a gene-centered view where the exon numbers and their position along the gene are represented in a horizontal axis above the gene name.
  • For large CNVs, please note that, since the CNV region might encompass several genes, making it impossible to plot all of them, we only show the position of the canonical transcript for each gene. Therefore, if a gene has no canonical transcript (e.g. annotated pseudogene) or if its canonical transcript doesn't overlap with the CNV, you may see genes listed in the Variant Table that are not shown in the CNV plot since their canonical transcript isn't the one that overlaps with the CNV.

Figure: In this example, the observed to expected read depth ratio in the region of the CNV is lower than 1 and below the 95% confidence interval (grey area). These results support the hypothesis of a deletion in the exon 20 of the BRCA1 gene.

Known CNVs

We display only the relevant CNVs for the classification according to the following criteria: 
  • CNV deletions: we retain those that fully overlap with the given CNV for gnomAD variants. For CNVs coming from clinical sources (Decipher, DBVar, ClinVar CNVs) we use the overlapping CNVs if they are benign and the contained CNVs if they are pathogenic.
  • CNV duplications: we keep only the CNVs encompassing the same coding genes. If the CNV is non-coding, then we retain the CNVs that have at least 85% of overlap.
 
 

Reads alignment visualization on JBrowse

Once you have selected a variant in the variant table, you can click on the JBrowse icon to view the alignment of the reads in the regions of the detected CNVs. The CNV called region is highlighted in yellow. The gene and the transcripts are represented above the aligned reads. 

 

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Browsing through the samples of a CNV analysis

You can search through the samples analyzed under the same CNV/SV analysis by visiting the results page of one and using the red arrows you can be directed to the next or previous sample:

 

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