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 marked at the top of the CNV Browser and the chromosome name is shown on the left. The user can change the size of the region shown by dragging:
In the chromosome track the user can choose which strand they want to see with all the related data, by clicking on the "STRAND" button. STRAND 1 (default) refers to the positive strand (5'-3' direction), while STRAND -1 to the negative one (3'-5' direction). Additionally, the browser offers the option to expand the chromosome-level visualization from the current chromosome to all chromosomes (and vice versa), by clicking on the “EXPAND TO ALL CHRS” button on the right-hand side of the bar. Each chromosome can be selected for visualization to inspect the identified variants.
The CNV calls track shows if it is a deletion or a duplication. Deletions are represented by an empty rectangle and duplications by a full one. The position in the reference genome and the length of the CNV are shown when the user hovers over the browser with the mouse on the rectangle.
Deletion
Duplication
The region of the CNV call is highlighted in orange. The purple area shows the 95% confidence interval of the read ratio (observed/expected reads). Each colored rectangle represents one of the target regions of the assay used to sequence the sample, and its position on the vertical axis indicates the read ratio for this region. Target regions whose read ratio falls within the confidence interval will be colored blue while those whose ratio falls outside the expected range will be red. The observed and expected read ratio is shown when the user hovers the mouse over the target region.
Below the read ratio is the coverage track which shows the depth of coverage across both the test sample (the sample currently under analysis) and the control samples used in this analysis. The test sample's coverage is shown in red and the others are in blue. The user can choose to view the coverage on a logarithmic or linear scale under the Filters panel.
The user can hover along the CNV and see the Coverage for the selected sample, the transcript and its exons.
The filters panel allows the user to visualize the CNV call region in the rest of the samples of the CNV analysis by checking the box of the sample name. Once checked, hover over the sample names on the filters and only these will be shown in the Coverage track.
Finally, the exonic structure of any genes the CNV overlaps with are shown in the Genes track under the coverage.
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
- 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.
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:
