Sample View

A new "Sample View" card has been added to VarSome Clinical. This presents a genome region browser, but one that is focused on displaying the variants (SNPs, indels, CNVs) identified in the current sample.

This sample browser incorporates the following new features:

• New conservation scores per position
• Germine Variant Classification selected transcript
• More filtering options
• Ability to switch strand and expand the visualization to all chromosomes to see all analyses data if the analyses are small enough. (less than 10k variants).
• Touch and gesture support
• Customisable colour palette 
• 5 track levels:

1. 1. Chromosome
   2. Conservation scores
   3. Transcripts
   4. Variants in the sample
   5. CNVs in the sample.

Browser interface settings

A user can customize the sample's region browser interface from the "Open Settings" option in the upper right corner. The provided settings work the same way as those on the "New Genome Browser" being introduced in VarSome. For more information about the customization of the browser please refer here.

Chromosome

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.

Conservation scores

The conservation score per chromosome position is displayed with different colours related to pathogenicity, and its value is presented as a bar. To inspect the conservation scores for a smaller region, the user can zoom in from the corresponding button on the upper right of the browser. Hovering over the conservation bars, the chromosome position is displayed inside a black box alongside the conservation score, extracted from PhyloP software.

Transcripts

The transcripts' track shows the MANE RefSeq transcript and the transcript selected for the Germline Variant Classification by default. Hovering over the transcript track the user is able to see useful transcript-related information such as the source, the transcript reference ID, gene name, exon number, number of codons and amino acids. 

A user can select which transcripts of interest want to be displayed by using the filtering options on the top right of the track. Moreover, a transcript of interest can be selected by clicking on the displayed option of the tooltip, and it will be visible regardless of the applied filters.

Variants in sample

The SNVs and indels of the sample are displayed as a lollipop graph with different colours related to pathogenicity. The zygosity state of each variant is presented at the edge of the lollipop display (homozygous variants as filled disks, while heterozygous as half-filled ones), and it corresponds to the one presented in the variants' table.

Hovering over a variant, a tooltip is presented containing information about the Germine Variant Classification class, the triggered rules, coding impact, zygosity, allelic balance etc. 

By clicking on the variant, a box is presented providing some additional options, such as a link to open the analysis in which the variant has been identified, a zoom-in option and the one to highlight this variant.

This track can be filtered based on pathogenicity class, zygosity and coding impact. To see the available options, click on the filters button on the top right of the track.

CNVs in sample

If a CNV sub-analysis has been launched for a sample, an additional track will be displayed for the identified CNVs. Each CNV is coloured based on the pathogenicity classification and either filled or not based on its type, insertion and deletion respectively.

Hovering over a CNV, a tooltip is displayed containing information about the Germine Variant Classification class, zygosity, type etc. 

By clicking on the CNV a box is displayed providing a zoom option for it.

Additionally, this track can be filtered based on pathogenicity class, type and analyses in which the CNVs are identified. To see the available options, click on the filters button on the top right of the track.