Somatic SV and CNV Grid

Features

• Review the somatic structural and copy number variants (e.g. deletion, loss, gain…) identified by the cancer pipeline and associated annotations
• Review the B-allele frequency, coverage and absolute allele count
• Apply certain filters (e.g. variant type)
• Search for specific variants within a certain chromosome, region or gene
• Sort the list of variants (e.g. by domain, genomic coordinate, copy number or size)
• Flag a variant for further review
• Add or remove a variant from the GTAB summary
• Add a comment and assign a biological classification or AMP tier to a variant
• Report whether the variant has been tested by another method i.e., Standard of Care Testing
• Report whether a variant is likely to be an artefact or a true variant

Variant Grid GuideDUX4 FusionsSearchingSortingVisualisationsFilteringAdvanced FilteringVariant InterpretationAdding Variants to the GTAB summaryPage Errors

An overview of the Variant Grid is shown in the following table

Key

#	Section	Description
1	Information Alerts	Relevant disclaimers and alerts will be shown here in a dropwdown.
2	Search	Search for variants within specific genomic regions, chromosomes or genes. Details on how to search can be found in the "Searching" tab.
3	Filters	Add or remove filters applied to the variant grid. By default, the variant grid will be filtered to display variants in genes belonging to Domain 1, Domain 2 and Domain 3.
4	Actions	Actions including "View Details" - viewing the variant details page, flagging, adding comments, and adding or removing the variant from the GTAB summary.
5	Domain and gene	Domain and HGNC gene symbol(s) which the variant affects. Affected genes in the highest domain are shown by default.
6	GRCh38 coordinates	Coordinates of the variant. Clicking the IGV icon will show the variant in IGV. If the genomic coordinates of a structural variant is shown as "Not available", the variant has been called by Pelops which detects the presence of a rearrangement, but not the precise breakpoint coordinates. Consequently, the partner break-end location also cannot be precisely determined, so Pelops returns a 1-2 kb region instead.
7	Chromosomal bands	The cytobands relating to the genomic coordinates of the variant. If the chromosomal bands of a structural variant is shown as "Not available", the variant has been called by Pelops as described above, and a chromsomal band cannot be provided as the precise breakpoint coordinate is unavailable.
8	Variant type / Copy number	The variant type e.g., Loss, Gain, Insertion and if applicable copy number of the variant.
9	Size	The length of the variant, shown in Kilobases.
10	Fusion / Reading frame	Fused genes and a prediction of the fusion outcome e.g. GENE1:GENE2 - ambigious. Only variants which potentially can produce a gene fusion will show fusion information.
11	Confidence / Support	CNVs will have a confidence value assigned to indicate whether the call is High or Low confidence. All CNVs called by Canvas with a confidence score of >=10 will be labelled as High and <10 labelled as low, while all CNVs called by Dragen with PASS in the VCF filter column will be labelled as High and non-PASS variants labelled as Low. Structural variants called by Manta will have paired- and split-read support shown, while structural variants called by Pelops will have supporting reads per billion shown. Internal tandem duplications in the FLT3 gene called by Pindel will have allele depth support shown.
12	VCF filter	Shows whether the variant has passed the pipeline filters. For variants that haven’t passed, the reason is shown in red e.g. ‘q10’ Quality below 10. This column is only populated for structural variants.
13	QC flag	Flags that indicate a variant with a higher likelihood of being a false positive call or unsubtracted germline variant e.g. ‘GE’ Variants with germline allele frequency >1% in an internal Genomics England dataset. This column is only populated for structural variants. Structural variants called by Pelops will have an ABP (ambiguous breakpoint) flag shown to indicate that it is not possible to determine the fusion breakpoint, and the partner region is returned as a 1-2 kb region instead.
14	Population frequencies (GESG/GECG)	Population germline allele frequency for the breakpoints of a given structural variant based on two internal panels of normals: GESG, which consists of germline variants coming from single germline analysis of about 2,200 samples, and GECG, which consists of the variants detected as germline in paired tumour-normal variant calling for about 2,500 cancer samples.
15	Classification	The assigned biological classification and AMP tiering of a variant. Click the pill to add or edit the classification and tiering of a variant.
Not shown	Origin*	Indication of the variant’s origin as specified by TiNC e.g. Somatic or Uncertain. This will only be available for cases that have gone through the TiNC workflow.

Tip: Open the transcript overlay

On your variant of interest, click any of the HGNC gene symbols shown under the Domain / Gene column (section 5 of the Variant grid guide) to open the transcript overlay (example shown below).

Following the update to Dragen (NGIS release Orion onwards), DUX4 fusions can be called by the Pelops variant caller. These variants will appear differently on the cDSS:

• The genomic coordinates of DUX4 fusions will be shown as "Not available", as Pelops has detected the presence of a rearrangement, but is unable to determine the precise breakpoint coordinate in DUX4. Consequently, the partner break-end location also cannot be precisely determined, so Pelops is returning a 1-2 kb region instead.
• The chromosomal bands will be shown as "Not available", as the precise breakpoint coordinate is unavailable a chromsomal band cannot be provided.
• DUX4 fusions will have an ABP (ambiguous breakpoint) flag shown in the QC flag column, to indicate they are called by Pelops and will not have a genomic coordinate provided for DUX4 and the partner gene will be returned as a 1-2 kb region instead.
• Supporting reads per billion (SRBP) will be provided as a measure of confidence in the confidence/support column.

Dragen v4

PLEASE NOTE: following the pipeline upgrade to Dragen v4, some findings are not UKAS accredited to ISO 15189. Dragen v4 software for calling somatic copy number variants (CNVs) and Pelops algorithm for identifying DUX4 rearrangements are not currently included in the schedule of accreditation issued by UKAS. Please refer to the schedule of accreditation for more information.

You can use the search bar to search for variants by:

• Gene symbol e.g., "TP53"
• Coordinates (chromsome, start coordinate and end coordinate) e.g., "17:7660779-7688538"
• Chromosome e.g., "17"

Searching

Searching will filter the variant grid to variants that match the search terms. If no variants are returned, there may be no variants in the chromosome, region or gene specified. The plots will also update in accordance with the filtered variant grid.

By default, all variants are sorted by Domain ascending and by variant coordinates. You can sort the list of somatic structural and copy number variants by domain, copy number and size. To change the order of the variants follow these steps:

To change the sorting of the variant grid from Domain to GRCH38 coordinates, follow these steps:

• Click the arrow icon on the column header to sort the grid by GRCH38 coordinates in ascending or descending order
• Click the three dots on the column header and select 'Sort by Coordinates ASC' or 'Sort by Coordinates DESC'
• To reset the variant grid to the default sorting order (by Domain) click the three dots on the column header and select 'Reset to default'

Sorting

Only one sort can be activated at the time. By default, we show the first 10 variants sorted by domain and coordinates. To see the remaining variants, scroll to the bottom of the page and new variants will continue to load.

The structural variant, B-allele frequency, coverage and absolute allele count plots are shown by default.

1. To make the visualisations full screen, click the expand icon.
2. To hide the visualisations, click the collapse icon icon.
3. To adjust the width of the plots while maintaining the variant grid, click and drag the light grey vertical divider line between the table and the plots.

Visualisations

Data has been hidden in the above visualisations to protect patient confidentiality.

To get more details about the information in the plots, see Visualisations

Warning

We have identified a bug in our plot generation, where genomic sex is being used rather than reported sex. If a cases genomic sex differs from the reported sex, the "expected coverage" line across chrX would display incorrectly.

Somatic SV and CNV Filters

• Domain
• Mode of Action
• Gene list
• Flag status
• VCF filter
• Supporting reads (SV only)
• Size
• Confidence (CNV only)
• Copy number (CNV only)
• Variant Type

By default, the variant grid is filtered by Domain 1, 2 and 3.

Applying filters

1. Click the '+' symbol next to 'Add filter'
2. Chose your filter of interest from the dropdown menu and click the '+' symbol
3. Click on the arrow dropdown and select your filter options e.g., Variant Type, Deletion. The variant grid will update accordingly

Removing filters

1. Individual filters can be removed by clicking the 'x' symbol next to the filter
2. Default filtering settings can be restored by clicking the 'Reset' button above the filter toolbar
3. Multi-select filters can be reset by selecting 'Clear'

Counts

The count on the top left shows the number of variants remaining after filters have been applied. The total number is the number of variants the pipeline identified before any quality checks have been applied.

Applying Multiple Filters

For information on applying multiple filters please see the "Advanced Filtering" section

We support applying multiple filters to the variant grid at the same time. The filters we support can be applied at the variant level and the gene level.

Filter	Variant Type	Level
Domain	SV, CNV	Variant
Flag status	SV, CNV	Variant
Size	SV, CNV	Variant
Variant Type	SV, CNV	Variant
VCF filter	SV	Variant
Supporting Reads	SV	Variant
Confidence	CNV	Variant
Copy Number	CNV	Variant
Mode of Action	SV, CNV	Gene
Gene list	SV, CNV	Gene

• When applying multiple filters at the same level, the filters are exclusive (See example 1)
• When a combination of gene level and variant level filters are applied, first we consider the variant level conditions and then apply the gene level filters which take the entire list of genes annotated to the variant into account (See example 2)
• If more than one gene level filter is applied in combination with a variant level filter, the gene must meet all filtering conditions (See example 3)

#	Filter 1	Filter 2	Filter 3	Result
1	Domain 1	Size min 500 KB	N/A	Domain 1 variants with a Size of >= 500 KB
2	Domain 2	Mode of Action: Oncogene	N/A	Any domain 2 variant with a gene labelled 'oncogene' (in any domain or undomained)
3	Domain 2	Mode of Action: Tumour suppressor	Gene List: NGTD M21	Any domain 2 variant with a gene labelled 'Tumour supressor' AND is a member of the NGTD M21 panel

Using the interpretation drawer, you can add interpretations and comments corresponding to a variant in the variant grid. To open the interpretation drawer, follow these steps:

1. Click the comment icon on any of the variants
2. The interpretation drawer will open on the right of the screen

Tip

Please refer to the following GTAB-related section to know how to add a somatic structural and copy number variant and its interpretation to the GTAB summary.

Variant QualityClassifying and TieringValidationActionabilityComments

Artefact AssessmentArtefact ReasonsArtefact Comment

To indicate whether the variant is likely to be a technical artefact or a true variant, follow these steps:

1. Under "Artefact assessment" click the dropdown arrow and choose the appropriate choice
2. The selection will automatically save and the "Saved" icon will appear once saved
3. The artefact assessment is added to the variant and will appear in the history below
4. All artefact assessment edits will be stored in the history

If a variant has been marked as a likely artefact, the interpretation drawer will display this additional field. To indicate the reason why the variant is likely to be a technical artefact, follow these additional steps:

1. Under "Artefact reasons" click the dropdown arrow and choose the appropriate choice from the options shown above
2. The selection will automatically save and the "Saved" icon will appear once saved
3. The artefact reason is added to the variant and will appear in the history below
4. All artefact reason edits will be stored in the history

If a variant has been marked as a likely artefact, the interpretation drawer will display this additional comment box. To add a supporting comment to your artefact assessment, follow these additional steps:

1. Under "Artefact comment" enter the text you wish to include
2. Click "Comment"
3. The artefact comment is added to the variant and will appear in the history below
4. All artefact comment edits will be stored in the history

Warning

Updating the artefact assessment to "True variant" will remove the artefact reasons and comment data from the interpretation drawer but it will still be available in the variant history.

Classifying and Tiering

To view or add classifications or tiers follow these steps:

1. Click the dropdown arrow and choose the biological classification and/or AMP tier from the menu
2. Click classify
3. The classification is added to the variant and will appear in the history below
4. All classification edits will be stored in the history

ValidationAssay TypeAssay Comment

To indicate whether the variant has been validated, follow these steps:

1. In the "Validation" section of the interpretation drawer, under "Has this variant or entity been tested by another method (either prior to or following receipt of this WGA)?" click the dropdown arrow and choose the appropriate choice
2. The selection will automatically save and the "Saved" icon will appear once saved
3. The validation information is added to the variant and will appear in the history below
4. All validation edits will be stored in the history

If your previous selection indicated the variant has been validated by another method, an "Assay type" dropdown will appear. To select which assay type(s) the variant has also been detected in, follow these additional steps:

1. Under "Assay Type", click the dropdown arrow and choose the appropriate choices
2. The selection will automatically save and the "Saved" icon will appear once saved
3. The assay type is added to the variant and will appear in the history below
4. All assay type edits will be stored in the history

If your previous selection indicated the variant has been validated by another method, an "Assay comment" box will also appear. To add a comment to support the assay types selected, follow these additional steps:

1. Under "Assay Comment", enter the text you wish to include
2. Click "Comment"
3. The assay comment is added to the variant and will appear in the history below
4. All assay comment edits will be stored in the history

Warning

Updating the validation to a "No" option will remove the assay type and comment data from the interpretation drawer but it will still be available in the variant history.

To enter the type of potential actionability associated with a variant, follow these steps:

1. In the "Actionability" section of the interpretation drawer, under "Type of (potential) actionability:" click the dropdown arrow and choose the appropriate choice(s)
2. The selection will automatically save and the "Saved" icon will appear once saved
3. Optional step: An "actionability comment" box will appear where you can add a comment to support the actionability type entry. If required, add your comments to the text field and click comment
4. Optional step: In the "Actionability" section under "How has/will this potentially actionable variant or entity been/be used?" click the dropdown arrow and choose the appropriate choice. Only one can be selected
5. Optional step: A "Utility comment" box will appear where you can add a comment to support the utility type entry. If required, add your comments to the text field and click comment
6. The actionability information is added to the variant and will appear in the history below
7. All validation edits will be stored in the history

Comments

To view or add comments follow these steps:

1. Add your comments to the text field and click comment
2. The comment is added and will appear in the history below
3. To edit the comment, click the three dots next to the date and click edit or delete. Note you can only edit or delete your own comments, for further information see Recording interpretation

You can add any somatic structural and copy number variant and its interpretation to the GTAB summary from the variant grid or interpretation drawer.

To add a somatic structural and copy number variant to the GTAB summary:

1. Click the "Add to GTAB report" icon on any of the variants
2. Go to the GTAB summary:
   • Click the "Go to GTAB report" link from the green message that will appear at the bottom of the variant grid confirming that the variant has been successfully added to the GTAB summary or
   • Click the "GTAB report" icon from the navigation sidebar

Info

At the moment, it is only possible to add variants one by one to the GTAB summary.

Refer to the GTAB summary section for more details.

When we fail to load the gene data needed for search and gene filters to work, you won’t be able to apply any gene list filters or search by gene. All other information on the page will still be available. When we fail to load all variant data, we will show a full page error. In both cases try reloading the page.