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Global Analysis Plots

Info

PLEASE NOTE: some findings in this section are not UKAS accredited to ISO 15189. Mutational signatures and the cluster analysis of somatic SNVs are not currently included in the schedule of accreditation issued by UKAS. Please refer to the schedule of accreditation for more information.

From this page, users are able to:

Circos Tumour mutational burden Mutational signature analysis Contextual analysis of somatic SNVs Variant allele frequency of SNVs, indels & length of indels (<50bp)
View the plot and its description
Select actionability options associated with the plot
Add actionability and usability comments to the plot
Add analysis comments to the plot
Add the plot to the GTAB summary

Tip

Click Zoom to expand the size of each plot and display its description.

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Info

The global analysis plots displayed have been modified or hidden to protect patient information. Variant Allele Frequency plots will appear differently in the DSS.

By clicking Add comment or View comments on the plot card of interest, the Interpretation drawer will open. From the Interpretation drawer of the selected plot you can:

  • Select actionability options associated with a plot
  • Add actionability and usability comments
  • Add analysis comments
  • View previous comments

Note

All of these functionalities are available for the tumour mutational burden and mutational signature analysis plots. The last two are also available for the circos plot.

Select Actionability Options and Add Actionability and Usability Comments

To select actionability options associated with a plot and add actionability and usability comments, in the Actionability section of the Interpretation drawer:

  1. Select one or multiple options from the Type of (potential) actionability dropdown list.
  2. The selection will automatically save and the Saved icon will appear once saved.
  3. Type a comment in the Actionability comment box to support the actionability options selected in the previous step and click Save comment .
  4. Select one option from the How has/will this potentially actionable variant or entity been/be used? dropdown list.
  5. The selection will automatically save and the Saved icon will appear once saved.
  6. Type a comment in the Usability comment box to support the options selected in the previous step and click Save comment.
  7. All changes will be stored in the Interpretation drawer history.

Tip

Please refer to the Comments section to know how to edit and delete previous actionability and usability comments.

Add Analysis, Actionability, or Usability Comments

To add an analysis, actionability, or usability comment to the plot:

  1. Type your comment in the Analysis, Actionability, or Usability comment text box.
  2. Click Save comment.
  3. The comment is added to the corresponding section together with the name of the user who added the comment and a date-timestamp to indicate when the comment was added to the plot.
  4. Only the last comment will be seen under the corresponding text box. Previous comments can be seen in the Interpretation drawer history.

Info

The Actionability comment text box only appears after selecting one option from the Type of (potential) actionability dropdown list. The Usability comment text box only appears after selecting one option from the How has/will this potentially actionable variant or entity been/be used? dropdown list.

Edit Previous Analysis, Actionability, or Usability Comments

To edit a previous analysis, actionability, or usability comment:

  1. On your comment of interest, click the icon next to the date-timestamp (icon shown below). Image
  2. Click Edit.
  3. Make your changes to the previous comment.
  4. Click Save comment.

Note

You can only edit your own comments.

Delete Previous Analysis, Actionability, or Usability Comments

To delete a previous analysis, actionability or usability comment:

  1. On your comment of interest, click the icon next to the date-timestamp (icon shown below). Image
  2. Click Delete.
  3. In the confirmation pop-up message that appears, click Delete.

Note

You can only delete your own comments.

Add plots to the GTAB summary

You can add plots and their interpretation to the GTAB summary from the Global Analysis.

To add a plot to the GTAB summary:

  1. Click the Add to GTAB report icon on the plot card or interpretation drawer of the selected plot. Image
  2. Click the GTAB report icon from the navigation sidebar to go to the GTAB summary. Image

Note

Only tumour mutational burden, mutational signature analysis, and circos plots can be added to the GTAB summary.

TINC cases

Note that some cases with high or undetermined levels of tumour in normal contamination will not have global analysis plots available.