GTAB Summary

From the GTAB summary, users can:

• Review patient information
• Review tumour and sample details
• Review all the somatic and germline variants that have been added to the GTAB summary
• Review the interpretation, comments, and classification of each variant added to the GTAB summary
• Make changes, add new information and GTAB comments to the interpretation and classification of each variant added to the GTAB summary
• Remove variants from the GTAB summary
• Review the plots that have been added to the GTAB summary
• Review the interpretation, and comments added to each plot included in the GTAB summary
• Make changes, add new information and GTAB comments to the interpretation of each plot added to the GTAB summary
• Remove plots from the GTAB summary
• Add clinical information to the GTAB summary
• Add GTAB outcome, recommendation, and attendees information to the GTAB summary
• Export the GTAB summary to a PDF document
• Review the audit history of any changes made to the GTAB summary

GTAB summary example

The example shown below has been generated using random data and for demonstration purposes only. Nevertheless, to avoid any potential match with real patient data some fields have been hidden.

Key

#	Section	Description
1	Patient information	Information about the patient as captured from TOMS, clinical indication from the Test Directory (defined during the test order), and Referral ID for the patient.
2	Tumour and sample details	Information about the tumour type, presentation, diagnosis date, tumour content (both from the lab as from the WGS data), and other details about the tumour sample.
3	Clinical information	Text box to write clinical information notes to the GTAB summary. Please refer to the Clinical information section to learn how to add clinical information notes.
4	Selected variants	Shows all the relevant information about the somatic and germline variants that have been added to the GTAB summary, including interpretation, comments, and classification of each variant. Please refer to the Selected variants section for more details.
5	Additional analysis	Shows all the relevant information about the tumour mutational burden and mutational signature analysis plots that have been added to the GTAB summary, including interpretation and comments for each of these plots. Please refer to the Global Analysis Plots for more details.
6	GTAB summary	Text boxes to write GTAB outcome, recommendation, and attendees information to the GTAB summary. Please refer to the GTAB summary section to learn how to add GTAB-related notes.
7	GTAB history	Audit history with all changes made to the GTAB summary.
8	Download PDF	Option to export the GTAB summary to a PDF document. Please refer to the Download PDF section for more details.

Clinical informationSelected variantsAdditional analysisGTAB summaryDownload PDFPage Errors

Add a Clinical Information Note

To add a clinical information note to the GTAB summary:

1. In the Notes text box, type your note.
2. Click Save note.
3. The note is added to the clinical information section together with the name of the user who added the note and a date-timestamp to indicate when the note was added to the GTAB summary.
4. Previous notes can be seen in the GTAB history (section 7 of the GTAB summary).

Edit Previous Clinical Information Notes

To edit a previous clinical information note:

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

Note

You can only edit your own notes.

Delete Previous Clinical Information Notes

To delete a previous clinical information note:

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

Note

You can only delete your own notes.

Selected variants

This panel (section 4 of the GTAB summary) allows you to review all the somatic and germline variants that have been added to the GTAB summary, including their interpretation, classification, and any comments added during the analysis of each variant.

#	Section	Description
4.1	Somatic small variants	Shows all the relevant information and annotations about the somatic small variant(s) that have been added to the GTAB summary. For more information about each field, please refer to the following sections: variant grid and variant interpretation for somatic small variants.
4.2	Somatic structural and copy number variants	Shows all the relevant information and annotations about the somatic structural and copy number variant(s) that have been added to the GTAB summary. For more information about each field, please refer to the following sections: variant grid and variant interpretation for somatic SV and CNV.
4.3	Germline small variants	Shows all the relevant information and annotations about the somatic structural and copy number variant(s) that have been added to the GTAB summary. For more information about each field, please refer to the following sections: variant grid and variant interpretation for germline small.
4.4	Hide/Expand comments list	Hide/Expand the comments list to hide or display the latest comments of each comment category added to the variants included in the GTAB summary. The Hide/Expand the comments list button is present for each variant and it only applies to the variant you are interacting with.
4.5	Actions	Actions including: editing variant interpretations of variants added to the GTAB summary and removing variants from the GTAB summary. The Actions buttons are present for each variant and the action selected only applies to the variant you are interacting with. Please refer to the Actions section to learn more about each option.

Info

By default, no variants will be shown in the GTAB summary. To know how to add a variant and its interpretation to the GTAB summary, please refer to the following sections: variant list somatic small, variant list somatic SV and CNV, and variant list germline small.

Actions

Edit Variant Interpretations from GTAB summaryRemove Variants from GTAB summary

Edit Variant Interpretations of Variants included in GTAB summary

To edit an interpretation of a variant added to the GTAB summary:

1. On the variant of interest, click Edit interpretation (icon shown below).
2. The Interpretation drawer will appear on the right of the screen.
3. View, add comments, and make the desired changes to the interpretation of the variant from the Interpretation drawer. For more information about each section of the Interpretation drawer, please refer to the following sections: variant interpretation for somatic small variants, variant interpretation for somatic SV and CNV variants, and variant interpretation for germline small variants.

Add GTAB Comments to a Variant

To add a GTAB comment to a variant added to the GTAB summary:

1. On the variant of interest, click Edit interpretation (icon shown below).
2. In the Interpretation drawer that will appear on the right of the screen, go to the Comments section.
3. Type your comment in the GTAB comment text box.
4. Click Save comment. The comment is saved as a GTAB comment together with the name of the user who added the comment and a date-timestamp to indicate when the GTAB comment was added to the variant.
5. The latest GTAB comment can be seen when expanding the comments list of the variant (section 4 of the Selected variants section of the GTAB summary) and in the variant history or the Comments section of the Interpretation drawer of the variant when opened from the GTAB summary.
6. Previous GTAB comments can be seen in the variant history or the Comments section of the Interpretation drawer when opened from the GTAB summary.

Comments section of the Interpretation drawer

The Comments section of the Interpretation drawer of a variant allows users to add generic variant level comments to a variant. When adding generic variant level comments from the Interpretation drawer when opened from a variant list, the comments added will be saved as Analysis comments and the Comments section will only show Analysis comments information. Whereas, when adding generic variant level comments to a variant from the Interpretation drawer when opened from the GTAB summary, the comments added will be saved as GTAB comments and the Comments section will only show GTAB comments information. This difference in the Comments section of the Interpretation drawer of a variant is to help users distinguish different general variant level comments added to a variant in different moments of the variant interpretation cycle.

Edit Previous GTAB Comments

To edit a previous GTAB comment:

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

Note

You can only edit your GTAB comments.

Delete Previous GTAB Comments

To delete a previous GTAB comment:

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

Note

You can only delete your own GTAB comments.

Remove Variants from GTAB summary

To remove a variant from the GTAB summary:

1. On any of the variants, click Remove from GTAB summary (icon shown below)

2. In the confirmation pop-up message that appears, click Remove.

Info

The variant will be removed from the GTAB summary but the variant will be present in the corresponding variant list and its interpretation saved and accessible from the Interpretation drawer.

Additional analysis

The additional analysis panel (section 5 of the GTAB summary) allows you to review the information about Tumour mutational burden and Mutational signature analysis plots that have been added to the GTAB summary, including their interpretation and any comments added during the analysis of each plot.

Info

By default, no plots will be shown in the GTAB summary. To know how to add a tumour mutational burden or mutational signature analysis plot and its interpretation to the GTAB summary, please refer to the following sections: Plot Interpretation and Add Plots to GTAB summary.

Note

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

Actions

Edit Plot Interpretations from GTAB summaryRemove Plots from GTAB summary

Edit Plot Interpretations included in GTAB summary

To edit an interpretation of a plot added to the GTAB summary:

1. On the plot of interest, click Edit interpretation (icon shown below).
2. The Interpretation drawer will appear on the right of the screen.
3. View, add comments, and make the desired changes to the interpretation of the plot from the Interpretation drawer. For more information about the Interpretation drawer for plots please refer to Plot Interpretation.

Add GTAB Comments to a Plot

To add a GTAB comment to a plot added to the GTAB summary:

1. On the plot of interest, click Edit interpretation (icon shown below).
2. In the Interpretation drawer that will appear on the right of the screen, go to the Comments section.
3. Type your comment in the GTAB comment text box.
4. Click Save comment. The comment is saved as a GTAB comment together with the name of the user who added the comment and a date-timestamp to indicate when the GTAB comment was added to the plot.
5. The latest GTAB comment can be seen when expanding the comments list of the plot and in the History or the Comments section of the Interpretation drawer of the plot when opened from the GTAB summary.
6. Previous GTAB comments can be seen in the History or the Comments section of the Interpretation drawer of the plot when opened from the GTAB summary.

Comments section of the Interpretation drawer

The Comments section of the Interpretation drawer of a plot allows users to add generic level comments to a plot. When adding generic level comments to a plot from the Interpretation drawer when opened from the Global Analysis, the comments added will be saved as Analysis comments and the Comments section will only show Analysis comments information. Whereas, when adding generic level comments to a plot from the Interpretation drawer when opened from the GTAB summary, the comments added will be saved as GTAB comments and the Comments section will only show GTAB comments information. This difference in the Comments section of the Interpretation drawer of a plot is to help users distinguish different general level comments added to a plot in different moments of the plot interpretation cycle.

Edit Previous GTAB Comments

To edit a previous GTAB comment:

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

Note

You can only edit your GTAB comments.

Delete Previous GTAB Comments

To delete a previous GTAB comment:

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

Note

You can only delete your own GTAB comments.

Remove Plots from GTAB summary

To remove a plot from the GTAB summary:

1. On any of the plots, click Remove from GTAB summary (icon shown below)

2. In the confirmation pop-up message that appears, click Remove.

Info

The plot will be removed from the GTAB summary, but the plot will be present in the Global Analysis and its interpretation saved and accessible from the Interpretation drawer.

Add GTAB Outcome, Recommendation, or Attendees Information Notes

To add a GTAB outcome, recommendation, or attendees information to the GTAB summary:

1. Type your note in the Outcome, Recommendation, or Attendees text box.
2. Click Save note.
3. The note is added to the corresponding section together with the name of the user who added the note and a date-timestamp to indicate when the note was added to the GTAB summary.
4. Previous notes can be seen in the GTAB history (section 7 of the GTAB summary).

Edit Previous GTAB Outcome, Recommendation, or Attendees Information Notes

To edit a previous GTAB outcome, recommendation, or attendees information note:

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

Note

You can only edit your own notes.

Delete Previous GTAB Outcome, Recommendation, or Attendees Information Notes

To delete a previous GTAB outcome, recommendation, or attendees information note:

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

Note

You can only delete your own notes.

Export the GTAB summary as a PDF

To export the GTAB summary into a PDF document:

1. Click Download PDF.

2. Select Draft or Final from the dropdown list.

   • The Draft version will be titled Pre-GTAB summary and include a DRAFT watermark and header on all pages of the document. The name of the PDF document will have the following format: YYYY_MM_DD draft summary referralID.
   • The Final version will be titled GTAB summary and will include FINAL in the header of all pages of the document and no watermark. The name of the PDF document will have the following format: YYYY_MM_DD final summary referralID. The Final version should only be used after GTAB.

3. Save the PDF in your preferred folder.

Note

Only the latest changes and comments made to each variant, plot, and the GTAB summary can be seen in the PDF generated (example below). To see previous changes and comments made to a variant or plot, open the Interpretation drawer of that variant or plot and check the History. To see previous changes made to the GTAB summary, check the GTAB history (section 7 of the GTAB summary).

Example of a GTAB summary exported as a PDF

The sample document shown below has been generated using random data and for demonstration purposes only. Nevertheless, to avoid any potential match with real patient data some fields have been hidden.

Gene order, CDS and protein change, and predicted consequence type

The order of the genes shown in the GTAB summary might differ from the one shown in the PDF version. The genes in the GTAB summary are ordered by domain/tier and the first two genes of the two highest domains/tiers are always displayed under the Domain/Gene or Tier/Gene columns (section 4 of the GTAB summary). In the PDF version of the GTAB summary, only the first two genes of the highest domain(s)/tier(s) are displayed and these are ordered alphabetically. Therefore, sometimes the gene order shown in GTAB summary and its PDF version might not always coincide. Nevertheless, the CDS and protein change as well as the predicted consequence type displayed in both the GTAB summary and its PDF version correspond to the changes and the consequence type predicted in the gene with the highest domain/tier.

Page errors

When the GTAB summary fails to load, you will see a full page error. If reloading the page doesn't resolve the problem, get in touch with support via the Genomics England Service Desk.