GTAB Report

From the GTAB report, users can:

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

Warning

The GTAB report feature and the generated PDF are not intended for pre- or post-GTAB reporting. If you choose to use the GTAB report feature or share the PDF generated for purposes other than as a GTAB report, please note that you do so at your own discretion and risk.

GTAB report 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 report. 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 report, including interpretation, comments, and classification of each variant. Please refer to the Selected variants section for more details.
5	Additional analysis	Additional analysis in the GTAB report is under development at the moment and the design shown above is prone to changes. The team is working hard to show this feature on the decision support system soon.
6	GTAB summary	Text boxes to write GTAB outcome, recommendation, and attendees information to the GTAB report. 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 report.
8	Download PDF	Option to export the GTAB report to a PDF document. Please refer to the Download PDF section to learn how to export the GTAB.

Clinical informationSelected variantsGTAB summaryDownload PDFPage Errors

Add a Clinical Information Note

To add a clinical information note to the GTAB report:

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 report.
4. Previous notes can be seen in the GTAB history (section 7 of the GTAB report).

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 report) allows you to review all the somatic and germline variants that have been added to the GTAB report, 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 report. 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 report. 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 report. 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 report. 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 report and removing variants from the GTAB report. 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 report. To know how to add a variant and its interpretation to the GTAB report, 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 reportRemove Variants from GTAB report

Edit Variant Interpretations of Variants included in GTAB report

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

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 form 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 report:

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 5 of the Selected variants section of the GTAB report) and in the variant history or the Comments section of the Interpretation drawer of the variant when opened from the GTAB report.
6. Previous GTAB comments can be seen in the variant history or the Comments section of the Interpretation drawer when opened from the GTAB report.

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 report, 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 report

To remove a variant from the GTAB report:

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

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

Info

The variant will be removed from the GTAB report but the variant will be present in the corresponding variant list 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 report:

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 report.
4. Previous notes can be seen in the GTAB history (section 7 of the GTAB report).

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 report as a PDF

Warning

The GTAB report feature and the generated PDF are not intended for pre- or post-GTAB reporting. If you choose to use the GTAB report feature or share the PDF generated for purposes other than as a GTAB report, please note that you do so at your own discretion and risk.

To export the GTAB report into a PDF document:

1. Click Download PDF.
2. Save the PDF in your preferred folder.
3. By default, the name of the PDF document will have the following format: YYYY_MM_DD report caseID

Note

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

Example of a GTAB report 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.

Page errors

When the GTAB report 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.