Recording Interpretation¶
There are a number of features designed to aid in the tracking of the analysis and interpretation of the case and the variants identified. This can be performed on the variant grid and in the interpretation section on the variant details page. These allow for variants to be flagged, commented on, classified and added for export. A history of any comments and classification can be seen in the variants history along with information on who provided the interpretation and when.
Flagging Variants¶
Functionality has been added to allow the ‘flagging’ of variants to highlight variants of interest. Flagging of variants can be done directly from the grid but clicking on the ‘Flag’ icon at the end of the variants row, or in the interpretation section of the variant details page. Filters can be set to show only flagged variants in the variant grid.
Commenting¶
Commenting can be accessed from the variant list by clicking on the speech bubble in the "Actions" column. This will open the interpretation drawer to the right of the screen. Generic variant level comments can be added by scrolling to the bottom of the interpretation drawer and entering text to the "Analysis comment" section and clicking save. From the variant details page, analysis comments can be added in the interpretation section by typing in the text box and clicking "Save Comment". Comments will be saved in the variant history along with the users full name and the date and timestamp.
Editing comments¶
- Comments can only be edited by the person who made the comment and can be done by clicking ‘edit’ alongside the comment made.
- If a comment is edited, the most recent version of the comment will be displayed in the variant history, and marked as "Edited". The date and timestamp will be updated to reflect when the comment was last edited.
Deleting comments¶
- If a comment is deleted, the content of the comment will be removed from the history, however the users full name, and the date and timestamp will remain, alongside a "Removed" stamp.
Info
To see a full audit trail of all edited and removed comments against a variant, please raise a ticket with the Genomics England Service Desk requesting an audit trail for the particular case.
Classification¶
A variant classification can be assigned to each variant analysed using the classification column on the variant grid or the interpretation section in the variant details. For somatic small variants the classification system follows the AMP guidelines alongside the biological classification of Benign, Likely Benign, Uncertain Significance, Likely Oncogenic and Oncogenic. For a classification to be saved, both an AMP and biological classification must be selected. For germline variants, the classification is based on the ACMG system and classifies a variant as one of Benign, Likely Benign, Uncertain Significance, Likely Pathogenic and Pathogenic. The classification can be made by selecting the classification from a drop down menu and clicking ‘Classify’ to save. This will also save a record in the variant history with the classification, name of person who classified and time and date. Classifications cannot be edited but new classifications can be made by reselecting from the drop down menu and clicking classify. This will change the overall classification but the prior classification(s) will remain in the variant history.
Add For Export¶
Clicking on the "Add to export" icon on the variant grid or variant details page will add the variant and it's interpretation to the report that can be exported. Refer to Export Preview section for more details.