CLASSIFICATION: Evidence and classification

Navigate to the CLASSIFICATION page by using the button in the left corner of the top bar (if no warnings are present, you will be taken to the CLASSIFICATION page automatically):

The CLASSIFICATION page contains all annotation, as well as tools for interpretation and classification of each variant. To start an analysis, click the green START [INTERPRETATION/REVIEW/MED. REVIEW] button in the top bar (right):

This reserves the variant or analysis for your user and marks it as ongoing for other users. If you don’t click start, the variant or analysis and any previous user comments or choices are read-only.

Different information is placed in separate sections (shown here in collapsed mode, see
Use collapsing ...):

The different parts are described in more detail in:

Example classification workflows

Recommended workflows for each variant on the CLASSIFICATION page, after clicking the START … button in the top bar:

Analyse new variants (no previous interpretation)

  1. Review the information in the QUALITY (ANALYSES workflow only), FREQUENCY, EXTERNAL and PREDICTION sections, add missing information and provide comments specific to each section when relevant.

    a. (Optional; in ANALYSES workflow): Clear analysis warnings using the work log.

  2. Evaluate the retrieved references and any references you add yourself in the REFERENCES section.

  3. In the CLASSIFICATION section:

    a. Review and choose ACMG criteria, add comments when necessary.
    b. Provide a summarising comment for the variant and set a classification.

  4. If in the ANALYSIS workflow:

    a. Move to next variant in the sidebar until no more variants are left.
    b. Switch to the REPORT page and make a clinical report for the sample.

  5. Once all variants have been interpreted (only one if in VARIANTS workflow):

    a. (Optional): Provide an overview comment or message for the next user using the work log.
    b. Press FINISH in the top bar and send to review/medical review or finalise.

Review previous interpretation

  1. Review the comments and choices made by the previous user in each section and make changes/additions as you see fit

  2. Once all variants are reviewed, review the report (if in ANALYSES mode) and finish the session as from point 4 above.

Use collapsing for overview and marking sections as done

To get a better overview of the comments you have added in the different sections for a variant, use the COLLAPSE ALL button in the top bar:

Alternatively, you may collapse each section individually by clicking on the section header. As the collapsed/expanded state of each section is saved along with your interpretation, this can be useful for marking sections as done if you need to quit for the day without being entirely finished with a variant.

Comments and attachments

Each section on this page has a comment field, which should be used for making notes about the particular evidence you find in each section.

Image attachments copied to the clipboard may be pasted into any of the section comment fields. Pasted images are added inline to the comment text, and can be zoomed in/out using the slider at the top left of each image.

In addition, files of any type (<50 MB) may be added to ella using the ADD ATTACHMENT button in the top banner:

Attachments added this way are available (through thumbnails) in the CLASSIFICATION section. NB: Attachments are given a number as name, the original file name is lost.

Throughout this page and often in card headers, you will find weblinks, usually to the sources of various annotation data, as well as buttons for exporting analyses or individual variants to Alamut. Weblinks are marked with a dotted line under the text, e.g.:

If you are in an offline environment, when you click one of these, instead of opening a browser or the program directly, the link is copied to your clipboard. To open the link:

  • For weblinks, click on the link, then (as you get the message COPIED LINK TO CLIPBOARD) open a browser on your local computer and paste (Ctrl+V) the contents into the address bar, then hit Enter

  • For Alamut, click either COPY ALL TO ALAMUT or COPY VARIANT TO ALAMUT in the top bar, then (as you get the message COPIED TEXT TO CLIPBOARD) paste (Ctrl+V) the contents in the Go to: input field at the top right of the Alamut main window:

Last Updated: 11/13/2018, 8:09:11 PM