Filling in a report
You fill in a report on the analysis's Report tab, the last tab in the interpreter. You add the variants you're reporting, file each under the right findings section, and write the clinical interpretation and any other sections the template provides.
Opening the report
Open the analysis in the Variant Interpreter.
Click the Report tab.
If the case has no report yet, one is created as a Draft from the workspace's default template when you open the tab (or when you first add a variant to the report). If the workspace has no default template, the tab says so; ask an admin to set one up.
The top of the tab shows the report's progress through Draft, Under review, Signed off, and Released, with the actions available to you. Below it are two cards: Reportable findings and Report Sections.
You can only change a report's findings and wording while it's in Draft. Once it's submitted, it must be returned to draft (or, after sign-off, reopened) before it can change. See Sign-off, release & amendments.
Choosing a template for a report
A new report uses the workspace's default template. If your workspace has more than one template, a Template menu appears below the progress steps while the report is in Draft.
To switch templates:
Choose a template from the Template menu.
In the Apply template dialog, click Apply template.
The report's sections are rebuilt from the new template:
Kept: the Clinical Interpretation and the report's findings.
Replaced: the wording in every other section is discarded and replaced with the new template's wording.
Findings filed under a findings section that the new template doesn't have move to its default findings section.
Choose the template before you edit the wording of sections such as Recommendations or Methods. Switching templates discards those edits.
When the template changes
A report keeps the sections it was created with, even if an admin later edits the template. If the template's structure has changed since the report was created (sections added, removed, renamed, reordered, or turned on or off), a Draft report shows a notice with an Update from template button.
Click Update from template and confirm to rebuild the report's sections from the current template. As when switching templates, the Clinical Interpretation and the findings are kept, and the wording in other sections is replaced.
Changes to a template's wording alone don't trigger the notice.
Adding variants to the report
You add variants while you review them. You can add a variant from:
The variant's Classification tab. Open the variant, go to the Classification tab and click Add to report. Click Remove from report to take it off again.
The Summary tab. Click Add to report on a priority finding's row. The button changes to In report; click it again to remove the variant from the report.
Variants on the report show an In report badge in the variant drawer.
You don't have to classify a variant before adding it, but the report prints each finding's classification, so classify every variant you report. The Reportable findings card shows how many of the included variants are classified, for example "3 of 5 classified".
Reviewing the included variants
The Reportable findings card lists every variant on the report under Included variants. Each card shows the variant type, its classification, the gene and coordinates, and the interpretation note.
The interpretation note is the variant's General Notes from its Classification tab. It's printed in the findings table, so write it as you want it to appear on the report.
Click a card to open the variant in the drawer. Use the drawer's previous and next controls to step through the findings.
To remove a variant, open it from the Report tab and click the remove icon in the drawer header, then confirm. The variant keeps its classification and stays in the analysis; you can add it back later.
Filing variants under findings sections
If the report's template has more than one findings section, each finding card has a Prints under menu. Choose the section the variant belongs in, for example Secondary Findings instead of Primary Findings.
Variants go into the default findings section when they're added, so check Prints under for each finding before you submit.
The cards are grouped under their section headings on the Report tab, in the order they'll print.
A findings section with nothing filed under it isn't printed, apart from the default section.
Writing the report sections
The Report Sections card has a rich-text editor for each section you can write in:
Clinical Interpretation: your overall interpretation of the case. It starts empty on every report.
Recommendations, Methods, Limitations, References, and any statements your lab added: these start with the template's standard wording, which you can edit for this case.
Sections that are filled in automatically (the letterhead, patient information, clinical phenotypes, the findings tables, and the sign-off) have no editor.
Your wording saves automatically a couple of seconds after you stop typing. If someone else changes the report at the same time, the Report tab loads the latest version and keeps your unsaved text so you can re-apply it.
Previewing the report
Click Preview at any time to open the Report preview panel. It shows the assembled report exactly as it will print, including the letterhead, the findings tables, and every section. Viewers can use the preview too.
Submitting for review
When the report is complete, click Submit for review. See Sign-off, release & amendments for what happens next.
Before you submit, check that:
every variant you're reporting is on the report and classified;
each finding prints under the correct findings section;
each finding's interpretation note reads as it should on the report;
the Clinical Interpretation is written and the other sections' wording fits this case.
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