Finalizing a case

The finalized case status locks the case to prevent further changes to interpretation notes, ACMG tags, variant tags, pathogenicity and case-level interpretations.

How to finalize a case:

1. On the Individual case page, click on the Case interpretation button located on the top bar.

2. In the Case interpretation widget, indicate the final result of the analysis:

1. Confidently Solved (Positive),

2. Likely Solved (Positive),

3. Further Investigation (Uncertain), or

4. Unsolved (Negative).

Case resolved

Confidently Solved, Likely Solved, and Further Investigation end-result categories correspond to the Resolved case status supercategory.

Case not resolved

Unsolved falls into the Not resolved status supercategory together with all the non-finalized cases.

The indicated case analysis outcomes are used to calculate the diagnostic yield.

3. In the Case interpretation widget, select which tagged variants to include in the Clinical Report (if any). Variants are described at the genomic DNA level.

You have the flexibility to reorder variants by drag-and-drop. The order of variants will be preserved in the Clinical Report within each variant table and/or section, defined by a variant tag and a variant type (e.g. SNVs tagged "In report").

Note: each variant in the Case interpretation widget is denoted at the coding DNA and protein level where applicable, otherwise, it's described at the genomic DNA level.

4. In the Case interpretation widget, you may add Interpretation notes, Gene interpretation, and Recommendations in the free-text format. This data is saved per case. If you’re using our customizable reporting solution, these fields will automatically populate in the Clinical Report.

In Gene Interpretation, you can import gene annotation from Curate (30.0+).

5. To complete the Case interpretation flow, press Save.

6. If you're using Emedgene for reporting, you may want to have a look at the Report Preview before finalizing a case. To do this, click on the eye button located rightmost on the Individual case page Top bar, select a template and click Preview.

You can download the report preview in a .pdf or .odt format.

7. Change Case status to Finalized.

Note: Finalizing a case will prevent users from making further changes to the case. To change information within the case (including variant tags and Variant Interpretation notes, Interpretation notes, Gene interpretation, and Recommendations, finalized variants, case analysis outcome, and Case Info, the case status must be changed from Finalized to another status.

8. To Generate Report, click on the printer button on the Individual case page Top bar, select Create New or choose a previously generated report (if any), then select a template and click Generate.

All the generated reports are saved per case and each can be downloaded in a .pdf or .odt format.

Note: for finalized cases, you can view the Case Result, Interpretation Notes and Finalized Variants in a new Finalize tab in the righthand panel of the case page. Another way to see the variants that were selected when the case was signed off is to select Finalized in the dropdown menu onthe Candidates tab.