Typical user actions

Connected Insights enables user actions that are common for interpreting oncology assays data. The sequence of steps can differ between laboratories, but typically includes the following actions:

Software Setup Actions

Perform the following actions during the initial setup of the software:

1. Configure secondary analysis data upload and sample data upload.

2. Configure settings (for example, QC metrics, variant interpretation, and transcripts).

3. Configure variant filters.

4. Configure the report template.

5. Configure the test definitions that store and automate the settings used for processing individual cases.

Case Review Actions

To review a case, perform the following actions:

1. Find the new case created by the data uploaded to the software.

• Case flags are used at this step to assign users and categories, perform searches, and filter as needed.

1. On the Overview tab, review findings in key genes, genome-wide biomarkers, and key QC metrics (if configured).

2. On the Visualize tab, review chromosomal and other events on the Genome View plot.

3. On the Variants tab, review variants as follows.

• Edit or create filters to customize the specific case information that displays.

• Use the Integrative Genomics Viewer (IGV) to review variant quality.

• Use tags to flag variants to support communication between variant reviewers.

1. Perform variant interpretation and include selected variants into the report as needed.

2. Use information from internal and external sources (for example, My Knowledge Base, JAX-CKB, and the COSMIC database) to facilitate the interpretation process. Reuse information stored for a variant that has been interpreted previously. When you remove and add variants, the draft report is automatically edited to reflect any changes.

3. On the Lab QC tab, review sample and variant quality information.

4. On the Report tab, review the draft report (if defined and enabled from the Configuration page).

5. Preview the final report and add the interpretation summary.

6. Approve the report (available only for the laboratory director role).

7. [Optional] Open the report and update or correct information.

The following illustration shows typical user actions in Connected Insights.