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 actions described below.

Software Setup Steps

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

1. Configure secondary analysis data upload and sample data upload. See section Data Upload for more details.

2. Configure settings (for example, QC metrics thresholds, report automation, preferred transcripts). See section Configuration for more details.

3. Configure variant filters following set-up and configuration instructions.

4. Configure the report template.

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

Case Review Steps

To create and review a case, perform the following actions:

1. Upload molecular data and associated sample and subject information.

2. Find the new case on the Cases page using search and filtering.

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

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

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

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

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

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

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

   3. Use tags to flag variants to coordinate with other variant reviewers.

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

   1. Use information from internal and external sources (for example, My Knowledge Base, 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.

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

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

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

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

A summary of case review in Illumina Connected Insights