Automation

User-defined automation can add assertions from your knowledge base and/or other knowledge bases automatically to a draft report.

Automation only applies to cases using a test definitions with automation turned on during case ingestion. Cases that were ingested before automation was turned on will not have assertions automatically added to their reports.

Automated assertions can be added for all types of variants with assertions in the supported knowledge bases, including the genome-wide biomarkers TMB, MSI, and GIS. Automation configuration settings determine which biomarkers are included in automation and which assertions for those biomarkers are added to the report.

You can also edit or remove assertions that were automatically added before approving a report. For more information, refer to Edit, Remove, and Archive Assertions.

Prerequisites

Before enabling automation, make sure that the following information is set up:

• Key genes and TMB, MSI, and GIS thresholds to limit reporting to certain biomarker scores. For more information, refer to Disease Configuration.

• Preferred transcripts to limit reporting to preferred transcripts. For more information, refer to Preferred Transcripts.

• Default filters to limit the variants being reported. For more information on creating variant filters and adding them as default filters in a test definition, refer to Variant Filters and Test Definition Setup.

Variant Selection

Select either of the following sets of variants to be reported:

• Variants that appear in a default filter and key genes (i.e., Key Findings of the Overview page).

• Variants that appear in a default filter.

The following are not reported:

• Any variant with a likely benign, benign, or likely neutral biological classification in a knowledge base (including My Knowledge Base and ClinVar).

• Any variant with no biological classification in any knowledge base (including My Knowledge Base and ClinVar), and biological classification predicted by the Oncogenicity Prediction tool is VUS, likely benign, or benign.

• TMB, MSI, and GIS with an unknown status.

Max number of variants eligible for reporting:

• If variant selection is Variants that appear in default filter and key genes, only the first 70 variants with assertions in your default filters that are in key genes are eligible for reporting.

• If variant selection is Variants that appear in default filter, only the first 70 variants with assertions in your default filters are eligible for reporting.

Knowledge Base Selection

You can select KBs you want to report assertions from. The following KBs are selectable:

• My Knowledge Base

• JAX-CKB

• CIViC

• OncoKB

You can also reorder KBs to prioritize assertions. Select and hold the icon to the left of the KB and move it up or down to reorder the KB list. Connected Insights uses the following information to prioritize which KB is used to report findings:

• Order in the KB list (for example, if you move My Knowledge Base above JAX-CKB in the KB list, then My Knowledge Base is prioritized)

• Case disease and assertion disease match (for example, if JAX-CKB is below My Knowledge Base in the KB list, but the case disease matches the JAX-CKB assertion disease, then JAX-CKB is prioritized)

Automatic Reporting Setup

1. On the Configuration page, select the General tab.

2. Select Report Automation, and then select Edit.

3. Select one of the following Report a biomarker when options:

   • Appears in a default filter and Key Genes (Key Findings)

   • Appears in a default filter

4. Select applicable knowledge sources from the following Report findings from options:

   • My Knowledge Base

   • JAX-CKB

   • CIViC

   • OncoKB For more information, refer to Knowledge Base Selection. After making your selections, a window displays indicating the reporting status for each classification.

5. Select Yes or No for the following questions:

   • Report assertions previously reported only?

   • Report therapeutic assertions with highest classification only, skipping anything in a lower classification?

   • Report therapeutic assertions that indicate response or resistance only?

6. Select Save.

7. Turn on automation within a test definition. For more information, refer to Test Definition Setup.