Variant Filters

The Variant Filters section describes how to add, configure, duplicate, or archive variant filters.

Add and Configure a Variant Filter

1. On the top toolbar, select Configuration.

2. Select the Test Components tab.

3. Navigate to Variant Filters and select New.

4. Navigate to the Condition Group section and enter the applicable genes in the Genes field.

5. [Optional] Select the Include genes from diseases check box.

6. Select Apply.

7. Select Include or Exclude from the drop-down list for each gene.

8. For Variant Category, select the field to open up a drop-down list of variants that can be included or excluded.

9. Select the check boxes next to the applicable variant types.

10. Select Add Criteria and select the applicable criteria from the drop-down list (for example, Cancer Hotspot Samples).

11. Select Include or Exclude from the drop-down list for the criteria.

12. To include or exclude additional criteria, repeat steps 10 and 11.

13. For AND or OR, select Add Condition Group to add any other applicable condition groups.

14. [Optional] Select Reset to undo the changes to the condition groups.

15. Select Save.

The Genomic Region criteria is not available when creating a filter from configuration but can be included when adding/editing filters in Variant grid . For more information, refer to Add and Configure a Variant Filter.

Edit a Variant Filter

1. On the top toolbar, select Configuration.

2. Select the Test Components tab.

3. For Variant Filters, select a filter.

4. Select Edit.

5. Update the applicable settings. For more information, refer to Add and Configure a Variant Filter.

6. Select Save.

Duplicate a Variant Filter

1. On the top toolbar, select Configuration.

2. Select the Test Components tab.

3. For Variant Filters, select the applicable filter.

4. In the right-hand pane, select Duplicate.

5. [Optional] Adjust the condition group settings. For more information, refer to Add and Configure a Variant Filter.

6. Select Save.

Archive a Variant Filter

1. On the top toolbar, select Configuration.

2. Select the Test Components tab.

3. For Variant Filters, select the applicable filter.

4. In the right-hand pane, select Archive.

5. To confirm, select Yes, change.

Default Filters

Connected Insights provides the following default filters to assist in preliminary test implementation:

Filter	Description
Pre-configured Demo Filter	Filters for rare coding small variants, copy number variants, unidirectional gene-fusions, and splice variants.
Pre-configured Small Variant Demo Filter	Filters for rare coding small variants.
Pre-configured CNV Demo Filter	Filters for CNVs.
Pre-configured Focal CNV Demo Filter	Filters for CNVs that exhibit a focal (>=7 CN, >3.5 FC, <2 CN, or <=0.5 FC) copy number change.
Pre-configured SV Demo Filter	Filters for unidirectional gene-fusions called via DNA data.
Pre-configured RNA Demo Filter	Filters for RNA splice variants and unidirectional gene-fusions.
Pre-configured TSO 500 RNA Demo Filter	Filters for RNA splice variants in AR / MET / EGFR and undirectional gene-fusions.
Pre-configured OVS1 + OP4 Demo Filter	Filters for rare gene disrupting small variants or splice variants in a known tumor suppressor gene.
Pre-configured AML Demo Filter	Filters for rare coding small variants, unidirectional gene-fusions, splice variants, and large ( >= 5 Mbp) structural / copy number variants in genes known to be involved in AML.