10. Using Interpretations in ReportsΒΆ

First open up the report tab by selecting the Open a new tab icon and selecting Report.

report tab

Figure 10-1: Opening the report tab.

We want to use the report template that is specific to the ACMG Guidelines, so select the plus icon next to the Template name dropdown menu to add a new template. From the dialog that appears, select VSClinical ACMG Gene Panel Template and type in a name (we use VSClinical ACMG Tutorial Template in this example). Reports can be used across projects and shared between users, but generally are configured to be specific to a given genetic test and its characteristics.

report template

Figure 10-2: Selecting the report template.

Next, it is helpful to associate the assessment catalog used for the ACMG Guidelines to the report to more easily transfer the classification and interpretations made in VSClinical. To do this, select the gear icon in the upper right-hand corner of the report tab, and select Configure Report Template from the dropdown. This opens the dialog that can be used to customize template entries regarding lab information, but at the moment we want to use this to select the assessment catalog used by the report from the dropdown menu in the ACMG Variant Catalog: field.

assessment catalog report template

Figure 10-3: Adding assessment catalog to report template.

Clicking OK will then close this dialog and return you to the main report tab. The first three sections of this report template all involve patient information which can be customized (see the advanced tutorial on Reports: VarSeq Reports Tutorial), but we are going to scroll down to the Primary Findings section to populate the results from the variant assessments.

From the Select a Variant Set dropdown menu in the Primary Findings section, select Primary Findings.

variant set match

Figure 10-4: Matching the variant set to the report section.

This will pull the variants that were part of the specified variant set into this section. In this example, we have the RAF1 variant from example 2. The other fields are very similar to the fields in the Interpretations section, and we can populate these fields with the same corresponding information that was saved to the assessment catalog by selecting the Lookup button next to Catalog Lookup:.

catalog match

Figure 10-5: Populating the variant entry with Interpretation Lookup.

This will populate the variant entry for the RAF1 variant with the information saved in the assessment catalog during the second example case.

populated entry render

Figure 10-6: The populated entry and render button.

Now that we have all of the information for this report, we can render it by selecting the Create the Report icon on the top of the report tab.

rendered report

Figure 10-7: The final rendered report.