16. Using Interpretations in ReportsΒΆ

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

report tab

Figure 16-1: 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: VSClinical ACMG Trio Template. Click OK.

report template

Figure 16-2: Selecting the report template.

Next, we will associate the assessment catalog used in VSClinical to the report to integrate the final classification and interpretations. 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 Variants Catalog: field. Select ACMG Catalog then click OK.

assessment catalog report template

Figure 16-3: Adding assessment catalog to report template.

This will return you to the main report tab. For the report, the first three sections of this template all involve patient information which can be customized (see the advanced tutorial on Reports: VarSeq Reports Tutorial, https://doc.goldenhelix.com/VarSeq/tutorials/varseq_reports/index.html), but we are going to scroll down to the Primary Findings section to populate the results from the variant assessment. From the Primary Findings dropdown, select Primary Findings.

variant set match

Figure 16-4: Matching the variant set to the report section.

This will pull the variants from the Primary Findings set into this section. In this example we have the SMAD4 variant. The other fields in this report can be populated from the corresponding information that was saved to the assessment catalog by selecting the Lookup button next to the Catalog Lookup. This will populate the variant entry for the SMAD4 variant with the information saved in the assessment catalog.

catalog match

Figure 16-5: Populating the variant entry with Interpretation Lookup.

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

populated entry render

Figure 16-6: The populated entry and render button.

This will then pull up the hidden table containing your Variant table, Compound Het Genes, Samples, as well as a tab titled NA19240 Report, open this tab. This tab contains the final report, which can be opened in an external browser, printed or saved as a PDF document using the export icon in the upper right corner of the report tab.

rendered report

Figure 16-7: The final rendered report.