3. Adding Variants to the ReportΒΆ

To add variants to a clinical report you must first create a Record Set, then flag variants you want to include in the report in the Variant Table.

  • Click on the Record Sets icon in the Table View toolbar and click on Create Variant Set... Figure 3-1. See Record Sets for more information.
Adding Variants

Figure 3-1: Creating Record Sets.

In this dialog you can give the record set a name, initials (abbreviation), choose a color, and set the sample option.

  • Leave the default options and click OK.
  • A Variants record set has now been created and added to the Variant Table View Figure 3-2.

Along with the Variants record set you just created, two additional record sets have been created for you:

  • One for variants to be flagged as Primary Findings and;

  • One set for variants to flagged as Incidental Findings.

    Adding Variants

    Figure 3-2: Record Sets in the Variant Table.

Once a record set is created variants can be added to the set by individually clicking on the box in the row for the record or by using options in the record set sub-menus.

As mentioned previously, a single variant has been added to each record set. For the Primary Findings record set, a disruptive inframe deletion (7:117199646 CTT/-) in the CFTR gene associated with the disease cystic fibrosis was flagged. In the Incidental Findings record set, a missense variant (17:41243800 C/T) in the BRCA1 gene associated with Breast-ovarian cancer was flagged.

Lets add a variant to a record set and observe how VSReports autofills information into the report template for flagged variants.

  • The variant (16:81942028 C/G PLCG2) has been added to the Incidental Finding record set Figure 3-3.

    Adding Variants

    Figure 3-3: Record Sets in the Variant Table.

Now that we have flagged variants in the Variant Table, we can include these variants in a clinical report.

  • Click on the Select a Variant Set dropdown box in the report view interface under the Primary Findings and then under the Incidental Findings sections and select the appropriate Record Set for each section. Figure 3-4.
Template Selection

Figure 3-4: Adding Groups of Variants to Report.

Now that you have added variants to the clinical report, you can classify variants using the Classification drop down dialog box Figure 3-5.

  • Classify the disruptive inframe deletion (7:117199646 CTT/-) in the CFTR gene as Pathogenic

  • Mark the the missense variant (16:81942028 C/G) in the PLCG2 gene as Unknown Significance

  • Classify the missense variant (17:41243800 C/T) in the BRCA1 gene as Likely Pathogenic

    Template Selection

    Figure 3-5: Adding Groups of Variants to the Report.

Note for the Exome Trio Report Template the Interpretation Summary has been autofilled with clinically relevant information from two sources:

  • RefSeq Genes (sequence ontology) and;
  • OMIM (textual description).

With the careful curation of the OMIM resource at the phenotype, gene and variant level, the following descriptive and filterable data points is joined to your reported variants:

  • Functional description of genes and phenotypes;
  • Lists of phenotypes linked to genes with supporting evidence and modes of inheritance of the phenotype;
  • Literature references with relevant PubMed and direct URL Links to relevant genetic resources such as testing guidelines, ontology and gene test registries; and
  • Descriptive interpretations for variants curated from published papers with family and disease context.

This information contained in the Interpretation Summary can be edited in the text dialog box prior to rendering the report.

Note

The information contained in the Interpretation Summary can all be found in the Variant Table. With some JavaScript know-how, VSReports users can extensively modify report templates to bring in other information contained in the Variant Table. Adding additional information from the Variant Table from other annotation sources is covered in the Report Customization section of this tutorial.

Once you are satisfied with the selections, click the Sync icon in the toolbar to render the report in HTML Figure 3-6. The rendered report will automatically open in a Web Browser tab. See VSReports for example reports.

HTML Report

Figure 3-6: Rendering a Clinical Report.

Click on the Export icon **Export** to export the report as a PDF document Figure 3-7. You will be prompted to enter the name of the output file. You can additionally open the containing folder (to view the HTML file directly) or open the HTML page in an external browser.

Exporting Reports

Figure 3-7: Exporting a Clinical Report.