13. The Final Report

One of the main value points of VSClinical’s ACMG/AMP reports is in the auto-population of data from your workflow into your clinical reports. In doing so, the results are faster reporting and allowing users to have control over the standardization of the reporting which reduces errors throughout the reporting process.

The report page shows the automatically populated fields and is organized first with Patient and Sample information from the Patient tab, then Biomarker Results from the 3 biomarkers we analyzed, then the Secondary Germline Findings of the germline variant we examined, Coverage Statistics again from the Patient tab, and finally any inline references collected from the entirety of the project with hyperlinks to the source data.

This is a good place to review the data, and any incomplete sections will provide warnings to the user under the Interpretations section in the sidebar. Since we do not have any incomplete or unsaved interpretations, the report is ready to be finalized, so select the green Sign Out & Finalize button.

report tab screen

Figure 13-1: The Report tab screen.

This will finalize the project and will not allow any changes to be made without first revoking the report freeze. This concept is reiterated with a follow-up dialog that makes sure the user want to finalize, so select Confirm Sign Out.

Next, click on the word icon below the Saved Exports of Report section so we can render a Word format report document.

We will make an adjustment to the template to customize our report. Select the open location button next to the Cancer Report Template V2.docx template and open the template. Note the warning that suggests saving any adjusted template files with a new name.

report template selection

Figure 13-2: Report template selection.

Here on the right is an example of an AMP based Clinical report. This report is easy to modify as the template is based on Microsoft word, which allows you to orient the template to fit your labs specific branding needs. The report can also integrate sample and patient level information if that data is present in a manifest text file or it can be added manually. Most importantly, the Reports can include interpretations for all variants and genes, somatic and germline, that were added to the VSClinical interface. Lastly, coverage statistics with low quality regions can be incorporated and in-line references are also cited.

Speed, autopopulate fields, standardization, references assessment catalogs, cancer KB boosts clinical report as a starting point, minimizing errors in the process paste and copy mistakes).

Final report

Figure 13-3: The final report exported.