Reports
BaseSpace Variant Interpreter provides tools to create a report from a case and export results to an external report in PDF and JSON file formats.
Selected variants are sorted across autopopulated tabs based on the interpretation category. Each tab lists the variants that have been added to or removed from the report. The Report Summary tab provides a free text field for adding notes to the report.
Completed case reports are available in PDF format or as JSON files containing additional data for the case.
The report template is defined as part of the test configuration. For more information, see Test Parameters and Using Report Sections.
Add Associations to the Report
Add gene and variant associations to the report during interpretation. Each reported variant requires a report category.
You can review and modify variant information before the final report is generated. For more information, see Review and Submit a Draft Report .
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From the Variant Details or Gene Details tab for the variant, select an association. |
NOTE
Subsequent changes made to the association do not automatically update on the report. To refresh the association data on the report, select the information icon for the association and then select Update to New Version after making a change.
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Select a report category. |
The category is assigned at the variant level and applies to all associations reported for the variant in the case.
Review and Submit a Draft Report
Before you submit the final report for approval, you can add a report summary, reassign categories, and change classifications for reported associations.
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From a Case, select the Reports tab. |
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[Optional] Select Proband Info to review subject metadata. |
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Select through the tabs and review the variants. |
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Select a variant and perform any of the following actions: |
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Choose whether to update association data. If new details are available, an information icon appears. To update the association, select the information icon and then select Update to New Version. |
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Choose whether to include a variant or association in the report. Excluded variants cannot be edited. |
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To exclude the variant, select Remove Variant from Report. |
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To restore an excluded variant, select Add to Report. |
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To remove an association, select Remove Association from Report. Each variant must have at least one association. |
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[Optional] Select a different variant category. |
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Select or change the variant classification. |
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Select Details to view more information about the variant association in Knowledge Network. |
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Add to or edit the association summary. |
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Drag associations to change their position in the list. |
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[Optional] Group variants. Only variants in the same category can be grouped. |
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To group variants, select a variant from the Group Variants menu, and then select a variant. |
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To ungroup variants, select None from the Group Variants menu. |
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Select the Report Summary tab and perform any of the following actions: |
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Add a summary description. The summary appears on the final report. |
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Select the Reference tab and perform any of the following actions: |
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Review references imported from Knowledge Network evidence citations. |
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Select Add Additional Reference, enter details for a new reference, and then select Add to Report. |
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Include or exclude references. |
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[Optional] Select Preview Mode to preview the PDF report. |
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[Optional] Select Download Case PDF to download a copy of the report. |
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Select Send for Review. |
The case status is changed to Ready for Review.
Approve a Report
Before you submit the final report for approval, you can add a report summary, reassign categories, and change classifications for reported associations.
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Select the Reports tab for the case, and then review the report details. |
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Select an approval status. |
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Approve—Generates the final PDF report and changes the case status to Complete. |
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Reject—Reverts the case status to In Progress. |
Edit an Approved Report
Edit a report to make changes to variant information.
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From the Reports tab of a completed case, select Edit Report. |
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Select the change type from the Report Status drop-down menu. |
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Amended—A minor correction (eg, spelling correction) is made but the report context does not change. |
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Addended—Information is added to the report but the report context does not change. |
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Corrected—A major correction (eg, change to pathogenicity) is made. |
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Enter a reason for the change. The change reason is displayed in the edited report. |
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Select Approve Report. |
Download a Completed Report
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To download a basic report in PDF format, do one of the following: |
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From the Reports tab, select Download Case PDF. |
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From the Reports column of the Complete cases list, select PDF. |
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To download case data in JSON format, select JSON from the Reports column of the Complete cases list. |
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To download older reports, point to the report name in the Complete cases list, and then select the PDF or JSON report from the reports list. |