Connected Insights requires you to provide a report template for each test definition to ensure consistency of reports produced across cases. This section summarizes the actions that can be performed with report templates to customize the look and content of PDF reports to your specifications.

• Create several report templates and use them in more than one test definition.

• Use a default report template provided by Connected Insights or customize the report as needed. These customizations include: – Changing the logo of the laboratory. – Changing the report name. – Reformatting the page and date. – Removing parts of the report related to the Nothing Reported section. This modification might be needed if the laboratory prefers not to report pertinent negatives. – Adding sample information alongside case and subject information. – Changing text in the Supplemental Information section.

For more information on the customization options, refer to Report Customizations.

Create a Report Template

1. On the top toolbar, select Configuration, and then select the Test Components tab.

2. Navigate to Report Templates and select New.

3. Select Download the template.

4. Save the base ODT template.

5. Edit the file with an applicable document editor. The document editor must be able to load v1.3 ODT files. For information on making custom edits to the report, refer to Report Customizations.

6. Select Upload template to re-upload the template with the recently made changes. Uploaded files must in the ODT format.

7. Select Confirm Report Creation when the report preview displays. Download the original report in the ODT format at any time. You can also archive and unarchive report templates. Archiving a report template makes it unavailable for use when creating a test definition.

Download Report Template

1. On the top toolbar, select Configuration, and then select the Test Components tab.

2. Select Report Templates, and then select Pre-configured Demo Report Template or Pre-configured Demo Report Template (Version 2).

3. After the report loads, select Download as ODT.

Test Changes After Report Template Customization

1. On the top toolbar, select Configuration, and then select the Test Components tab.

2. Navigate to Report Templates and select New.

3. For Create your new report, select Upload template.

4. Using file explorer, navigate to the template with the changes and select Open.

5. Review the PDF preview to make sure that the modified report displays as intended.

This section provides information on how to create and customize reports using a template.

In Connected Insights, use the default report template or introduce customizations to configure the reports according to your specifications. For more information on using the default report template, refer to Report Templates.

The following applications can be used to customize the report:

• LibreOffice v7.5 or later

• Carbone Studio Illumina recommends using LibreOffice to customize the report. For more information on the customizations that can be done with LibreOffice, refer to the writer guide on the LibreOffice website. Carbone studio and its documentation are updated regularly. Please ensure any command used in an ODT is compatible with Carbone version 4.22.4 or earlier.

Use LibreOffice or an equivalent ODT editor to do common report customizations, including:

• Changing the logo in the header.

• Changing the report name.

• Updating the date and time format.

• Adjusting the font size and color.

• Reordering and removing sections.

• Inserting or removing information, such as single or aggregate data and the Genomic biomarkers table asterisk.

• Changing the paper size.

• Update Methodology Description and Gene List.

• Show Findings by Tier

Change the Logo

1. Prepare the image file that is going to be inserted into the template.

   • Make sure that the image is between 200 and 600 pixels so that it can fit within the header.

   • Make sure that the image file size is less than 50 KB to avoid a delay in report generation.

2. Open the template in the ODT editor.

3. Replace the Laboratory image in the header as follows. a. Select the Laboratory image within the header of the first page. b. Replace the image with the formatted image from step 1. If you are using LibreOffice, right-click and select Replace. For more information on LibreOffice functions, refer to the writer guide on the LibreOffice website. The location and size are adjustable after the image is placed in the header.

   ❗ The default template includes a different header style for the first page and subsequent pages.

   c. Select the image in the header of the second page. d. Replace the image with the formatted image from step1. If you are using LibreOffice, right-click and select Replace.

   For more information on LibreOffice functions, refer to the writer guide on the LibreOffice website. This replacement causes the header image to change in subsequent pages.

Change the Report Name

1. Open the template in the ODT editor.

2. At the top of the template of the first page, replace the following text with the new report name: {d.reportData.reportLabels.report:ifEM():show('Report'):upperCase()}

   ❗ The default template includes different report name text for the first page and subsequent pages.

3. Repeat step 2 for the second page. This replacement causes the report name to change in subsequent pages.

Change Date and Time Format

1. Open the template in the ODT editor.

2. At the top of the template, find the following code that generates the report updated time text: {d.subjects[0].reports[0].reportDetails.updateDate:formatD('YYYY-MM-DD HH:mm')}

3. Replace YYYY-MM-DD HH:mm with the desired format (for example,YYYY-MM-DD).

Localize Time and Date

1. Open the template in the ODT editor.

2. Find and replace every instance of (UTC) with {d.reportData.localDates.timezone.shortName}. This will replace "UTC" with the local time zone abbreviated name (for example, "PT" for Pacific Time).

3. Find the following code that generates the updated date and time text: d.subjects[0].reports[0].reportDetails.updateDate

4. Replace every instance with d.reportData.localDates.reportUpdateDate

5. Find the following code that generates the report approval date and time text: d.reportData.reportHistory[i].approvedDate

6. Replace every instance with d.reportData.reportHistory[i].approvedDateLocal

Change Font Color and Size

1. Open the template in the ODT editor.

2. Change the font color and style using the font characteristics function for an individual text section.

   ❗ Color and size are changeable, but the font style and type cannot be altered.

3. [Optional] If you must update the font color and size for the whole document, adjust the paragraph style.

Reorder Sections

1. Open template in the ODT editor.

2. Identify the sections that must be rearranged.

3. Select and copy all relevant text or tables in that section.

   ❗ The sections of the template primarily consist of tables. Make sure that the entire table is selected when reordering a section. If you do not,then formatting issues can occur.

4. Enter a paragraph break between the sections where the copied section is being placed.

5. Paste the copied section to the new location.

6. Make sure that all of the information is present and formatted correctly.

7. Delete the original section.

8. Repeat steps 1–7 for any other sections that must be reordered.

Remove a Section

1. Open the template in the ODT editor.

2. Select the section of the report that you want to remove.

   ❗ The sections of the template primarily consist of tables. To remove the section, make sure that the entire table is selected. If you do not, then formatting issues can occur.

3. Delete the section.

Insert Information

Insert single data (for example, Methodology) or aggregate data as follows.

1. Open the template in the ODT editor.

2. Place the cursor where you want the new information to appear.

3. Add the applicable code or text used to generate new content or enter free text that you want to appear in all of the generated reports. For example, enter {d.createdDate:formatD('YYYY-MM-DD')} for the date the report was created or {d.reportData.therapies[]:aggCount} to add a count for the number of therapy assertions included in the report.

Remove the Genomic Biomarkers Table Asterisk (Remove Pertinent Negative)

1. Open the template (version 1) in the ODT editor.

2. Search for and delete the following line (use Ctrl+F to search): {$lbl.gbTableFooter:ifEM():show('*Contains disease related genes only')}

3. Search for the following and delete only the asterisk (*): ('Nothing reported')}*

Remove the Nothing Reported genes list

1. Open the template (version 2) in the ODT editor.

2. Search for the following line (use Ctrl+F to search): {$lbl.nothingReportedV2:ifEM():show('Nothing Reported')}

3. Use the ODT editor delete the table row containing the searched for text above.

Change Supplemental Information Description

1. Open the template in the ODT editor.

2. Search for supplemental information in the search field at the bottom of the template. You can also select Ctrl+F to search.

3. Make the desired edits. For more information on complex edits, refer to the ODT editor help documentation. The following edits are common:

   • Change an existing term heading or its definition by updating the text within the single quotation marks for a given term or definition. For example, {$lbl.geneList:ifEM():show('Gene List')} can be changed to the following: {$lbl.geneList:ifEM():show('Genes Included In This Test')}

   • Add static text (for example, laboratory contact information) by placing the cursor outside of the braces ({ }) where the status text begins. Then, type the text. If needed, press Enter to start a new line. Refer to the following example:

   • Before editing:

     {d.dataSourceVersions}{d.dataSourceVersions:ifEM():showBegin()}{$lbl.notProvided:ifEM():show('Not provided')}{d.dataSourceVersions :showEnd()}

   • After editing:

     {d.dataSourceVersions}{d.dataSourceVersions:ifEM():showBegin()}{$lbl.notProvided:ifEM():show('Not provided')}{d.dataSourceVersions :showEnd()} Contact Information Name of Laboratory +1 (123) 555-1234 Email@Email.com

Change Paper Size

1. Open the template in the ODT editor.

2. Select each paragraph style and adjust the page size to the required size needed for printing.

Change Methodology Description and Gene List

1. Open the template in the ODT editor.

2. Search for and delete the following line (use Ctrl+F to search):{d.reportData.methodology.assayDescription:convCRLF()}

3. Replace line with desired methodology text used for the specified workflow. Example text can be found in the default PDF generated from a case in ICI.

4. Search for and delete the following line (use Ctrl+F to search):{d.reportData.methodology.assayGeneListText:convCRLF()}

5. Replace line with desired gene list.

Show Findings by Tier

1. The version 2 template can conditionally display findings at the beginning of the report based on the Tier/Actionability level. The default shows all levels in this section. To only display Tier I and Tier II (or equivalent).

2. Open the template in the ODT editor.

3. Search for the following line (use Ctrl+F to search):classification.actionabilityOrder:ifGTE(7.0)

4. Change 7.0 to 5.0 in the instances of the line.

5. Search for the following line (use Ctrl+F to search):classification.actionabilityOrder>6.9999

6. Change 6.9999 to 4.9999 in all instances of the line.