Setting Up Tests in Clinical Reporter

Charlene Son-Rigby -

Setting up a Panel Test

Setting up a Trio or Quad Test

Setting up a Single Whole Exome or Genome Test

Setting up a Duo Test 

 

Clinical Reporter allows you to set up and manage panel, exome and family tests, including generating a final interpretation report.

Note: this guide explains how to set up a test using the Opal user interface. Higher volume clinical labs may prefer to set up tests programmatically. Please contact support@fabricgenomics.com for information on our API.

 

To access Clinical Reporter, on the Opal home page click on “Clinical Reporter”. You will be directed to the Clinical Reports page.

The Clinical Reports page lists all of the interpretation reports in your workspace. You can filter the list based on Report ID, Accession ID or Report Status.

Note: prior to creating a new report, your sequence file must already be uploaded with a Variant Report from Opal Annotation Engine 4. You can upload sequences by clicking “Upload Genome” on the Home Page. If the sequence file you want to interpret already has an annotation report, but it is from Pipeline 3 or older, contact support@fabricgenomics.com to submit it to for re-annotation. You will need to provide the Genome ID.

After uploading your sequence, navigate to the Home Page, and click “Clinical Reporter”.

When you click the green “+New Report” button, you have these options in the dropdown menu:

  • Panel: Launch a Panel-based Test
  • Panel Trio: Launch a Panel-based Test with Family Trio data
  • Solo: Launch a Single Whole Exome or Genome Test
  • Trio: Launch a Trio Family Test
  • Quad: Launch a Quad Family Test

 

Setting up a Panel Test

Panel Test

When you select the Panel option, you will be presented with the below New Clinical Report page.

    1. Enter Patient Accession ID (optional)
    2. Select Assay Type (if enabled in workspace for quality control)
    3. Select the Panel.
    4. Select the Filtering Protocol. The Filtering Protocol is important to manage the types of variants you want to include in your report, and the level of quality you need to report on a variant. For instance, you probably want to exclude intronic regions from your panel and you may also want to exclude variants with low coverage.

You can set up Filtering Protocols by selecting this option on the Home Page. We have also included a Public Filtering Protocol called “Protein changing in coding regions” that filters introns and non-protein changing variants.

 

    1. Click the checkbox if you want to include COSMIC evidence in your interpretation results. Select this for cancer tests.
    2. Select the sample. To do this, navigate to the Project then Genome you want to report on. Selecting a genome when creating a new report is optional. A sample can be added to the report at a later time.
      • Note that the annotation process for a sample must be complete before selecting the sample. The sample needs to have been annotated using Opal Annotation Engine 4.
    3. Click the blue “Save” button.

 

Note on using Public Panels. Fabric Genomics has curated a number of panels to accelerate your panel development process. You can review these panels in Panel Builder’s Public Panels. If you want to use a Fabric Genomics Panel, you need to clone it. For more information on using Fabric Genomics' curated panels, see the Panel Builder section of the User Guide.

You will be directed to the Clinical Reports page with the list of Panel Reports in your workspace. Your new panel report will have a status of Processing then a status of Ready for Interpretation. Processing time is typically less than two minutes.

Adding Patient Information to a Report

To add patient information to a report, click the Actions dropdown menu for your report, and select “Edit Patient Information”. You can also use this option to update patient information at any time before the report is approved.

  1. In this screen, you can enter patient information including Accession ID, Name, Ordering Physician, Indication for Testing and Specimen Type.
  2. If you want to upload patient information using a spreadsheet instead, click the Upload File link. Templates for Excel and CSV are provided in the Upload File dialog.
  3. Once you have entered the desired patient information, click “Save Fields”. 

Patient information fields can also be customized. Please contact support@fabricgenomics.com for more information.

Adding a Sample to a Report

To add a sample to a report, click the Actions dropdown menu for your report, and select “Add Sample”. You will see the New Panel Report page, with the information for your current report already entered in the page.

  1. Navigate to the Project then select the Genome you want to report on.
  2. You can also change information for your test such as the panel or filtering protocol.
  3. Click “Save”.

Once you have added the sample to the report, the test setup information cannot be changed. Only the patient information can be changed, as described in the "Adding Patient Information to a Report" section above.

Assigning A Workspace Member to a Report

To add a workspace member to a report, click the Actions dropdown menu for your report, and select “Assign”. The workspace member will be displayed in the Clinical Reports page, and workspace members' assigned reports can be filtered for using the Assigned To filter at the top of the page.

 

Panel Trio Test

The process for setting up a panel trio test is the same as for a panel test, with the addition of specifying the parents and the proband in the pedigree diagram. This will set up a a test where variants can be reviewed in the context of parental information and modes of inheritance.

Setting up a Trio or Quad Test

The process to set up a family test is simple. In the current version of Clinical Reporter, you can interpret and report out on Trios and Quads with unaffected parents. If you have affected parents, use the Duo family test setup.

Family Reports use the VAAST analysis to prioritize variants by ranking. VAAST is Fabric Genomics' advanced algorithm for ranking disease-causing variants and genes. More information on VAAST is provided in the Advanced Genome Analysis Using VAAST section.

Trio Test

When you select the Trio option, you will be presented with the below New Trio Report page.

  1. Enter the Patient Accession ID (optional)
  2. Select Assay Type (if enabled in workspace for quality control)
  3. Click the checkbox if you want to include COSMIC evidence in your interpretation results. Select this for cancer tests.
  4. Choose one of these options:
    1. Create a New Report. Click on the members of the pedigree and select sequences for the family members and the proband in the modal. This will launch VAAST; the analysis will take a few hours to run before it is ready for interpretation.
    2. Select an Existing VAAST Report. Note that the VAAST Trio analysis must already be complete for you to select this option. For information on setting up a VAAST Trio analysis, see VAAST Family Workflows.
    3. Wait to select a pedigree or existing VAAST report until after the report has been created.
  5. Click the blue “Save” button.

You will be directed to the Clinical Reports page with the list of Reports in your workspace. Your new report will have a status of Processing then a status of Ready for Interpretation. Processing time is typically less than two minutes if the VAAST run was already complete.

 

Quad Test

For a Quad Test, select the Quad option from the New Report drop down menu. The process is the same as the setup for the Trio Test with the added step of including data from a sibling.  You will need to specify whether the sibling is affected or unaffected.

 

VAAST analysis and Clinical Reports can also be set up automatically using our API. Please contact support@fabricgenomics.com for more information.

 

Adding Patient Information to a Report

To add patient information to a report, click the Actions dropdown menu for your report, and select “Edit Patient Information”. You can also use this option to update patient information at any time before the report is approved.

  1. In this screen, you can enter patient information including Accession ID, Name, Ordering Physician, Indication for Testing and Specimen Type.
  2. If you want to upload patient information using a spreadsheet instead, click the Upload File link. Templates for Excel and CSV are provided in the Upload File dialog. Information for the proband can be uploaded.
  3. Once you have entered the desired patient information, click “Save Fields”.

Patient information fields can also be customized. Please contact support@fabricgenomics.com for more information.

Adding a Pedigree or VAAST Analysis to a Report

To add a pedigree or VAAST Analysis to an existing report, click the Actions dropdown menu for your report, and select “Add Sample”. You will see the New Panel Report page, with the information for your current report already entered in the page.

  1. Select one of the following options:
    • New Report: Click on the family pedigree and select the members of the pedigree
    • Existing VAAST Analysis: Navigate to the Project then select the VAAST analysis you want to use.
  2. You can also change information for your test such as the assay type. 
  3. Click “Save”.

Once you have added the sample to the report, the test setup information cannot be changed. Only the patient information can be changed, as described in the "Adding Patient Information to a Report" section above.

Assigning A Workspace Member to a Report

To add a workspace member to a report, click the Actions dropdown menu for your report, and select “Assign”. The workspace member will be displayed in the Clinical Reports page, and workspace members' assigned reports can be filtered for using the Assigned To filter at the top of the page.

 

Setting up a Single Whole Exome or Genome Test

The Solo test setup is a little different from the panel and family tests. When you select the Solo option, you will be presented with the New Solo Report window.

 

  1. Enter the Patient Accession ID (optional)
  2. Select Assay Type (if enabled in workspace for quality control)
  3. Click the checkbox if you want to include COSMIC evidence in your interpretation results. Select this for cancer tests.
  4. Choose one of these options:
    • New VAAST Analysis: Launch a new VAAST analysis to prioritize variants by ranking. VAAST is Fabric Genomics' advanced algorithm for ranking disease-causing variants and genes. More information on VAAST is provided in the Advanced Genome Analysis Using VAAST section
    • Existing VAAST Analysis: Use an existing VAAST analysis in a clinical interpretation
    • Solo Report without VAAST: Perform a clinical interpretation without a VAAST analysis
    • Wait to select a pedigree or existing VAAST report until after the report has been created.

 

For a Solo test with a new VAAST analysis:

  1. Click the Affected Person pedigree box and select the sample.
  2. Click the blue “Save” button.
  3. You will be directed to the Clinical Reports page. Your new report will have a status of Processing then a status of Ready for Interpretation. Due to the new VAAST analysis run, it may take a up to 10 minutes before this report is ready for interpretation

For a Solo test with an Existing VAAST analysis:

  1. Click the Existing VAAST Analysis tab
  2. Select the Project then Genome you want to report on. Note that the annotation process for a sample must be complete before creating a clinical report on that sample. The sample needs to have been annotated using Opal Annotation Engine 4.
  3. Click the blue “Save” button.
  4. You will be directed to the Clinical Reports page. Your new report will have a status of Processing then a status of Ready for Interpretation. Processing time is typically less than two minutes.

For a Solo test without VAAST:

  1. Click the Solo Report without VAAST tab
  2. Select the Project then Genome you want to report on. Note that the annotation process for a sample must be complete before creating a clinical report on that sample. The sample needs to have been annotated using Opal Annotation Engine 4.
  3. Click the blue “Save” button. You will be directed to the Clinical Reports page. Your new report will have a status of Processing then a status of Ready for Intepretation. Processing time is typically less than two minutes.
  4. From the Actions drop down menu, select Review Report.
  5. In the Interpret Variants page, click the “+Add Variants” button. This will lead you to Clinical Variant Miner to select variants for your interpretation.

Adding Patient Information to a Report

You can also add patient information to a report. On the Clinical Reports page, click the Actions dropdown menu for your report, and select “Edit Patient Information”. You can also use this option to update patient information at any time before the report is approved.

  1. In this screen, you can enter patient information including Accession ID, Name, Ordering Physician, Indication for Testing and Specimen Type.
  2. If you want to upload patient information using a spreadsheet instead, click the Upload File link. Templates for Excel and CSV are provided in the Upload File dialog.
  3. Once you have entered the desired patient information, click “Save Fields”.

Patient information fields can also be customized. Please contact support@fabricgenomics.com for more information.

Assigning A Workspace Member to a Report

To add a workspace member to a report, click the Actions dropdown menu for your report, and select “Assign”. The workspace member will be displayed in the Clinical Reports page, and workspace members' assigned reports can be filtered for using the Assigned To filter at the top of the page.

 

Setting up a Duo Test

The Duo test setup allows you to select a proband and a relative, and specify whether the relative is affected. The Duo workflow uses a VAAST run for the proband, then allows the user to analyze different potential modes of inheritance with genotype filters for the proband and relative.

When you select the Duo option from the +New Report menu, you will be presented with the New Duo Report window.

  1. Enter the Patient Accession ID (optional)
  2. Select Assay Type (if enabled in workspace for quality control)
  3. Click the checkbox if you want to include COSMIC evidence in your interpretation results. Select this for cancer tests.
  4. Choose one of these options:
    • New VAAST Analysis: Launch a new VAAST analysis to prioritize variants by ranking. VAAST is Fabric Genomics' advanced algorithm for ranking disease-causing variants and genes. More information on VAAST is provided in the Advanced Genome Analysis Using VAAST section
    • Existing VAAST Analysis: Use an existing VAAST analysis in a clinical interpretation
    • Wait to launch or select a VAAST report until after the report has been created.

For a Duo test with a new VAAST analysis:

  1. Click the Affected Person pedigree box and select the sample.
  2. Now select the relative's sample in the window below the pedigree box. 
  3. Check the box if the relative is affected
  4. Specify the relative's relationship to the proband
  5. Click the blue “Save” button.
  6. You will be directed to the Clinical Reports page. Your new report will have a status of Processing then a status of Ready for Interpretation. Due to the new VAAST analysis run, it will take a few hours before this report is ready for interpretation

For a Duo test with an Existing VAAST analysis:

  1. Click the Existing VAAST Analysis tab
  2. Select the Project then Genome you want to report on.
  3. Now select the relative's sample in the window below the pedigree box.
  4. Check the box if the relative is affected
  5. Specify the relative's relationship to the proband
  6. Click the blue “Save” button.
  7. You will be directed to the Clinical Reports page. Your new report will have a status of Processing then a status of Ready for Interpretation. Processing time is typically less than two minutes.

Adding Patient Information to a Report

You can also add patient information to a report. On the Clinical Reports page, click the Actions dropdown menu for your report, and select “Edit Patient Information”. You can also use this option to update patient information at any time before the report is approved.

  1. In this screen, you can enter patient information including Accession ID, Name, Ordering Physician, Indication for Testing and Specimen Type.
  2. If you want to upload patient information using a spreadsheet instead, click the Upload File link. Templates for Excel and CSV are provided in the Upload File dialog.
  3. Once you have entered the desired patient information, click “Save Fields”.

Patient information fields can also be customized. Please contact support@fabricgenomics.com for more information.

Assigning A Workspace Member to a Report

To add a workspace member to a report, click the Actions dropdown menu for your report, and select “Assign”. The workspace member will be displayed in the Clinical Reports page, and workspace members' assigned reports can be filtered for using the Assigned To filter at the top of the page.

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