Example PGx Workflow

Step 1:  Login

Login to Ovation Using Your credentials.

  • Logging in will bring you to your organization’s Dashboard - this is a great place to go to see what tasks are pending for you.

Step 2:  Click Projects

Step 3:  Select the Project

Step 4:  Accession a sample for PGx testing

PGx Workflow Overview

  1. Accessioning
  2. DNA Extraction
    1. Pass = Continue to CNV/Genotyping
    2. Reject = Queue backup sample
  3. CNV
    1. Create Batch, Dilution, CNV, Results QC
      1. Fail = Requeue for CNV
  4. SNP/Genotyping
    1. Create Batch, Dilution, SNP, Results QC
      1. Fail = Requeue for SNP/Genotyping
  5. Results are combined in Ovation and released for Report Generation.
  6. Report Returned for Review and Approval
    1. Approved Report = 
      1. Release for Billing
      2. Release to Provider Portal

DNA Extraction

Step 5:  Begin Workflow

  • You can View Queued Samples, or begin a New Workflow, but the simplest way to begin is to click the bar in the bar graph to begin a new workflow.
  • Select Workflow, and click Create.

Step 6:  Create Batch

  • Ensure Appropriate Controls are selected, ensure Sample to add is checked.  
  • Click Submit
  • Click Return To Workflow

NOTE: Uncheck any samples that should not be added to the batch.

Step 7:  Batch Plating

  • Click Create a New Container
  • Select Appropriate Container
  • Scan Container Barcode (If one exists)
    • Alternatively, click Add
  • Assign Locations
    • If locations are to be assigned manually, click Assign Manually.
    • Sample List will open, click sample location and select sample to add to the position.
  • Click Submit
  • Click Return To Workflow

DNA Extraction

Step 8:  DNA Extraction

  • Select Source Container
    • Input candidate(s) should populate with Available Containers.
    • Scan or Type container ID to Add.
  • Enter any appropriate Metadata such as lot numbers of reagents, etc.
  • Select Results Container (Elution Plate).
    • Create a New Container or scan the barcode of Results Container.
    • Sample positions will be automatically assigned once the activity is submitted.

NOTE:  You can add a data file by dragging and dropping into the Additional Files area.

  • Click Submit
  • Click Return To Workflow

You have completed DNA Extraction!

Click Workflows to Move to CNV and Genotyping

CNV Testing

Step 9a: Click the bar graph for the appropriate test and select workflow to begin.

Step 10a:  Create Batch 

  • Select appropriate samples to add to the batch.
    • Alternatively, you can upload a sample sheet to add samples in bulk.
  • Click Submit, and Return to Workflow.

Step 11a:  Batch Plating 

  • Input candidate(s) should populate with Available Containers.
    • Scan or Type container ID to Add.
    • Create New Container if no ID exists.
  • Select the appropriate container type.
  • Plating locations will be assigned automatically.
    • Alternatively, you may upload a plating configuration.
Tip:  You must plate the samples in the order assigned, to maintain traceability in Ovation.

Step 12a:  Create Run Plate

  • Scan bar-code on the Elution plate, or enter the Input container.
  • Select Plating configuration from the drop-down menu and click Submit.

CNV Testing

Step 13a:  Enter Results

  • There are 2 results files to enter in order for Ovation to parse data appropriately.
    • Raw Results - Intended to be an unaltered instrument output file.
      • The file will validate provided it is one of the accepted file types.
      • The file will be stored by Ovation but not used to determine QC.
    • Analysis file - Intended to be a specific analysis file with the extension .txt.
      • The file will validate provided that it is a .txt file.
      • The file headers that Ovation is looking for are displayed in the file drop window.
      • If appropriate headers are found, and all samples in the batch are located, the file will be accepted.
      • If appropriate headers are found but any of the following circumstances exist, the file will be accepted, and data can be submitted.
        • Missing a sample from the batch
        • Missing any data in any column
        • Additional samples or columns found not in batch

CNV Testing

Tips:
  • Incorrect File types, or files with inappropriate header columns will prompt an error message.
  • If file is appropriate file type, and samples in the batch are found in the file, you will see Validated successfully.  
  • If you see warnings, it can mean that some of the fields in the file do not contain data, however, warnings do not stop from continuing workflow.
  • FILE COLUMN HEADERS MUST MATCH THE EXPECTED HEADERS EXACTLY, OR FILE WILL NOT VALIDATE AND DATA WILL NOT PARSE APPROPRIATELY.
  • All Targets contained in the field must be registered targets with Reporting Service.

Congratulations!

You’ve just completed the CNV Workflow

Your Results are Ready for QC

CNV Results QC

Step 14a:  Results Sample Review (QC)

  • Click the sample that you would like to review.
  • Once clicked, the sample will open in the pane on the right.
  • Review assay results, click appropriate review.
Tip:  Assays accepted by laboratory set threshold values will default to accept.
    • Accept (green check)
    • Reject (red crossed circle)
    • Ignore (crossed out eye)
  • Once reviewed, the radio button will appear checked.
Tip:  You can review assays in the left panel by clicking the radio button next to the sample, or all samples at once by clicking the radio button at the top of the column.
  • Once all samples are reviewed, click Submit to send data for report generation.
  • Generated Reports will be sent to provider contact information (set on Accession tab of Requisition).

Tip:  PGx reports will not be sent for report generation until both CNV and Genotype data has been submitted via QC.

SNP/Genotype Testing

Step 9b: Click the bar graph for the appropriate test and select workflow to begin.

Step 10b:  Create Batch 

  • Select appropriate samples to add to the batch.
    • NOTE:  Alternatively, you can upload sample sheet to add samples in bulk.
  • Click Submit, and Return to Workflow.

Step 11b:  Batch Plating 

  • Input candidate(s) should populate with Available Containers.
    • Scan or Type container ID to Add.
    • Create New Container if no ID exists.
  • Select the appropriate container type.
  • Plating locations will be assigned automatically.
    • Alternatively, you may upload a plating configuration.
Tip:  You must plate the samples in the order assigned to maintain traceability in Ovation.

Step 12b:  Create Run Plate

  • Either scan bar-code on the Elution plate or enter the Input container.
  • Select Plating configuration from the drop-down menu and click Submit.

SNP/Genotype Testing

Step 13b:  Enter Results

  • There are 2 results files to enter in order for Ovation to parse data appropriately.
    • Raw Results - Intended to be an unaltered instrument output file.
      • The file will validate provided it is one of the accepted file types.
      • The file will be stored by Ovation but not used to determine QC.
    • Analysis file - Intended to be a specific analysis file with the extension .txt.  
      • The file will validate provided that it is a .txt file.
      • File headers that Ovation is looking for are displayed in the file drop window.
      • If appropriate headers are found, and all samples in the batch are located, the file will be accepted.
      • If appropriate headers are found, but any of the following exist, the file will be accepted, and data can be submitted.
        • Missing a sample from the batch
        • Missing any data in any column
        • Additional samples or columns found not in batch

SNP/Genotyping Testing

Tips:  
  • Incorrect File types or files with inappropriate header columns will give an error message.
  • If the file is the appropriate file type, and samples in the batch are found in the file, you will see Validated successfully.
  • If you see warnings, it can mean that some of the fields in the file do not contain data, however, warnings do not stop from continuing workflow.
  • FILE COLUMN HEADERS MUST MATCH THE EXPECTED HEADERS EXACTLY OR FILE WILL NOT VALIDATE AND DATA WILL NOT PARSE APPROPRIATELY.
  • All Targets contained in the field must be registered targets with Reporting Service.

Congratulations!

You’ve just completed the SNP/Genotype Workflow

Your Results are Ready for QC

SNP/Genotyping Results QC

Step 14b:  Results Sample Review (QC)

  • Click the sample that you would like to review.
  • Once clicked, the sample will open in the pane on the right.
  • Review assay results, click appropriate review.
Tip:  Assays accepted by laboratory set threshold values will default to accept.
    • Accept (green check)
    • Reject (red crossed circle)
    • Ignore (crossed out eye)
  • Once reviewed, the radio button will appear checked.
Tip:  You can review assays in the left panel by clicking the radio button next to the sample, or all samples at once by clicking the radio button at the top of the column.
  • Once all samples are reviewed, click Submit to send data for report generation.
  • Generated Reports will be sent to provider contact information (set on Accession tab of Requisition).
Tip:  PGx reports will not be sent for report generation until both CNV and Genotype data has been submitted via QC.

Report Sign-off

Step 15:  Report Sign-off

  • Once a report is generated, click the Sign Now button to review and sign the report.
  • Prior to sign-off, the generated report is in Draft status.
  • Review the report.
  • Apply electronic signature by entering the password in the Provide Password box and click Approve.
  • Once Approved, an updated version of the report is created.
    • You can toggle between draft and approved reports using the drop-down box under the report name.

Congratulations!

You’ve just completed the PGx Workflow

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