TITLE: LIS-001 INSPECT CLIA User Manual version 1.0
AUTHORS: Adam N Baer, Shashank  Sathe

[DESCRIPTION]
Document Title: INSPECT CLIA User Manual
Document No. LIS-001
Document version: 1.0

User guide for the INSPECT (Instant Service Platform for Emergency COVIDTests) CLIA LIS application for use by EXCITE (Expedited COVID IdenTification Environment) Lab.  

INSPECT is a companion LIS to testing performed with Thermo Fisher or Perkin Elmer testing testing kits.  Workflows and procedures differ for each kit.  Please refer to the corresponding test kit lab documents when using INSPECT and this guide.

Sections are divided into end user application use and admin setup and maintenance.  Please refer to lab documents for details on lab testing processes.  Only trained users will be given access to the INSPECT system.  Please contact an Admin user and lab supervisor to set up a login and user training.

Admin use is restricted to users granted access to administer the INSPECT application and access to AWS services.  Please contact an Admin and AWS support staff as applicable for access to admin functions.  Use is restricted to individuals trained on admin functions.

[GUIDELINES]
NA

[STEPS]
SECTION: Standard (Thermo) Workflow
4. Upload platemap file.
SECTION: Standard (Thermo) Workflow
3. Pre-Scan Barcodes.

SECTION: Standard (Thermo) Workflow
3.1. Select Pre-Scan Barcodes from the workflow steps listed in boxes:   

SECTION: Standard (Thermo) Workflow
3.2. Follow the instructions on the page to enter or scan in barcodes.  Turn on the newline setting on the barcode scanner. This will automatically enter a new barcode on a new line. Select the source of the samples entered from the drop down menu.  All samples scanned will be assigned to the same source.  Once all samples for the source are entered, click the submit button and you will be redirected to the home page with a message showing the number of samples that were pre-scanned in to the INSPECT database.  Repeat this process for each set of samples for each source.  

SECTION: Standard (Thermo) Workflow
4.2. Click the "Choose File" button to add the platemap file.  Enter the ID for the Hamilton machine used.  Enter your name.  If the platemap contains sequencing or environmental samples, select the appropriate source from the drop down menu, otherwise, do not select a source.  If the sample plate contains only ANX samples, click the checkbox before submitting the plate.  INSPECT will look for any MAWI barcodes on the plate and error if any are found, since mixed plates are not allowed.

  

SECTION: Standard (Thermo) Workflow
4.3. If using the Visionmate barcode reader, upload all the associated Visionmate platemap files using the "Choose Files" button.  Enter the ID of the Visionmate machine used.
  

SECTION: Standard (Thermo) Workflow
4.4. Click "Assign Plates" and the sample barcodes in the platemap will be assigned sample information from the UCSD student app, INSPECT Forms database, REDCap, or other associated databases.  The page will redirect to a progress bar and a success message will be displayed showing the number of samples that were successfully associated and if any samples were not assigned sample information.  Contact an admin if any error messages are displayed.  There is a set 15 minute time limit for this step in INSPECT, so if the assignment and database lookups take longer than 15 minutes a timeout error will show.  If a platemap times out please troubleshoot the SEP IDs listed on the platemap file and please separate all SEPs listed into separate platemap files and upload the files.

  

  

SECTION: Shared Workflow
13. Assign Storage Box
SECTION: Shared Workflow
14. Discard Storage Box
SECTION: Standard (Thermo) Workflow
5. RNA Elution
SECTION: Standard (Thermo) Workflow
6. Plate Compression
SECTION: Standard (Thermo) Workflow
7. qPCR Reaction
SECTION: Standard (Thermo) Workflow
8. Submit qPCR Results
SECTION: Standard (Thermo) Workflow
9. Techinical Review
SECTION: Shared Workflow
11. Licensed Review
SECTION: Shared Workflow
12. Results Submission:
SECTION: Shared Workflow
15. Sample Rejection
SECTION: Troubleshooting
27. Troubleshooting (LAs and CLSs)
SECTION: Troubleshooting
28. Troubleshooting (Admin troubleshooting and database management)
SECTION: User Login and Sample Tracking
29. User Login
SECTION: User Login and Sample Tracking
31. Sample Tracking (Index page)
SECTION: Standard (Thermo) Workflow
5.2. Enter the appropriate lot numbers or "N/A" used for the MS2 Phage, Wash buffer, Binding Solution, Binding Bead, EtOH (used in the second wash plate), and nuclease-free water (used in the elution plate).  Scan or enter in the Sample Extraction Plate Barcode and RNA Elution Plate Barcode in the appropriate boxes and click the "Assign Plates" button.  This will link the SEP and REP in the INSPECT database.  Click the Assign Plates button on the bottom of the form to link the plates.  A message will display giving success or failure confirmation, and reason for failure, if applicable.

  
 



SECTION: Version Control
32. CodeCommit Version Control
SECTION: Version Control
32.1.  All INSPECT code is stored on the AWS CodeCommit version control module. Please see the CodeCommit User Guide for more information about use and commands. Only Admin users will have AWS console access.  To gain console access, contact an Admin user and include AWS application support staff as applicable. 
SECTION: Version Control
32.2. Each INSPECT application is stored as a separate repository.  The repositories will have branches for any changes made based on projects or updates.  The latest version of the Master branch will store the code currently in on the production server.  Other branches will be merged with the Master only after testing and approval.
SECTION: Version Control
32.3. All updates must be tested before deploying.  Coding review is not required, but it is recommended that best coding practices for Django are followed.  
SECTION: Standard (Thermo) Workflow
5.1. Select the RNA Elution button from the menu:

     

SECTION: Standard (Thermo) Workflow
6.1. Select the Plate Compression button from the menu:

  

SECTION: Standard (Thermo) Workflow
6.2. Enter the EpMotion ID to determine which compression program is used, if EXC_JNS_004, EpMotion1a, EXC_EPM_001, EXC_EPM_002 is entered INSPECT will use the EpMotion compression procedure.  If anything else is entered, INSPECT will use the Bravo compression protocol.  Enter the REP plate IDs in the correct order since the order of the plates entered and well positions on the 384 well plate are dependent on the order of the REP plates entered.  Enter or scan in the RWP ID in the RNA Working Plate Barcode field.  Click the Assign Plates button on the bottom of the form to link the plates.  A message will display giving success or failure confirmation, and reason for failure, if applicable.

   

 

SECTION: Standard (Thermo) Workflow
4.1. Select the "Submit Platemap" button from the menu:
  
   

SECTION: Standard (Thermo) Workflow
7.1. Select the qPCR Reaction button from the menu:

  

SECTION: Standard (Thermo) Workflow
8.1. Select the Submit qPCR Results button from the menu:

  

SECTION: Standard (Thermo) Workflow
9.1. Select the Technical Review button from the menu:

  

SECTION: Shared Workflow
13.1. Select the Assign Storage Box button from the menu:

  

SECTION: Shared Workflow
14.1. Select the Discard Storage Box button from the menu:

  

SECTION: Standard (Thermo) Workflow
7.2. Enter the Probe Mix Lot #, Enzyme Type, Enzyme Mix Lot #, Mosquito ID, and Tip Spool Serial # in the appropriate boxes.  Make sure the qRT-PCR Plate Barcode is correct and is linked to the correct RWP Barcode.  Click the Assign Plates button on the bottom of the form to link the plates.  A message will display giving success or failure confirmation, and reason for failure, if applicable.

  

SECTION: Standard (Thermo) Workflow
8.2. Upload the qPCR results file.  Make sure that the RT-qPCR plate ID in the file matches an existing RT-qPCR plate in INSPECT and that the results have not yet been uploaded, or the file will not be able to be uploaded.  If any samples matching the QRP ID have results in INSPECT the file cannot be uploaded since results will not be over-written.

  

SECTION: Standard (Thermo) Workflow
9.2. Input the qRT-PCR Plate Barcode ID into the box and click the Start button to begin the review process:

   
 

SECTION: Standard (Thermo) Workflow
9.3. Review the results following POA-007 Data Analysis and Interpretation for SARS-CoV-2 Assay, including Data Delivery Review.  The SOP contains the latest tables and diagrams outlining results thresholds and decision tree assessment calls.  

Each result has a drop down menu allowing the user to select the corrected result for each sample.  If any changes are made, comments must be added explaining the change.  All original results from the QRP result file will be stored in the database for reference (INSPECT Decision field).  Select the Confirm button once all samples are reviewed and any comments are added.


   
 

SECTION: User Login and Sample Tracking
29.1. All user activity requires a login and is recorded by the INSPECT system.  Each user is tracked through their username for any action performed.  Each individual user is tied to a trained member of the laboratory staff; shared logins are not allowed. Each user must be set up by an Admin after training has been completed.  All logins are created by an Admin user.  Only admin users can set or change passwords, so any password changes must be submitted to an Admin user.  All login credential information must be sent via Secure email, please see the Admin section of this document for more details.
SECTION: User Login and Sample Tracking
29.2. To log in, navigate to the index or home page for the INSPECT site https://inspect.ucsd.edu/qpcr_test/ and enter your login credentials (note that the index page redirects to the login page as listed in the address bar below): 

  

 

SECTION: User Login and Sample Tracking
31.1. After successful login, the index page loads displaying the navigation bar on the top, the workflow selections on the left bar and Sample Tracking and Summary information in the center.  Your username will be displayed on the right top corner, clicking the arrow next to it will allow you to log out.

  

SECTION: User Login and Sample Tracking
31.2. The Overall Testing Summary table shows all sample data from the INSPECT database.  This includes the total number of samples run, the number of negative and positive samples, and the list of samples and plates to be requeued.  Clicking on the Samples To Be Requeued or Plates To Be Requeued button will give a list of the samples or plates marked to be requeued.
Example of plates to be requeued:
  
Example of samples to be requeued:
  

SECTION: User Login and Sample Tracking
31.3. The Daily Sample Summary displays the samples from today and what sources they have associated.  
 


  

SECTION: User Login and Sample Tracking
31.4. The Plate Tracker table displays plates processed in the last 2 days.  This tracker helps the lab keep track of which plates have been run for each step and track any plate failures or requeues.  

  

SECTION: Shared Workflow
11.1. Licensed review is performed by a CLS according to POA-007 Data Analysis and Interpretation for SARS-CoV-2 Assay including Data Delivery Review.
SECTION: Troubleshooting
27.1. Access the TroubleShoot link via the top navigation bar.


Troubleshooting can be used to revert a plate of samples back to a specific step in the workflow, removing any downstream data.  Never troubleshoot a plate that has ANY samples that have results submitted.  Please contact an Admin to help troubleshoot a plate with samples that may have been submitted.

Troubleshooting is irreversible, once a plate has been troubleshot it cannot be recovered.  If a plate is accidentally troubleshot or the original data from a plate needs to be recovered for any reason, please contact an Admin.
SECTION: Troubleshooting
27.3. Enter the plate ID to troubleshoot.  A SEP or REP or RWP or QRP ID is may be used to start the process.  Note that all samples on a plate will be affected by troubleshooting.  Enter the reason for troubleshooting the plate, i.e. file upload issue, system down, entry error, etc.  Select the step to troubleshoot the plate to, or select "Requeue" to requeue the plate.  Once again, Troubleshooting is irreversible, once a plate has been troubleshot it cannot be recovered.  If a plate is accidentally troubleshot, please contact an Admin.

  

SECTION: Troubleshooting
27.5. Confirm troubleshooting on the following page, INSPECT will show information and counts for all samples and other possible associated plates.  Note that all data displayed in this screenshot is testing data and not present in the INSPECT CLIA production database.

  
After reviewing the selected plate and associated sample information, confirm using the "Confirm" button at the bottom of the page.

  

SECTION: Troubleshooting
28.2. Restoring a plate that has been troubleshot: 

All plates that have been troubleshot are stored in the qpcr_test_troubleshoot table.  The entries may be restored by a staff user with access to the database back end only. 
SECTION: Troubleshooting
28.3. Updating demographics:

If sample demographics are not entered into the database when a sample is plated and the platemap file is uploaded to INSPECT, the demographics must be updated manually before results may be released.  Samples may be edited through the admin interface by admin users.
SECTION: Troubleshooting
28.1. The Admin interface:

Admin sites are hidden and only accessible by Admin users.  To access the admin site to display data tables, ask a staff user for the link to the admin interface.  Users, groups, and data tables are accessible on the admin interface.  The development instance (inspect-training.ucsd.edu) has the same data structures as the production database, but all users, groups, and data tables differ based on the database connection.  Admin users may test any changes on the development server before applying them to the production server.
SECTION: Shared Workflow
13.2. Enter the SEP and SSB plate IDs in the fields provided and click "Submit"

  

SECTION: Shared Workflow
14.2. Enter the SSB ID for the box being discarded and click "Submit"

  

SECTION: Shared Workflow
15.1. Navigate to the Reject Specimen workflow page by using the top navigation bar.  The following page will be displayed showing a link box to scan rejected tubes (LAs) and another to confirm specimen rejection (CLSs only). Click the appropriate link box.

  

SECTION: Shared Workflow
15.2. Scan Rejected Barcodes (LAs)

Enter or scan the rejected tube barcodes, multiple may be entered, and click the "Reject Listed Tubes" button to continue.

  


SECTION: Shared Workflow
15.3. Select the specimen disposition from the drop down menu.  Enter the reason for rejection in the appropriate text box for each specimen and click the "Confirm" button.  Once the samples are confirmed, database information, such as the employee ID will be added for each specimen.  If the specimen is not present in the UCSD student application, INSPECT Forms, or test order database, the sample will not be displayed for the CLSs' reject confirmation list.  Samples without database information cannot be rejected through this workflow.  If any errors occur, please contact an admin user immediately and do not enter any tubes for rejection.

  

SECTION: Shared Workflow
15.4. Rejection Confirmation (CLSs)

Follow instruction to identify any duplicate tubes or multiple database entries.  Add comments when applicable to help track duplicate tubes. If no duplicate tube barcodes are present, click "Continue" to proceed to the following page.

  

SECTION: Shared Workflow
15.5. Review the rejected specimen information and add comments as necessary.  Use the table and information provided to inform the partners about rejected specimen.  Once the partners have been notified, check the boxes on the left for the entries in the table and click the "Submit Checked Tubes" button.  A csv file will be generated listing all the rejected specimen information.  Review the information in the csv and store it in the appropriate location.  If any errors occur, please inform a system admin immediately and do not confirm any rejected specimen.

  

SECTION: INSPECT CLIA System Architecture
1.   

SECTION: Version Control
32.4. Update procedure

Proposed updates coded by the development team and applied tested on development servers only. Code is stored in the CodeCommit repository under a development branch while being developed.
A validation procedure will be created and written with test cases for testing the update and any components affected.
The validation procedure must be approved before testing by a CLS or the lab director.
Testing is performed according to the approved validation protocol by the designated tester.
Results and necessary supporting information is reviewed and must be signed off by a CLS or the lab director.
The code is updated on the production server by a designated admin user.
SECTION: Shared Workflow
11.2. Click on "Submit Results" on the top menu bar to see pending results submissions and tubes ready for licensed review.  If no samples are pending submission or licensed review the page will look like the following screen shot below.  If there are samples pending licensed review the number will be listed in the licensed review box.  If there are samples pending submission they will be listed by source.

  
SECTION: Shared Workflow
11.3. Click the licensed review box to list each set of samples for review by SEP plate.  The control samples and results will be listed, if the control sample results are not as expected the plate may be rejected by clicking the red "Reject" button.  Click the green "Continue" button to review sample results from the SEP listed.

  

SECTION: Shared Workflow
11.4. If there are any duplicate samples on the SEP plate they must be resolved before continuing.  Please add comments to help keep track of duplicates when applicable.  If there are none, click "Continue" to  review the the rest of the samples.

  

SECTION: Shared Workflow
11.5. Review results for each sample.  Detected samples' results will be highlighted in red, not detected in green, invalid in grey, and inconclusive in yellow, including control samples.  Samples with "Undetermined" results highlighted in white are samples that failed to upload any results or have a bug preventing results from updating correctly.  If any samples in review have "Undetermined" results please contact an Admin user immediately and do not continue to review the plate.  The Licensed Result column drop down may be changed for any sample if the results are inconsistent with the ct values noted.  Please add comments if any results are changed for tracking purposes.  Once review for all results is complete, click the "Confirm" button.

  

SECTION: Shared Workflow
12.2. Click on "Submit Results" on the top menu bar to see pending results submissions and tubes ready for licensed review.  If there are samples pending submission they will be listed by source.  This will also include ELR submissions and manual submissions.  ELR submissions will send automatically on a set schedule.  Manual results will generate a csv file that needs to be emailed securely to the partner.  Click a source to continue to results submission.

  

SECTION: Shared Workflow
12.4. Review the results and select the tubes to submit using the check boxes on the left side.  Click the "Submit" button on the bottom to generate a csv file for manual submission or to send the results via ELR.  The color scheme is the same as Licensed Review, Detected samples' results will be highlighted in red, Not Detected in green, Invalid in grey, and Inconclusive in yellow, including control samples.  Samples with "Undetermined" results highlighted in white are samples that failed to upload any results or have a bug preventing results from updating correctly.  If any samples in review have "Undetermined" results please contact an Admin user immediately and do not continue to submit results for the plate.

    

 

SECTION: INSPECT Updates
33. Procedure to Qualify Updates to the INSPECT system
SECTION: INSPECT Updates
33.1. Proposed updates coded by the development team and applied tested on development servers only. Code is stored in the CodeCommit repository under a development branch while being developed.
SECTION: INSPECT Updates
33.2. Once the code updates have been developed and tested on the development servers/systems, follow steps in INS-003 Clinical Laboratory Equipment for Performance Qualification.  If applicable, forms INS-003-F2, F3, and F4 may be used to record the qualification procedure.  All qualification or validation procedures must be approved and signed off by a CLS, Quality Assurance officer, or the Laboratory Director before qualification may begin.
SECTION: INSPECT Updates
33.3. Test cases for any added components must be created and performed to qualify any added components.  If any existing components are modified, test cases must be created to ensure all connected components will function properly after the update is applied.
 

SECTION: INSPECT CLIA System Architecture
2. Selecting a Workflow:

Select the workflow from the left side navigation bar, this will link to the menu displayed in the following step where each workflow step may be selected.

  
The top navigation bar also has a Workflow drop down that is linked to the two selectable workflows.
SECTION: PE Workflow
20. Uploading Platemap(s)
SECTION: PE Workflow
19. Pre-scan Barcodes
SECTION: PE Workflow
19.1. Select Pre-Scan Barcodes from the workflow steps listed in boxes:   
SECTION: PE Workflow
19.2. Follow the instructions on the page to enter or scan in barcodes.  Turn on the newline setting on the barcode scanner. This will automatically enter a new barcode on a new line. Select the source of the samples entered from the drop down menu.  All samples scanned will be assigned to the same source.  Once all samples for the source are entered, click the submit button and you will be redirected to the home page with a message showing the number of samples that were pre-scanned in to the INSPECT database.  Repeat this process for each set of samples for each source.  
SECTION: PE Workflow
20.1. Select the "Submit Platemap" button from the menu:
  
   
SECTION: PE Workflow
20.2. Click the "Browse..." button to add the platemap file.  Enter the ID for the Janus machine used.  Enter your initials.  Enter the lot numbers for the qPCR kit and Chemagic kits.  Click "Submit" to upload the platemap.

  

SECTION: PE Workflow
21. RNA Elution
SECTION: PE Workflow
21.1. Click the RNA Elution box:

  

SECTION: PE Workflow
21.2. Enter the Chemagic ID, lot number for the Chemagic kit, and the sample extraction plate (SEP) barcode.  Enter the RNA elution plate barcode to be assigned and click the "Assign Plates" button. A message will display giving success or failure confirmation, and reason for failure, if applicable.

  

SECTION: PE Workflow
22. Generate REP Platemaps
SECTION: PE Workflow
22.1. Click on the "Generate REP Platemaps" box:

  

SECTION: PE Workflow
23. qPCR Reaction
SECTION: PE Workflow
23.1. Click on the "qPCR Reaction" box:

  

SECTION: PE Workflow
24. Submit qPCR Results
SECTION: PE Workflow
24.1. Click the "Submit qPCR Results" box:

  

SECTION: PE Workflow
25. Technical Review
SECTION: PE Workflow
25.1. Click the "Technical Review" box:

  

SECTION: PE Workflow
26. 
 

SECTION: PE Workflow
22.2. Enter the REP ID and click the "Generate Platemap" button to generate the platemap:

  

INSPECT will generate a platemap to input into the Janus machine for plate compression.
SECTION: PE Workflow
23.2. Click the "Browse..." button and upload the QRP platemap.  Enter the ID of the Janus and the lot number of the qPCR kit and click "Submit" to link the RT-qPCR plate to the RNA Elution Plates listed in the RT-qPCR plate.

  

SECTION: PE Workflow
24.2. Upload the qPCR results file.  Make sure that the RT-qPCR plate ID matches an existing RT-qPCR plate in INSPECT and that the results have not yet been uploaded, or the file will not be able to be uploaded.  If any samples matching the QRP ID have results in INSPECT the file cannot be uploaded since results will not be over-written. A message will display giving success or failure confirmation, and reason for failure, if applicable.

  

SECTION: PE Workflow
25.2. Input the qRT-PCR Plate Barcode ID into the box and click the Start button to begin the review process:

   

 

SECTION: PE Workflow
25.3. Review the results following PES-006 Perkin Elmer System Data Analysis and Interpretation for SARS-CoV-2 Assay, including Data Delivery Review.  The SOP contains the latest tables and diagrams outlining results thresholds and decision tree assessment calls.  

Each result has a drop down menu allowing the user to select the corrected result for each sample.  If any changes are made, comments must be added justifying the change.  All original results from the QRP result file will be stored in the database for reference.  Select the Confirm button once all samples are reviewed and any comments are added.  

Verify that the correct amount of samples are displayed, that all the controls have the correct calls, and that the Inspect calls are correct.

Red= Detected
Green= Not Detected (shown below)
Grey= Invalid (shown below)
Yellow= Inconclusive  
  

 

 

 


SECTION: INSPECT Updates
34. Testing system critical components

SECTION: INSPECT Updates
34.1. The following steps are a guide to testing the core or critical components of INSPECT.  These steps may be taken to test end-to-end sample processing to ensure INSPECT functions correctly after an update.  

These steps are NOT intended to be a full validation of the INSPECT system and all components, but can be used to qualify updates made to the production server or the core system of INSPECT.  Additional components can include, but are not limited to, rejecting specimen, troubleshooting plates, and searching results.  

Samples used for these steps can be the same samples for each step for end-to-end qualification.  If testing on a development server, use only testing data to avoid any PHI or PII on the development servers.

Unless testing involves components that assign well positions or other updates that would require testing a whole plate or multiple plates, partial plates may be used for testing.
 

SECTION: INSPECT Updates
34.2. Pre-scan barcodes:

Add a list of barcodes to the database using the pre-scan function.  Select a pre-scan source from the drop down.  
 

SECTION: INSPECT Updates
34.3. Upload platemap(s):

Generate a testing platemap csv file and enter your name and the Hamilton ID.  Select a source from the drop down to assign a source to all samples on the plate not identified in the databases.  Upload a Visionmate plate and enter the Visionmate ID, if applicable.

Be sure that all samples on the platemap are present in the UCSD student app or INSPECT Forms database, or the test order data table (orders from Redox partners).  Any samples not identified in the databases will not have an associated source field and cannot proceed to result reporting steps (which may be preferred, depending on testing).
 

 

SECTION: INSPECT Updates
34.4. Assign the REP platemap(s):

Link a testing REP platemap to the testing SEP.  Enter lot and ID information for all fields.  Make sure all instrument IDs are valid equipment IDs.
 

SECTION: INSPECT Updates
34.5. Assign REP plates to a compression plate:

Up to 4 REP plates can be compressed into 1 RWP.  For testing, use as many testing REPs as are necessary. Make sure to enter a valid EpMotion ID.
 

 

SECTION: INSPECT Updates
34.6. Link the RWP to a qRT-PCR Reaction Plate:

Enter lot and ID information for all fields.  Make sure all instrument IDs are valid equipment IDs. Enter the RWP plate ID and testing qRT-PCR plate ID.
 

SECTION: INSPECT Updates
34.7. Upload qPCR results:

Upload a testing qPCR results csv file.  Make sure that the RT-qPCR plate ID in the file matches an existing RT-qPCR plate in INSPECT and that the results have not yet been uploaded, or the file will not be able to be uploaded.
 

SECTION: INSPECT Updates
34.8. Technical Review:

Enter the barcode for the testing RT-qPCR plate.
 

 

SECTION: INSPECT Updates
34.9. Additional components to INSPECT can be tested independently.  All added components must be tested before being added to the production server and used for patient testing.


SECTION: Shared Workflow
12.1. Results Submission is performed by a CLS according to POA-007 Data Analysis and Interpretation for SARS-CoV-2 Assay including Data Delivery Review.
SECTION: PE Workflow
18. To start the PE workflow, click the "PE qRT-PCR Workflow" button.  Follow steps outlined in PES-001 SARS-CoV-2 ASSAY USING THE PERKIN ELMER SYSTEM.

  
  

SECTION: Troubleshooting
27.4. Table showing each troubleshooting step and what the actions that will occur in INSPECT will be.  Also shows common reasons for troubleshooting to each step, there may be additional reasons to troubleshoot plates to each step as well.

 
            Troubleshooting   Step   Actions   Reason       Requeue Plate   All   samples associated with the plate will be labelled as "Requeue" for   Technical and Licensed Result and will not be able to be reviewed or   submitted.   Plate   Failure, control failure      Licensed Review   Licensed   result is reset to the Techinical Review result for all samples associated   with the plate.  Licensed Reviewed   Datetime is set to "None".   Change   any Licensed results BEFORE results are submitted      Technical Review   Licensed   result is reset to the Techinical Review result and Techincal review result   is reset to the Decision Tree result for all samples associated with the   plate. Licensed Reviewed and Techinical Review Datetime are set to   "None".   Change   any Technical Review results BEFORE results are submitted      RT-qPCR Results   Licensed   result and Techinical Review result is reset to "Undetermined" for   all samples associated with the plate.    All results values for all targets are reset to -1.  Licensed Reviewed and Techinical Review   Datetime are set to "None".    qpcr_file_received_datetime is set to "None".   Errors   in results file, incorrect result file associated with QRP plate      RT-qPCR   QRP   ID is removed and QPCR Datetime is set to "None".  Licensed result and Techinical Review   result is reset to "Undetermined" for all samples associated with   the plate.  All results values for all   targets are reset to -1.  Licensed   Reviewed and Techinical Review Datetime are set to "None".  qpcr_file_received_datetime is set to   "None".   Remove   QRP association from samples on a RWP      Plate Compression   The   RWP ID is removed and the RWP and QRP wells are reset for all samples   associated with the plate.  QRP ID is   removed and QPCR Datetime is set to "None".  Licensed result and Techinical Review   result is reset to "Undetermined" for all samples associated with   the plate.  All results values for all   targets are reset to -1.  Licensed Reviewed   and Techinical Review Datetime are set to "None".  qpcr_file_received_datetime is set to   "None".   Reset   plate compression for all REP associated with RWP, plates were incorrectly   assigned at the compression step      RNA Elution   The   REP ID and all lot numbers associated with samples on the plate are removed.   RWP ID is removed and the RWP and QRP wells are reset for all samples   associated with the plate.  QRP ID is   removed and QPCR Datetime is set to "None".  Licensed result and Techinical Review   result is reset to "Undetermined" for all samples associated with   the plate.  All results values for all   targets are reset to -1.  Licensed   Reviewed and Techinical Review Datetime are set to "None".  qpcr_file_received_datetime is set to   "None".   REP   was assigned to the incorrect SEP, incorrect lot numbers were entered or   scanned      Sample Extraction   All   data associated with the plate will be completely removed from INSPECT.  WARNING: This will also remove the pre-scan   information, which cannot be restored except by a System Admin.   Incorrectly   uploaded platemap, incorrect source or demographics, incorrect sample   barcodes     
 
SECTION: Troubleshooting
27.2. Some common reasons for troubleshooting a plate include but are not limited to:
Incorrect assignment of plates (SEP to REP, etc).
Issue generating platemaps at sampling step
Problems during qPCR run (Regents, machines, etc). Needing to run the plate again.

SECTION: Shared Workflow
12.3. For each source, each plate will be listed separately for submission.  Click the Continue button to view and check the results before submitting.

  

SECTION: Shared Workflow
17. CLS Dashboard

The CLS dashboard shows samples that have been submitted and are pending submission.  It also shows Rejected samples, and all samples that have been tested but do not have assigned sources or demographics information and cannot be reported.  

 

SECTION: Shared Workflow
17.2. Pending samples/submissions:

The dashboard will display a count of all samples for the current date (or a Sampling Date entered into the dashboard) and what step of the testing workflow they are in.  A csv database dump can be output by clicking the Download Report link.

  

SECTION: Shared Workflow
17.3. Unclaimed Results, Rejected Samples and Un-Identified Samples Breakdown:

The dashboard also displays counts for all samples for the last 48 hours or a given date range (enter on the left side, Sampling date1 and Sampling date2 then click search) that have been Rejected or have not been submitted. Unclaimed results will show a count of the samples that have a source associated but lack demographics; click the header to show a table of the sample information and results.  Unidentified samples will show a count of all the samples that do not have a source associated listed by the pre-scan source; Click the header to show a table of the sample information and results for these samples.

  

Example table showing unclaimed results, may also be output as a .csv file:

  

SECTION: PE Workflow
20.3. The sample barcodes in the platemap will be assigned sample information from the UCSD student app, INSPECT Forms database, REDCap, or other associated databases.  The page will redirect to a progress bar and a success message will be displayed showing the number of samples that were successfully associated and if any samples were not assigned sample information.  Contact an admin if any error messages are displayed.  There is a set 15 minute time limit for this step in INSPECT, so if the assignment and database lookups take longer than 15 minutes a timeout error will show.  If a platemap times out please troubleshoot the SEP IDs listed on the platemap file and please separate all SEPs listed into separate platemap files and upload the files.

  

  
SECTION: INSPECT System Maintenance
35. System Backup and Recovery
SECTION: INSPECT System Maintenance
35.1. INSPECT system backup is handled by AWS.  The system image is backed up daily and can be restored from the AWS image.  To restore an image of the INSPECT system from AMI contact a network admin and the AWS support team (currently Jit and team at ExperTech).  Details on the AMI and recovery can be found here: https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/AMIs.html and here: https://aws.amazon.com/backup-restore/
SECTION: INSPECT System Maintenance
35.2. If the INSPECT system is recovered from a backup or the codecommit repository, follow section 31, Testing system critical components to verify the system works as expected before processing any clinical samples. 
SECTION: Shared Workflow
14.3. Once discarded, the flag "is_destroyed" is set to True for all samples associated with the plate.  A record is created in the qpcr_troubleshoot table with the information from the original entry.
SECTION: Shared Workflow
10. Receiving Test Orders (ELR)
SECTION: Shared Workflow
10.1. EHR messages are received from Redox and are parsed by INSPECT using an automated process.  The messages are received in json format and information is taken from the message fields and added to the test_order and PI tables in the INSPECT database.  

If we have more unidentified samples from an ELR partner than expected, check Redox for errors in the log files.  If no errors are present on the INSPECT side, please contact the partner and have them check their messages.  If both sides do not have error messages, please contact Redox support for more information.

Troubleshooting any issues with ELR or EHR messages must be handled through Redox, since they control encrypting/decrypting and sending messages.  Contact an Admin for any issues with Redox or messaging.
SECTION: User Login and Sample Tracking
30. Adding users to the database:

An Admin user can add additional users to the database.  Generate a unique secure password for the user and input the user name and password in the fields and click "Save"

  

You will be prompted to add personal info, use a UCSD email for users whenever possible, and can assign groups to the user as needed to access different parts of INSPECT.  Do not assign a user superuser permissions.  Staff users will only be assigned to trained system Admin users.  

  

Groups are assigned to users needing the following functions:


 
 
 
 

Do not assign any additional user permissions, access to INSPECT functions and admin functions are all controlled by groups and staff user designation.  Click the "Save" button at the bottom of the form to add the information and group(s) to the user.
 
 
 
SECTION: Shared Workflow
17.1.  

The Re-Sync Database button allows a user to check all pending samples that are missing demographics information against all connected databases (UCSD student app, INSPECT Forms, and REDCap (SASEA and SYHC Mobile Testing Sites)) to attach any updated demographics information.  The re-sync will also update any samples in the qpcr_test table with information from the test_order table from messages received from partners' ELR systems, like Redox.

Click the button to begin the resync process.  A progress bar will be displayed showing the number of samples being re-sync'd and the total sample to re-sync.  Note that this process has a 15 minute timeout.

  

SECTION: Shared Workflow
16. Search Functions

INSPECT has 3 different search functions that can be accessed through the "Search" button in the top menu bar.

  

SECTION: Shared Workflow
16.1. Searching the INSPECT database (all users)

Enter 1 or more search queries into the fields listed.  Searches may be combined, i.e. searching for all "Detected" results across a date range.  Rejected samples will search using the date time rejected (technical review datetime), all other searches will use the sampling datetime (plating).  A maximum of 5000 results may be returned.  If any more results are returned an error message will be displayed.

  
Error displayed when more than 5000 results are returned:

  

The search results will displayed as a table on the results page:

  

SECTION: Shared Workflow
16.2. PII Search (CLS only)

The PII search will query records in the PI table and the qpcr_test table.  Since PI is displayed, only CLSs and admins have access to the PI search.  Enter a tube barcode or employee or student ID to search.  The results will display 2 tables, the top table will display the PI information and the bottom table will display the qpcr_test table information:

  

SECTION: Shared Workflow
16.3. App Search (CLS only)

The app search will query additional databases, including the UCSD student app, and INSPECT Forms.  Enter a tube barcode to search; this search only accepts tube barcodes, not employee or student IDs.  The search results will include the information from the app and specify which app the record was found in.

  

SECTION: Troubleshooting
28.4. Pulling results for research or queries:

The most straightforward way to pull any information from INSPECT is by using the search function.  If results from the search function are unable to satisfy a lab or research query, samples may be queried from the Admin interface.  Each of the data tables in INSPECT may be searched by their primary key and additional fields listed in the admin.py file in the django project.  Tables are listed under the QPCR_TEST database.  Additional databases are also listed as headers:

  

Example of searching for a tube barcode in the qpcr_test table admin page:

  

SECTION: Troubleshooting
28.5. 
SECTION: Standard (Thermo) Workflow
9.4. You can change the final result by clicking on the drop down arrow in the box, for example, if a sample is actually Invalid (due to RP Ct value > 35). If you change a result, add a comment to say why. 

 

SECTION: Standard (Thermo) Workflow
9.5. Verify that the correct amount of samples are displayed, that all the controls have the correct calls, and that the Inspect calls are correct.

Red= Detected (shown below for a Positive control sample)
Green= Not Detected (shown below)
Grey= Invalid (shown below)
Yellow= Inconclusive

Positive (Control) Example: 
 

Invalid Example: 
 

 

 

SECTION: Standard (Thermo) Workflow
9.6. Verify that all samples meet criteria and that Inspect is making the correct calls. See below charts for gene calls. Cq Confidence is not listed in INSPECT, however, these cutoffs are automatically applied when the qpcr results are uploaded.  If Cq Confidence needs to be reviewed, refer to the qpcr results file for the values.

 
       ORF, N, S Gene            Cq Cutoff         Cq Confidence         Target Call             < 37         > 0.7         Detected            < 37         < 0.7         Not Detected            > 37         < 0.7         Not   Detected            > 37         > 0.7         Not Detected            MS2 Gene            Cq Cutoff         Cq Confidence         Target Call            < 37         > 0.3         Detected            < 37         < 0.3         Not Detected            > 37         < 0.3         Not   Detected            > 37         > 0.3         Not Detected      
       RNAse P Gene            Cq Cutoff         Cq Confidence         Target Call            <   35         > 0.7         Detected            < 35         < 0.7         Not Detected            >   35         < 0.7         Not Detected            > 35         > 0.7         Not Detected      

       Control Sample         Orf         N         S         MS2 or RP         Target Call            Negative Control         Negative         Negative         Negative         Positive         Not Detected            Positive Control         Positive         Positive         Positive         Negative         Detected              Negative Control         Negative         Negative         Negative         Negative         Invalid            Positive Control          Positive         Positive         Positive         Positive         Invalid       

       Clinical Sample         Orf         N         S         MS2 or RP         Target Call            1         Positive         Positive          Negative         Positive         Detected            2         Negative         Negative         Negative         Positive         Not Detected            3         Negative         Negative         Negative         Negative         Invalid            4         Positive         Negative         Negative         Positive         Inconclusive            5         Positive         Positive          Positive          Negative         Detected