8/30/23 CA TB LWP Weekly Meeting Notes

Anne Gaynor:

Angela Starks: --

Zenda Berrada:

Sarah Buss:

Lauren Cowan: --

Varvara Kozyreva:

Gretl Glick:

Joan Mangan: --

Mathew Sylvester:

Stephanie Johnston: --

Steven Yu:

Katelyn Chen:

TB LWP: Issue Log

Published Link: https://app.smartsheet.com/b/publish?EQBCT=1136271a8d2e4fa184ebc0833df46742

Smartsheet: https://app.smartsheet.com/sheets/8q4pGFcfXc4mmgCw5Q4CQ43j93G6ChHCjxQ5pGm1

TB Testing Updates Target Deadlines

• Validation schedule for expected TB Testing:

  • tNGS should be available for ordering in StarLims Production by Jan 1, 2024

  • WGS: should be available for ordering in StarLims Production by October 1, 2023

  • PSQ: Will no longer be available for ordering as of December 31, 2023

Notes

• Potential update to TRF:

  • TB Genotype would be opt in

  • Genotyping would not be separate option

  • TRF updates:

    • tNGS would this be applied at same time as WGS updates in lwp

    • Potential to include molecular DST

    • Varvara: Would be logical to do WGS for culture

  • APHL: Interim TRF: may not be feasible by end of September

    • Long-term: Would need to develop TRF by Dec 2023 when Pyrosequencing is removed

  • SY: Zenda wanted to provide PSQ for as long as possible; Would PSQ be hard stop after December?

    • VK: Yes, PSQ would not be offered after December

    • AS: Impacts on TAT will need to be communicated to submitters for WGS

  • VK: if this can be built by November, would it be available for ordering?

    • APHL: Interim solution would not be feasible by November, potentially develop updates for long-term solution which would remove PSQ but would add WGS

  • VK: Can test orders be manually mapped in SL if not mapped? SY: if test is not mapped, can potentially manually change in SL to correct test;

    • Would need to confirm with ICC

    • Would rely on manually update

    • KC: Once test is in pre-log, team can change it to other test in panel

    • Would need to verify results syncing

  • PSQ would be available through Dec; WGS would be available in Sep

  • SY: W/o PSQ option, would not be able to automate test ordering

  • KC: Remove PSQ from NEW TRF, and would only add PSQ manually

    • ADD: Sequence based DST performed

  • AG: All isolates will be WGS for DST and genotyping, in addition to phenotypic

    • Are labs selecting WGS or is it default test by submitters in October?

    • VK: Always would add wgs

    • If WGS test is default happening (even if not ordered), would need to send results for reporting

  • SY: Would this be confusing for user in LWP? To be able to order WGS, but may need to provide guidance that WGS would be done if PSQ

  • Is there ever an instance where WGS is done by the time CDPH gets isolate? Unknown

  • Alternative workflow where sent to MI (low volume) --edge case

    • CDPH would need to re-do DST genosequencing if previously conducted by submitting lab

  • WGS would be performed for both clinical or surveillance? Yes, would be performed for both

  • ICC: Can one test be mapped to 2 different workflows? Conditional logic may need to be applied in LimsConnect

  • SY:

    • Proposed potential phases:

      • Phase 1: Update/test/deploy new TRF and PDF results report

      • Phase 2: Update/test/deploy discrete results parsing

• Additional discussions/resources availability needed to determine project schedule

  • Determine Potential reporting options for WGS results Reporting on PDF Results Report (if it is added by CDPH staff as a test when it is ingested into SL;

    • SY: Potential risk of confusion if submitter places order, but does not have WGS available for ordering

• VK: Genotyping: Interest in capturing information

  • Potential updates to AOE [current AOEs not stored discretely in SL; stored as a blob in questions/genotyping panel]

    • Potential data completeness/quality concerns by submitters

    • May be used by submitters, but not reviewed by CDPH/cdc

  • CDC: Have other submitters been asking for this optional fields? This has been available since 2016, so would submitters enter this data? This data could be entered post test in different system, so is this needed in ETOR?

    • Labs and programs may use AOE information differently

  • Potentially include opt-out for genotyping as a way to determine workflow

    • If genotyping is required, may be directed to MI for testing

  • If CDPH does genotyping, then would submitters have option to edit data? Yes

Next Steps & Action Items

• APHL: Confirm LWP functionality with ICC

  • If test ordered in LWP, can this trigger different workflows?

  • If WGS is added manually to test panel in StarLims by CDPH lab staff, will the results sync back to the LWP (e.g. be included on the PDF results report for review by submitter)?

• APHL: Assess ICC resource availability, determine development, deployment schedule

• CDPH: Provide updated Test Requisition Form for review to APHL/ICC