12/13/23 CA TB LWP Weekly Meeting Notes

• Anne Gaynor

• Angela Starks

• Zenda Berrada

• Sarah Buss

• Lauren Cowan

• Varvara Kozyreva

• Gretl Glick

• Joan Mangan

• Mathew Sylvester

• Laura Carlton

• Stephanie Johnston

• Steven Yu

• Shawnte George

• Katelyn Chen

• Allison Stewart

• Amy Tieku

• Catherine Evans

• Olga Yayloyan

• Esita Harper

OOOs

• Steven OOO:

  • Dec 11, 22-25

• Gretl OOO: 12/22-1/2

• Katelyn- TBD 12/19-20

• Matt OOO: Nov 29-Dec 8

• Shawnte: 12/22

• Allison: 12/19-1/2

• APHL Offices: Closed the last week of December (12/25-29, Jan 1)

• ICC Offices closes ( Dec 25- Jan 2)

TB LWP: Issue Log

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

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

1. Issue 137: LWP Specimen Source Mapping: Needs to be extracted/conversion/translations from SL

   1. Mapping estimated date of completion 12/11/23 IN PROGRESS

2. Issue 143: TB WGS & TNGS Mapping Updates; Predecessor> TRF updates being completed:

   1. Updated spreadsheet attached to log, no questions from Catherine IN PROGRESS

3. Issue 161: Confirm process for tNGS if ordered in LWP prior to being completed in CDPH StarLims Production READY FOR RETEST

   1. 12/6 Options were discussed the consensus would be to use option 1 workflow. Option 1: TNGS is "ordered" prior to it being ready in CDPH SL, lab manually switches to PSQ. This would reduce the impact of having to retest, they could make changes in batch mode.

4. Issue 149: PDF version of  [order] TRF @vova. READY FOR RETEST

   1. 12/6: Client Validated, noticed Apostrophe change in Comments lab result section, Shawnte reached back out to ICC for edits.

5. Issue 161: Option 1- TNGS is "ordered" prior to it being ready in CDPH SL, lab manually switches to PSQ OPEN

TB Testing Updates Target Deadlines

• CDPH: Validation schedule for expected TB Testing:

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

    • 11/22/23: Validation in progress (placeholders in place?): Current Target: Jan 31, 2024

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

    • 11/22/23: WGS not yet in production: Validation will be completed by 11/30/23; SL Production Deployment for WGS: ~12/1/23

    • 11/29/23: ~CA to follow up with LIMS specialist to give updated timeframe by 11/30/23

    • 12/5/23: TB WGS assay moved from StarLIMS testing to staging environment.

    • 12/7/23: Moved to StarLims Production COMPLETE

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

    • 11/22/23: WGS will be used in place of PSQ; If TNGS is ordered, will manually switch to PSQ

      • SB: Will PSQ be available for ordering by submitters post Dec? Once WGS is live, PSQ will not be available for submitters to order, but will need to available for lab to use/switch to if TNGS is ordered

      • CDPH is creating placeholders in production before TNGS is fully validated --

      • Need to verify PSQ can be returned if TNGS with ICC/Gretl.

      • 12/6: Verified that the PSQ would return, working similar to a reflex test.

  • WGS go-live--roll out to submitters/ready for ordering:

    • Webinar for submitters: Jan 2024

    • Ideal path forward: Go-Live when validation is complete, in SL production, and LWP is ready for production deployment

    • 12/6: Final package is under review with the Lab Director.

    • RISK: TB Testing SHUTS DOWN if PSQ runs out--which may happen in January

• Project Schedule: https://app.smartsheet.com/b/publish?EQBCT=ea47c05f36e245439ca44e53c66696a1

TB LWP: WGS & tNGS TRF Updates

• TRF FINAL: Updates to the TRF in progress by ICC

  • TRF Updates: Draft completed in FB1, QC1--Available for review: https://qc1.labwebportal.com/cdph/#/auth/login

  • Discussion on the timing of web page updates concerning the availability of PSQ and TN for submitters. Consideration of a tiered approach for whole genome sequencing versus TN NGS rollout.

Outstanding Questions

Next Steps & Action Items

• When LWP goes into Production the WGS should be live and in production and http://www.aphl.org/tbdst will be updated for both WGS and TNGS (once in production)

• PSQ will no longer be available for ordering