12/6/23 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, 25, ~22,

• Gretl OOO: 12/22-1/2

• Matt OOO: Nov 29-Dec 8

• Sarah: 12/3-6 OOO

• Anne OOO: 12/4-7 OOO

• Shawnte: 12/22

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

• ICC Officces 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: OPEN

3. Issue 149: PDF version of  [order] TRF @vova.

   1. 11/22: Dependent on all updated of TRF being completed OPEN

   2. 12/4: Additional test requested data not visible on TR section

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.

  • 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.

  • 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

    • 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

Additional TRF Changes

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