12/13/23 CA TB LWP Weekly Meeting Notes

OOOs

• Steven OOO:

  • Dec 14

  • Dec 11, 22-25

• Gretl OOO: 12/19 ( am) 12/22-1/2

• Varvara: 12/20- conflict

• Katelyn- 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 Closed

   2. 12/13: list is available to download from Smartsheet. See most recent date

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

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

   2. 12/13: Ready in QC 1 ready for retest

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.

   2. 12/13: CDPH SL manual process to be tested.

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

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

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. Enough reagent to March

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

  • Targeted Testing complete 12/22/23

  • SB deployment 1/10/24

  • Production 1/16/24

TB LWP: WGS & tNGS TRF Updates

• TRF FINAL: Updates to the TRF complete.

  • 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

TB webinar for submitters, need to set a date for training.

User guide updates: Ann to send most recent Word version , to begin working on updates

Website: Varvara to work on draft update

New Issue: Contact verbiage when selecting culture, is not on the TRF during ordering, but prints out on the PDF. Varvara will log an official ticket.

Next Steps & Action Items

• When LWP goes into Production the WGS should be live and in production and APHL will be updated for both WGS and TNGS (once in production)

• PSQ will no longer be available for ordering

Round trip testing

Kathelyn/Steve

December 22, 2023

TB Webinar for submitters

TBD

TBD- before Production Deployment

User Guide Updates

Ann/ APHL

TBD

Website update

Varvara

TBD- before Production Deployment