12/27/23 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

• Gretl OOO: 12/19 ( am) 12/22-1/2

• 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 161: Confirm process for tNGS if ordered in LWP prior to being completed in CDPH StarLims Production RESOLVED

   1. 12/27: Confirmed that the manual process works

2. Issue 165: Incorrect mapping of comments and culture type OPEN

   1. 12/20: Comments were made in Smartsheet that the fields can not be split. Steven will reach out to LIMS and verified that they are indeed the same stored field in LIMS. Follow up with Katelyn and Varvara

   2. 12/27: Updates submitted on smartsheet, will need to follow up with ICC

3. Issue 168: TRF Update; Submitter Requested test OPEN

   1. 12/20: update that the field has been correct

   2. 12/27: Issue reopened because this is sometimes not working for Seq DST Code, can’t seem to figure out the pattern

4. Issue 170: Preapproval question mandatory for mixed non-viable cultures OPEN

5. Issue 171: User Password asking for reset every time they sign in

   1. User resetting pw everytime they sign on OPEN

6. Issue 172: TBGenotyping CDC_WGS

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

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

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

    • 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.

    • 12/20 Approved; Share with CDC , Sync with Vavara

    • 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

    • 12/20: Need an update from Katelyn on progress with testing and if we are still on track.

  • SB deployment 1/10/24

  • Production 1/16/24

    • 12/20: Discussion on if we had to push out, the latest we would like to propose is 1/23

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

Next Steps & Action Items

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

  • 12/20: TBD, planning. Target one week out from set go-live date. 1/9 preliminary communication with submitters.

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

  • 12/20: Gretl to review and provide updates. Coordinate timing of release, goal is to have ready to present at webinar and switch to new version

• Website: Varvara to work on documents that will drive website changes

  • 12/20: Varvara working on documents ( workflows, etc) to send

Round trip testing

Kathelyn/Steve

December 22, 2023

Feedback on follow up for issues 164, 165 and 168

Katelyn/Vavara

December 21,2023

User Guide Updates

Ann/ APHL

TBD- before Production Deployment

Website update

Varvara/APHL

TBD- before Production Deployment