11/29/23 CA TB LWP Weekly Meeting Notes

Anne Gaynor:

Angela Starks:

Zenda Berrada: X

Sarah Buss: X

Lauren Cowan:

Varvara Kozyreva: X

Gretl Glick: X

Joan Mangan:

Mathew Sylvester:

Laura Carlton:

Stephanie Johnston:

Steven Yu: X

Shawnte George: X

Katelyn Chen:X

Allison Stewart: X

Amy Tieku:

Catherine Evans:

Olga Yayloyan:

Esita Harper: X

OOOs

• Steven OOO:

  • Dec 11, 25, ~22,

• Gretl OOO: 11/28-12/5/2023; 12/22-1/2

• Matt OOO: Nov 29-Dec 8

• Sarah: 11/28-29; 12/3-6 OOO

• Anne OOO: 11/29-12/1; 12/4-7 OOO

• Laura OOO: 11/28-12/1

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

TB LWP: Issue Log

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

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

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

  • Due date: Is a dependency for assay development, would like to review prior to mapping specimen source

  • CE: Still in progress, Target: 11/8/23.

  • 11/22: Request for an update from Catherine via Esita , due to issue being open for several monthsopen

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

• Issue 146: Change to bold “Sequencing-Based DST (performed by default)”: Done in QC1, Ready for review; 11/22: Add please see details webpage closed

• Issue 149: PDF version of  [order] TRF @vova.11/22: Dependent on all updated of TRF being completed open

• Issue 155: Sediment Option Order closed

• Issue 156: Instructional text closed

• Issue 157: Material Type Modifier closed

• Issue 158: Missing Field closed

• Issue 159: Change instructional text to remove AFB smear positive text--edits closed

• Issue 160: Duplicate instructional text closed

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

  • 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: Web Portal

  • 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.

Additional TRF Changes

• CDPH Proposed Updates:

  • Modifications:

    When Material type Modifier is selected the “Material Approved by CDPH” prompt disappears. This change was implemented.

  • MDL contact information prompt was removed as duplicate prompt, as well as the second sentence of the prompt that asked for a submission reason and sample type was removed.

11/22/23:

• Please note: The 11/16/23 version of the TRF will be considered final. Any proposed NEW updates will be applied as a post-production update and will be captured as enhancement request moving forward.

Next Steps & Action Items

• ICC: Provide current list of TB Specimen Sources and any associated mappings for review: 11/8 overdue

• ICC Issue 143 can now begin work due to TRF final being approved.

• ICC: Issue 149 PDF can being work due to TRF final being approved.

• CDPH: Follow up with LIMS specialist on new WGS timeframe.

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

• 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