11/15/23 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:

OOOs

• Steven OOO:

  • Thursday Nov. 23^rd – Tuesday Nov 28^th

• Gretl OOO: 11/28-12/5/2023

• Matt OOO: Nov 29-Dec 8

• APHL Offices Closed: 11/23/2023

TB LWP: Issue Log

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

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

• 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

• Issue 144: CA TB: PDF order not generating for PR submitter--Resolution in progress

  • Fixed, PDFs are generating, reviewing to identify any OIDs which need to be regenerated

• Issue 145: Default selection for WGS Genotyping test: Done in QC1, Ready for review

• Issue 146: Change to bold “Sequencing-Based DST (performed by default)”: Done in QC1, Ready for review

• Issue 147: Elevate General Comments title: Done in QC1, Ready for review

• Issue 148: Question mark after shipping question: Done in QC1, Ready for review

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

• Issue 150: Spell out WGS in WGS Genotyping title: Done in QC1, Ready for review

• Issue 151: Updates to Material Type; add new specimen types under Other [See notes below]

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

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

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

• 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

Additional TRF Changes

• Changes to sediments/specimens:

  • CDC has approved the following change to the workflow:

    • Add AFB negative sediment and have that open up a Material approved by CDPH yes/no box. 

    • Add processed tissue, mixed culture and non-viable culture as separate options under “Other” and map to ordering tNGS directly. 

    • Added to Issue Log --Issue 151

• CDPH Proposed Updates:

  • Modifications:

    1. Move “Sediment-AFB Negative” from “Other” to “Sediment”

    a.      if “Sediment-AFB Negative” selected:

                                                        i.     show selection “*Material approved by CDPH”: Yes/No

    AND

                                                       ii.     display message:

    1. Under “Other” add additional options:

    a.      Processed tissue

    b.      Mixed culture

    c.      Non-viable culture

    d.      Other (add comment field, if selected)

    1. Rename “Other” to “Other (e.g. tissue, mixed culture)”

  • Need to discuss with APHL/CDC: Some of these proposed changes are not allowable sediments

• If user selects Culture, maps to WGS panel

  • If user instead selects mixed culture, map to tNGS

  • If user selects processed tissue, mixed culture and/or non-viable culture under “Other” and order/map to tNGS panel

Questions

Next Steps & Action Items

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

• ICC: Olga will apply updates for review in QC1

  • CDPH will review in QC1 and provide any updates needed (please submit any updates to the Smartsheet Issue log): https://app.smartsheet.com/b/form/7e797e47d0f247619f27252242d6d530

• Next:

  • CDPH/GG will review in QC1, identify any additional changes needed

    • Please provide summary of changes needed and submit to the SmartSheet TB Issue Log: https://app.smartsheet.com/b/form/7e797e47d0f247619f27252242d6d530

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