11/1/23 CA TB LWP Weekly Meeting Notes

Anne Gaynor: X

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

Andrew (ICC):

Katelyn Chen: X

Catherine Evans:

Vova:

Olga: X

OOOs

• Steven OOO:

  • Monday Nov. 6^th

  • Friday Nov. 10^th (Veterans Day)

  • Monday Nov. 13^th

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

• Gretl OOO: 11/2-11/6, 11/28-12/1/2023

• Sarah OOO: Nov 9

• APHL closed Veteran’s Day: Nov 10

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

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

TB LWP: WGS & tNGS TRF Updates

• Finalized TRF for review/development

  • https://aphlinformatics.atlassian.net/l/cp/WM2SWjwF

  • TRF FINAL: Updates to the TRF in progress by ICC

    • TRF Updates: Draft completed in FB1, QC1--Available for review: Web Portal

• Updates needed:

  • Move “Phenotypic DST (pDST) is recommended to be performed in conjunction with sequencing-based DST, unless pDST has already been performed or will be conducted elsewhere. Please choose pDST test below (leave blank if not needed)” to appear as part of the Additional Test Option(s).

  • Insert space b/w elsewhere and Please

  • Update: Updated!

    • Sequencing-Based DST (performed by default)

      Please see detailed testing algorithm on test information webpage.

  • Please choose a pDST test below (leave blank if not needed)” to appear as part of the Additional Test Option(s).

•  Logic Updated: Display ALL three test options, but apply condition logic:

  • If First-line pDST (RIF, INH, PZA, EMB) is chosen, then First-line pDST for 4-month RPT-MOX regimen (RIF, INH, PZA, MOX) should be removed

  • Second-line pDST (MOX, AMK, CAP, ETA, KAN, RFB)

  • If First-line pDST for 4-month RPT-MOX regimen (RIF, INH, PZA, MOX) is chosen, then First-line pDST (RIF, INH, PZA, EMB) should be removed

     

• All test options should be displayed if any material (sediment, culture, etc) is selected

  • Update needed: If material selected is sediment, only 1 test option is displayed [First-line pDST for 4-month RPT-MOX regimen (RIF, INH, PZA, MOX)]

  • Update needed: display all test options

• Add title: “Additional Test Option” to each test option

• Add “WGS Genotyping (performed by default and data submitted to the CDC).

  This testing is performed by default on culture submissions or isolates obtained from submitted sediments and will be submitted to the CDC for analysis/National Surveillance.” before/above text “*Please confirm that you would like TB DST Reference Center to perform WGS Genotyping”

• Please confirm that you would like TB DST Reference Center to perform WGS Genotyping *

  OPTION SHOULD be defaulted/auto-selected: Yes, please perform default testing

• Update: Has sequencing-based DST been performed by CDPH or CDC on a sample from this patient previously?

Update text:

• Phenotypic DST (pDST)

  • pDST is recommended to be performed in conjunction with sequencing-based DST, unless pDST has already been performed or will be conducted elsewhere. Please choose a pDST test below (leave blank if not needed).

• WGS Genotyping

  • WGS Genotyping is performed by default on culture submissions or isolates obtained from submitted sediments and data will be submitted to the CDC for analysis/National Surveillance.

Submitting Lab Results Section:

• Update needed: Pop-up text should be changed to: "Sample should be sent to CDC for MDDR and not to MDL for sequencing-based DST"

• Change text “Indicate reason(s) for sequencing-based DST below, if applicable” to “Please select any that apply”

  • Remove “Other reason(s), please specify” from list

TB Mapping Documentation

• Review/update TB TRF > CDPH Starlims Mapping

  • See Mapping spreadsheet--any follow up items?

  • Pending confirmation from ICC of Specimen Sources mappings list and any associated transformations/updates applied in SL

Questions

Next Steps & Action Items

• ICC: Provide current list of TB Specimen Sources and any associated mappings for review: 11/1

• 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

• APHL: ICC to provide summary of universal changes which may be applied to both MDL/VRDL AND TB LWPs for review to Steven/TB Team prior to applying to TB LWP so we have consensus and awareness of changes, potential impact, and historic documentation

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