Page Comparison

Anne Gaynor:

Angela Starks:

Zenda Berrada: X

Sarah Buss: X

Lauren Cowan:

Varvara Kozyreva: X

Gretl Glick: X

Joan Mangan:

Mathew Sylvester: X

Laura Carlton:

Stephanie Johnston:

Steven Yu:

Andrew (ICC):

Katelyn Chen: X

Catherine Evans: X

Amy Tieku: X

Vova:

Olga:

OOOs

• Steven OOO:

  • Friday Nov. 10^th (Veterans Day)

  • Monday Nov. 13^th

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

• Gretl OOO: 11/28-12/15/2023

• Sarah OOO: Nov 9

• APHL closed Veteran’s Day: Nov 10

• Matt OOO: Nov 29-Dec 8

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: https://qc1.labwebportal.com/cdph/#/auth/login

• Updates identified 11/1/2023--Review in QC1”:

  • 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

• 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

11/8/23: Updates Identified:

• Under WGS Genotyping:

  • Yes, please perform default testing >>This radio button should be defaulted/auto selected

• Ask Olga: Under order test tile, the tile is now capturing the date--is this automatically updated based on the version; If so, can we include the format [DATE] version?

Additional TRF Changes

• Changes to sediments/specimens:

• 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, could instead map to tNGS

• Option: If user selects “Culture” AND IN Submitting Lab Results AOE the user selects Mixed Culture OR (and/or) Non-Viable Culture then the panel ordered should be to Add “M_TBDST_tNGS” Panel and “M_TBtNGS_Aux” Panel.

  • N.B.: Currently AOEs are not stored in SL

  • Ideally Mixed Culture or non-viable culture should be stored in SL

    • Potentially use Materials Comments to store or misc comments field in other tabs (user would need to search in SL)

    • Potentially concatenate all AOEs data and store in Comments 1 tab?

• Long-term: Would be good to capture and store this information discretely for tracking/auditing purposes (storing as comment tab would make it difficult to discretely parse)

  • About 7% of tests ordered fall under this use case

• Next step:

  • APHL will discuss with CDC to determine if options are allowable; will then determine next steps for development/which option should be implemented

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

• 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

• 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

  • Sarah N Buss Will follow up with CDC to determine if additional specimen types/material type modifiers are allowable for testing (will determine development option if allowable)

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