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Notes

OOOs

  • Steven OOO:

    • Dec 11, 25, 26

    • Thursday Nov. 23rd – Tuesday Nov 28th

  • Gretl OOO: 11/28-12/5/2023

  • Matt OOO: Nov 29-Dec 8

  • APHL Offices Closed: 11/23/2023 & 11/24/23

  • 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

  • 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

TB LWP: WGS & tNGS TRF Updates

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

11/14/23 CDPH Requested changes via email

  1. Regarding adding new material types under “Other”, we discussed further internally and decided against putting the Mixed Cultures under “Other” because the Material Type Modifier that are displayed under “Culture” are still applicable to Mixed cultures. Would you be Ok to use the checkboxes for "Mixed culture" & "Non-viable culture" under Submitting Laboratory’s Results as was discussed at last call? In terms of mapping, if either "Mixed culture" or "Non-viable culture" selected under Submitting Laboratory’s Results, add “M_TBDST_tNGS” Panel and “M_TBtNGS_Aux” Panel (for Cultures, this would overwrite previously added panels “M_TBDST_WGS” and “M_TBWGS_Aux”).

We still would like to add some additional Material Type Modifiers under “Other” to capture Processed Tissues that currently not captured. And also to move Material Type Modifier “Sediment-AFB Negative” to “Sediment” Material. Please see the attached layout that reflects all proposed changes. Hope those would be minimal. We can also revisit the discrete parsing concerns that you had and APHL concerns about the timeline before moving with those proposed changes.

  • CDPH: Proposal is to use AOE answers to determine which test is ordered in SL

    • Answers would be concatenated in SL “Comment 1” questions tab

    • SL could be queried for Comment 1 (Comment 1 would only be used to store AOE data for mixed culture/non viable culture”)

    • Impact and being able to parse this data discretely in SL

    • Is this CLIA compliant --are there any concerns about being to trace/audit if test ordered in SL

  • APHL: is there a way to capture this information in the LWP and capture this as part of the Material Type Modifer?

  • Would need to add another section (b/w) Material Submitted and Material Type Modifier

    • If user selects Culture, create new section “Culture Type” [Mandatory field] and have option to select

      • Pure Isolate

      • Mixed Culture

      • Non-Viable Culture

      • Map all to “Comment 1” in SL

    • Functionality: Selection should be default to Pure Isolate in Culture Type; user can only select 1 option in culture type

  • Sediment-AFB Negative: Potential for CDC to remove it as an acceptable specimen type (not yet decided)

  • Is it possible to include header “Sequencing-Based DST as part of Test Requested *

    Sequencing-Based DST (performed by default); similar to how Phenotypic DST (pDST) appears as section header

Questions11/15/23:

  • NEW TRF Version received from CDPH

  • New issues created in Issue Log

Next Steps & Action Items

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

  • CDPH: Send over a new TRF with all the changes captured discussed on 11/15

  • ICC: Provide LOE for changes requested (if low LOE will move forward with proposed changes)

  • ICC: Olga will apply updates for review in QC1

  • Next:

...