Page Comparison

OOOs

• Steven OOO:

  • Dec 11, 25, 26 ~22,

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

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

• 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.

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

    Status
    colour Yellow title open

• Issue 143: TB WGS & TNGS Mapping Updates

  Status
  colour Yellow title Open

• Issue 144: CA TB: PDF order not generating for PR submitter --CLOSED

  Status
  colour Green title Closed

  • 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

  Status
  colour Green title Closed

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

  Status
  colour Yellow title Open

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

  Status
  colour Green title Closed

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

  Status
  colour Green title Closed

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

  Status
  colour Yellow title open

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

  Status
  colour Green title Closed

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

  Status
  colour Green title Closed

• Issue 152: Add Field: Culture Type to TRF

  Status
  colour Green title Closed

• Issue 153: Remove Mixed & Non-Viable options from “Submitting Lab Results” Section

  Status
  colour Green title Closed

• Issue 154: Add Sediment- AFB Negative in Material Type Modifier>Sediment Section

  Status
  colour Green title 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

  • 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

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

  • 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

• 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.

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

• • .

• Adding of link to TRF

11/22/23:

• NEW TRF Version received from CDPH

• New issues created in Issue Log

• 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

  Status
  colour Red title overdue

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

• ICC: Olga will apply updates for review in QC1

  • NEW Issues:/updates to be applied to TRF:

    • Issue 137: List of specimen sources for TB LWP and Starlims, request for an update from Catherine

    • Issue 146: [RE-opened] ADD Header “Sequencing-Based DST (performed by default)” (I know you indicated you can't bold it, but can we add a Header and bold the heeaderheader?)

    • Issue 151: TB TRF: Updates to Material Type; add new specimen types under Other

    • Issue 152: TB TRF: Add Field: Culture Type to TRF

    • Issue 153: TB TRF: remove Mixed and Non-viable culture options from “Submitting Laboratory’s Results” section

    • Issue 154: Add  Sediment-AFB Negative in Material Type Modifier >Sediment Section

• 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

• When LWP goes into Production the WGS should be live and in production and http://www.aphl.org/tbdst will be updated for both WGS and TNGS (once in production)

• PSQ will no longer be available for ordering