Page Comparison

Anne Gaynor: --

Angela Starks:

Zenda Berrada: --

Sarah Buss: X

Lauren Cowan:

Varvara Kozyreva: X

Gretl Glick: X

Joan Mangan:

Mathew Sylvester:

Laura Carlton:

Stephanie Johnston:

Steven Yu:

Andrew (ICC):

Katelyn Chen: X

Catherine Evans: --

Vova: X

OOOs

• Steven OOO: Oct 9, 12, 16, 30 (or 31st)

• Sarah OOO: 10/6, Oct 10-12 (limited availability, on site meetings)

• Indigenous People’s Day: Oct 9 (APHL is open)

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

  • Mapping working session scheduling

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: No changes, approved for development

    • Next: Determine project schedule for development updates

  • SL Updates in progress

  • TRF Updates --relatively quick to complete, additional time needed for SL Mapping/ User/Regression testing

• Updates pending from ICC/Catherine re: Steven’s question below:

  • “When we last spoke about the genotyping panel you mentioned by default, that for this panel alone, you could make it so that there is no external contact associated with it (we wanted this because for most cases there would not be sending a report). However, would an alternative solution be to include the external contact but leave “Send COA” unchecked specifically for just this panel?

     

    I’m not familiar with the “Send COA” but I think if it’s unchecked in LIMS, nothing goes to report delivery queue and subsequently, no report goes to the lab web portal. Do you know if this is correct and if so, is this something you would be able to do?

    I’ve pasted the original request below for your reference.

     

    WGS Genotyping

    Selection under *Please confirm that you would like TB DST Reference Center to perform WGS Genotyping: =

    • “Yes, please perform default testing”: Add “M_TBGenotyping_CDC_WGS” Panel.

    • “No, submitter will be responsible for submitting necessary isolate and/or data elsewhere”: Remove “M_TBGenotyping_CDC_WGS” Panel.

     

    Report to ETOR from M_TBGenotyping_CDC_WGS panel will only happen in case of inability to generate successful WGS data (in order to request isolate re-submission); for this:

    • When M_TBGenotyping_CDC_WGS panel is ordered, remove the external contact for that panel only, this way, by default, no reports will be issued through this panel when it’s closed out. We would manually put in the external contact when necessary”

     

Notes

• Potential different mapping for TB Reference Center

  • CDPH to discuss internally and confirm potential updates (will provide any updates, if relevant).

  • Review Mappings: 10/11/23: during the 2pm call

• CDPH: Order of tests ordered when synced to SL?

  • KC: Some of the related panels, would be nice to set a priority for for additional testing (#1 or #2) --is this available functionality in the LWP? Accession -01, or -02--can we set it to having certain tests? Some panels may not always be added; main panel (Auxilliary test) should be added before the supplemental panel

  • Example:

    • Selection under “Material Submitted” = “Culture”: Add “M_TBDST_WGS” Panel [This would be -01 or after main panel, added first] and “M_TBWGS_Aux” Panel [This would be -02, added as a supplementary panel]

    • Will follow up with Catherine

    • If functionality is available, then CDPH can provide preferred order of adding tests to panel for accession numbering

CDC Monthly call

• CDC Monthly checkpoint: Call re-scheduled for 10/5/23

  • Will include updates on tNGS and WGS Validation statuses for TB Ref Ctr.

Next Steps & Action Items

• ICC/APHL: Confirm project schedule for TRF Development & Mapping: 9/27/23

• ICC/APHL: Working on finalizing the project schedule