10/11/23 CA TB LWP Weekly Meeting Notes

Anne Gaynor: --

Angela Starks:

Zenda Berrada: --

Sarah Buss:

Lauren Cowan:

Varvara Kozyreva:

Gretl Glick: X

Joan Mangan:

Mathew Sylvester:

Laura Carlton:

Stephanie Johnston:

Steven Yu:

Andrew (ICC):

Katelyn Chen:

Catherine Evans:

Vova:

OOOs

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

• Sarah OOO: 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

     

TB Mapping Documentation

• Review/update TB TRF > CDPH Starlims Mapping

  • See Mapping spreadsheet

Questions

• 10/4/23: Pending ICC input:

• 2 questions from CDPH:

  • “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?"

  • CDPH would like to know if it is possible to set the order in which tests are added to the main panel so that the accession numbers roughly always correspond to the same -01...-05 accession numbers/testing panels.

    • CDPH: 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]

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

Next Steps & Action Items

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

• ICC/APHL: Working on finalizing the project schedule