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:
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:
Under “Other” add additional options:
a. Processed tissue
b. Mixed culture
c. Non-viable culture
d. Other (add comment field, if selected)
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
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
11/15/23:
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
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 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 heeader?)
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
ICC: Provide current list of TB Specimen Sources and any associated mappings for review: 11/8
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 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 heeader?)
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
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