2023-05-11 LabMCoP Meeting notes

X

Nancy Cornish

CDC

X

Manjula Gama-Ralalage

CDC

-

Riki Merrick

APHL

X

Christina Gallegos

APHL

-

Amy Liu

Inductive Health / APHL

X

Raj Dash

Duke / CAP

X

John Snyder

National Library of Medicine (SNOMED CT)

X

Andrea Pitkus

UW

X

Kathy Walsh

Labcorp

-

Rob Hausam

Hausam Consulting

-

Doug Franklin

APHL

-

Pam Banning

3M

Upcoming OOO

Yes

• Riki 5/4 - 5/12 - what about the call on 5/4 and 5/11 - leave on the books - Christina to run and record

• John 5/17 - 5/25

• Raj week of 5/15

• APHL Week 5/22-5/26

Question from CLSI

Yes

Working on a document for proper collection of respiratory specimens for microbiology testing and one of our member shared the coding below with us. https://aphlinformatics.atlassian.net/wiki/download/attachments/1915519082/How-To-Collect-NMT-Specimen-for-COVID-19.pdf?api=v2; https://aphlinformatics.atlassian.net/wiki/download/attachments/1915519082/NMT-Specimen-Collection-Infographic.pdf?api=v2

She has a number of concerns about the coding, the tests and what we are calling the specimen collection. Here is the link for SNOMED Coding: https://browser.ihtsdotools.org/?perspective=full&conceptId1=181203001&edition=MAIN/2023-03-31&release=&languages=en

Example: Anterior nares (both anterior nares) which makes sense since both sides should be sampled. - add synonym for anterior nasal cavity swab

Example: middle turbinate instead of mid-turbinate - it is modeled to point to the middle turbinate - we need to update that to be a new term for the mid-section (on the anterior/posterior axis) of the cavity between hard palate and the inferior turbinate structure - it goes to the middle of it| Swab specmen from nasal mid-turbinate

We also have description for NP Swab (along the top of the ):

Anterior nose swab (squamous epithelial vs respiratory epithelial (which is what is getting infected): https://www.cdc.gov/coronavirus/2019-ncov/testing/How-To-Collect-Anterior-Nasal-Specimen-for-COVID-19.pdf

add synonym for anterior nasal cavity swab)So we ned to update the modeling

Reporting Biomarkers to Cancer registries

Lab Test Naming Conventions

Andrea planning this

• SHIELD call topic (maybe June 13)

  • TRUU Lab

  • LOINC

Specimen CMT - review of terms with questions

• 5/11/2023:

• FecalFluid - duplicate term

  • SPM-4 is the same but collection method is required for one of the terms

  • usually collected for C-diff testing - need to be passed per rectum not colonoscopy(as opposed to colonoscopy which includes saline fluid that flushes the colon - can lead to false positives = not a good specimen)

  • removed duplicate term for specimen collected from colonoscopy (row 213)

• Washings_Tracheal - duplicate term (x3)

  • one preferred, two discouraged but definitions are the same

  • usually go through trach site for specimen with a suction device - not sterile as opposed to a needle in trachea (not done anymore) - most collections are done through an endoscope usually BAL - comment added

  • no real distinction between tracheal or pre-bronchial lavage

  • discourage term with pre-bronch HL7 code for description (row 374)

  • Nancy to look at the American Thoracic Society guidelines

• Lavage - duplicate terms*

  • different HL7 table terms (Lavage-KELOI vs. Wash-WASH)

  • same source site requirement, SPM-9 requirement but one requires SPM-5 (specimen type modifier) - need to ask about this riki.merrick

  • specimen type (SPM-4) - should it be just ‘body fluid’ or should the ‘440674008 - specimen obtained by lavage (specimen)’ - specimen obtained by the procedure but procedure is already listed in SPM-7 - would be redundant to use this code.

    • Need to think more about this

    • Email discussion:

      • ‘440674008 - specimen obtained by lavage (specimen)’ is the FSN and has a syn. of “Wash fluid sample”. However, “lavage fluid sample” wouldn’t become the FSN, but it could be added to 440674008 as a new synonym. -There may always be some confusion around the use of the concept.

      • Decision?: To use the existing term for SPM-4 (440674008) and the procedure term of ‘irrigation’ would be in SPM-7

Specimen CMT - Hosting Options

• How can we publish the content in the dB?

  • Allow access somehow to query the dB

  • as access or excel

  • Using FHIR conceptMap similar to https://build.fhir.org/conceptmap-example-specimen-type.html - based on this profile: https://build.fhir.org/conceptmap.html

  • riki.merrick to ask Eric if he still has that or how he built it:

  • ANSWER FROM ERIC:

    • if you look in the xml source https://build.fhir.org/conceptmap-example-specimen-type.xml.html . you can see how it is mapped. 

    • I am not sure if you mean the table rendering or creating the concept map from a spreadsheet or CSV file.  The FHIR build tool did the table rendering for that mapping, I think I entered the data by hand, or Grahame did it. It would not be hard to create a script to create a concept map from an excel or csv file if needed.  The table needs to be large enough to make it worthwhile though. you could even create formula cells in the spreadsheet to generate the XML or json for each item. and then copy to a text editor and append to the Metadata fields.

Specimen CMT - education

No

Specimen CMT - potential pilot sites

Yes

• Goal is to have some implementers lined up by April - so who to reach out to?

  • Review where we are: Vendor Connections - updated some notes there

Specimen CMT - tracking implementation impact

• Setting baseline

• Define metrics

No

• Setting baseline

Specimen CMT - Compare to NHS Medical Terminology testing

No

Future projects for this call after CMT

No

• In general the call is intended as a forum for ANY messaging related issues to work out.

• In the past we have

  • reviewed containers re-vive that - and how does that interact with devices (UDI identification?)

  • review code systems around additives (HL70371 and SCT substance and product hierarchies)

  • started work on cross-mapping between HL7 method codes and SNOMED CT procedure / technique concepts

    • American College of Surgeons is working on procedure protocol and synoptic data elements / surgical synoptic reports - we could work with them together on that