2024-05-16 LabMCoP Meeting Notes

X

Nancy Cornish

CDC

X

Manjula Gama-Ralalage

CDC

X

Riki Merrick

APHL

X

Christina Gallegos

APHL

X

Amy Liu

Inductive Health / APHL

 regrets

Raj Dash

Duke / CAP

X

John Snyder

National Library of Medicine (SNOMED CT)

Andrea Pitkus

UW

X

Kathy Walsh

Labcorp

Rob Hausam

Hausam Consulting

Doug York

APHL

Pam Banning

 3M

X

Sandy Jones

CDC

Upcoming OOO

• We are now using https://aphlinformatics.atlassian.net/wiki/spaces/LMCOPL/calendars and everyone can just keep it updated

  NOTE: you will need to use type “Event” if you do not have a confluence account

Previous Action Items

• Nancy Follow up:

  • EDTA Stopper top

    • EDTA sufficient or do we need to specify K2 or K3?

    • Nancy can review the list in SNOMED from John

    • Need to check on completeness against the Anne/Nancy list (compare with ARUP)

      • Nancy/Anne’s list is 10 years old - may not want to compare with this outdated list and use ARUP and Labcorp lists

      • Raj: I found this at a phlebotomy certification course website: What Color Tubes Are Used for Which Tests in Phlebotomy – PhlebotomyU

        • Here's a nice one-pager (University of Colorado Health): https://www.testmenu.com/universityhospital/TestDirectory/SiteFile?fileName=sidebar\CLNLAB-2020-03-13-Blood-Tube-Color-Chart.pdf

        • Cleveland Clinic: Blood Collection Tubes - Collection | Cleveland Clinic Laboratories

    • https://phlebotomygeeks.yolasite.com/resources/PRINT OUT COMMON TUBES.pdf

      • but color is manufacturer dependent, which is why we named the tubes by the additives

      • there are container types in SNOMED under 706049005 |Blood tube (physical object)|

      • Have a start here: https://aphlinformatics.atlassian.net/wiki/download/attachments/2018312270/ContainertypesListRikiEmailed20171013.xlsx?api=v2

      • K1 or K2 might be important to differentiate

    • We should leave the top color out of it, since that is manufacturer specific

  • Contact United Network for Organ Sharing for input on donor terms (pre-coordinated or not?) = Contact - UNOS

    • Riki filled out the form - No repsonse

    • ISBT 128 | ICCBBA | Technical Documents

    • Scott’s response: “When the SNOMED representative referred to the existence of “donor codes,” they might be referring to the ISBT-128 coding standard that’s managed by ICCBBA. Please see their website: ISBT 128 | ICCBBA, and navigate to view their technical documents: ISBT 128 | ICCBBA | Technical DocumentsFDA’s regulations for human cells, tissues, and cellular and tissue-based products (HCT/Ps) in 21 CFR part 1271 require assignment of a “distinct identification code” to facilitate tracking HCT/Ps (see 21 CFR 1271.290(c)) but I don’t believe this is relevant to your question.”

    • Might be a topic for SNOMED International

    • We may need to reach out to laboratories/industry to see if the donor codes are needed (we need to show that these codes are needed.)

• Amy follow up - check if she has all of these

  • nasal sinus fluid definition

  • surgical insertion site peritonealDialysisTunnelSite

  • surgical insertion site peritonealDialysisSite

• Riki’s Follow up - none of these got done yet

  • liquid-based cytology specimen vial = https://us-request.ihtsdotools.org/#/requests/preview/354843?fromList=truehttps://request.ihtsdotools.org/#/requests/edit/786429

  • submit a code for formalin10

  • work with John

    • new term for pacemaker insertion site sample

      • in SCT there are only swabs for insertion sites (line, drain, chest tube, vascular catheter) - this should be fixed

      • we should model it after 435971000124108 | Body fluid specimen from peritoneal dialysis insertion site (specimen) and require method, which should be aspirate

    • For wound modeling (see 2023-11-30 LabMCoP Meeting Notes ) create a few pre-coordinated specimen terms

      • to cover the wound causes as children under: 119365002 | Specimen from wound (specimen)

      • another child term for aspirate under 445611000124106 | Specimen from bite wound (specimen), since that is preferred over the existing swab

    • IDSA has a guidelines for wound cultures (deep and superficial - related to surgical wounds) - link sent to Amy

• John:

  • 460621000124104 |Superficial surgical incision wound (morphologic abnormality)| - created in US extension in 2019. Is this needed? If so, then LabMCoP/APHL should promote it to SNOMED International to retain US SNOMED identifier. John submitted this to be promoted: https://request.ihtsdotools.org/#/requests/edit/959920?fromList=true

  • SNOMED guidance related to morphological abnormality: Morphologic Abnormalities vs. Findings - SNOMED CT Editorial Guide - SNOMED Confluence

Reporting Biomarkers to Cancer registries

Yes

National Program of Cancer Registries (NPCR) | CDC

One pager

NAACCR IG in V2.5.1 and FHIR IGs support synoptic Cancer protocols, but FHIR IG has not been implemented, V2.5.1 is in production; Neometrics is configured and once they migrate to V5.1 they will start reporting that

Working with Epic and CAP to inform their clients that use Beaker - they can turn on modules that produces the NAACR V5 format

Currently working on hospital onboarding with DataPult

• How can we help?

  • Any input on use of FHIR

  • NAACCR V5.1 has not been balloted, but is widely implemented - have done crosswalks with LRI IG (and ELR IG) before, but we should redo the crosswalk against LRI base E5 - APHL can create the comparison once we have the LRI base in IGAMT

  • Association of Pathology informatics - get them involved with implementations, maybe create a checklist for the steps needed for implementation

  • Reach out to LIS vendors for Anatomic Pathology Labs

    • Epic (already working with)

    • Oracle

    • Sunquest

    • Vital Access (smaller specialty labs) - already reporting via AIMS

• Update from CAP Cancer Summit with ONC and NCBI and CMS

  • CAP has synoptic report - SCT codes for all templates for questions and answers (Scott Campbell has modeled all of that )

• Dataflow:

  • Cancer Checklist is completed in the template by the pathologist

  • Challenges:

    • available to licensed users only

    • currently labs are storing the synoptic data in a textblob, which means we are loosing the discrete coded data

    • could maybe add in checklists for the gross exam of the specimen?

Specimen CMT - review of terms with questions

• Next Step- Amy to review and update the dB and identify any other outstanding items and bring it to the group

• SkinLesionSwab

  • need a definition, usage type

  • sometimes a preferred specimen type, can be a scraping, etc.

• ShuntTip - delete term

  • non specific

  • not certain if you would culture the shunt tip - if infected, then you would pull the whole shunt out. You would culture the CSF, not the tip

  • Search is coming up with TIPS (see below)

  • Not a preferred term - preferred specimen is CSF (for culture, cell count, glucose, gram stain, DIFF, etc.)

• Chat:

  • Kathy: le·sion/ˈlēZH(ə)n/nounMEDICINEa region in an organ or tissue which has suffered damage through injury or disease, such as a wound, ulcer, abscess, or tumor.

  • John: Transjugular intrahepatic portosystemic shunt (TIPS)

  • Christina: https://www.facs.org/for-medical-professionals/news-publications/journals/case-reviews/issues/v3n7/farazdaghi-successful-surgical-removal/

  • Nancy: Ventriculoperitoneal Shunt - StatPearls - NCBI Bookshelf (nih.gov)

Specimen CMT pilot implementers

• Review where we are: Vendor Connections

  • no update

Specimen CMT - Hosting Options

• How can we publish the content in the dB?

  • Allow access somehow to query the dB

  • as access or excel or csv

  • Using FHIR conceptMap similar to Conceptmap-example-specimen-type - FHIR v6.0.0-cibuild - based on this profile: ConceptMap - FHIR v6.0.0-cibuild

  • @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 Conceptmap-example-specimen-type.xml - FHIR v6.0.0-cibuild . 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.

    • There will be a call Clinical Architecture on May 3rd to discuss moving specimen CMT to Symedical

    • Manjula will take a look at the concept map

Specimen CMT - education

Specimen CMT - tracking implementation impact

• Setting baseline

• Define metrics

Specimen CMT - Compare to NHS Medical Terminology testing

LOINC to SNOMED CT mapping

Future projects for this call after CMT

• 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

  • Look at other HL7 tables that we would want to migrate SCT (i.e., Specimen Condition table, etc.)