2026-06-18 LabMCoP Meeting Notes

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Nancy Cornish

CDC

Manjula Dharmawardhana

CDC

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Riki Merrick

APHL

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Christina Gallegos

APHL

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Amy Liu

Inductive Health / APHL

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Raj Dash

Duke / CAP

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John Snyder

Pragmatic Terminologies, LLC

Andrea Pitkus

UW

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Kathy Walsh

Labcorp

Rob Hausam

Hausam Consulting

Pam Banning

 3M

Elissa Passiment

Kristina Betz

CDC - NHSN

Jake Bunn

CDC

Marissa McMeen

CDC

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Richard Santiago

FL DOH

Upcoming OOO

• Reminder: 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

• Nancy is out for 2 weeks

Working with DHQP for NHSN reporting

Nancy

Follow up list:

• Urine culture results for HAI requriements

• Gather current means to record bottle volume

  • Biomeriuex

    • it records the volume for each bottle, but not coming across with the instrument, no code set, lab has to record it on their own - willing to help

  • SHIELD - no feedback received

• Provide feedback on NHSN IG: https://measures-ci.nhsnlink.org/artifact-listing.html - Submit Jira to GET INFO FROM LAST MINUTES!!!

Question on Karius Testing

Riki/Christina

FL DPH (and CDPH) have questions about how to best encode reports from Karius (using NextGen Sequencing for a multitude of organisms) - this is a LDT

They are currently using:

• Order LOINC: LP437401-5 Metagenomic NGS - DNA + RNA - used in https://loinc.org/103566-6/ - but only for CSF - they need cell-free plasma and BAL / however they are not reporting on non-infectious disorders, so could use 97601-9 for ordering too?

• Observation LOINC: 97601-9 Microorganism of interest sequence [Presence] in Specimen - if they are reporting orgnism concepts, then the scale for this one is wrong!

• Result SNOMED: Various types of SCT codes (e.g., organism, disorder), but they would prefer to use substance concepts instead

Discussion:

• state reportable labs are based on the organism, but SNOMED CT does not have a means to connect the substance (DNA/RNA) to the organisms

• US is working with Australia to link substance to organism hierarchy so that connection can be made (already a 1 year project) - in the short term organizations would have to provide that mapping until this is implemented in the SNOMED model

• in the long run we think using substance concepts makes sense for this kind of tests

• How would a change to substance concepts impact reporting requriements?

  • the requirements are for reporting the detection of or suspecting of reportable organisms

• this test is not FDA approved, so the cut-off values don't really have undergone the sensitivity determination like FDA appproved tests do for comparison against other methods

• We don’t like this test because it might be misleading, as it only detects fragments - might not be a viable organism

• in FL get a few Karius reports a month

• Next Steps:

  • review the list of results and figure out where current gaps in organism hierarchy are AND identify the substance concepts that are still missing in SCT

  • do education to get LIS and EHR-s and surveillance systems to support more than one hierarchy for results - bring this to the SHIELD Standards and Vocab WG:

    • organism

    • qualifer

    • clincial findings

    • substance

  • let Karius know that in the future we will have substance concepts, but it is going to be a little while

  • need to also review the LOINC and potentially adjust that

Follow up from AndesVirus codes question

Riki

• https://www.linkedin.com/feed/update/urn:li:activity:7463943614830694400/ about codes related to Ebola and Hantavirus outbreaks is asking if we have all the codes we need for reporting, highlighting the need for

• Andes Virus disorder codes

  • Andesvirus causes Hantavirus Pulmonary Syndrome

• Andes Virus organism hierarchy modeling? - John and Riki will reach out to Steven Bradfute to get the low-down on the taxonomy and then figure out how to model the disorder concepts and create submissions for anything new

Below not discussed today:

• pathway for requesting CPT codes

• pathway to getting ICD-10-CM codes (when ICD-11 codes exist)

• Overall thoughts on setting up a code request process (across all SDOs) for emergencies (how do we ensure that Emergency Response teams include properly coded reporting in their work?)

Call adjourned 12:03 PM EDT

BELOW NOT DISCUSSED

Specimen CMT - Hosting Options

Riki

Any Updates on FU with:

Clinical Architecture: They could create conceptMap based on the content model they built, need to follow up about FHIR server usage

ONC: Pull up email from Carmela

Specimen CMT terms

Christina

Review collection method concepts (initiated by USCDI valueset creation: https://hackmd.io/38xa1BZ7TjaPMao6LJHuCA#Proposal ):

retired concepts:

24139008 Endoscopy of urinary bladder (procedure)
176178006 Diagnostic cystoscopy (procedure)
397394009 Bronchoalveolar lavage (procedure)
1388791008 Urine collection after prostatic massage (procedure)
1571000284107 Arterial sampling catheter procedure (procedure)
78181000284104 Cornea impression (procedure)

not in procedure hierachy:

258429002 Rectal scrape specimen
261665006 Unknown

Using preferred name, not FSN (these should not be an issue in the final version, since FSN or preferred name would be pulled based on the concept code, correct?):

122462000 Drainage procedure
14766002 Aspiration
232595000 Bronchoscopic lavage

only NHSN terms left for questions:

CMT Governance process

CMT proposed maintenance process

Start writing this up on this confluence page: Specimen CMT Update Process

Questions from Zulip thread that should be covered by the process we come up with here:

1. Requests for terms used in practice that are not yet in the Cross Map Table?

2. Requests for any corrections or needed updates to terms?

3. What type of version control will be leveraged for releases and major/minor updates?

4. How do you plan to incorporate SNOMED CT Release Updates into Cross Map updates/releases?

5. At what frequency will updates occur? For example, will you process SCT updates once yearly and have a subsequent Cross Map release yearly with changes or more or less often?

6. How do you communicate differential changes between releases? Is a differential file produced or is it expected that users will be able to find changes on their own?

7. What type of customer support for downloads is expected? Will the release entity provide or is it expected of the site hosting the content for download? Both need to work colLABoratively to ensure no blockers arise for users/consumers.

User Guide starter Specimen Cross-Mapping-Table (Specimen CMT)

Follow up items

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

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

    • ISBT 128 | ICCBBA | Technical Documents

      • https://www.isbt128.org/_files/ugd/1a7593_edfd176861c94dca94c34eff8fa3ad0d.pdf - for organs

    • Riki has some contact now with European bloodbank and biobanks = Home - BBMRI-ERIC working with the folks that define their minimum data set: MIABIS - BBMRI-ERIC - these folks shared the follwoing for the reject reason topic, but it seems they differentiate between source site and the organ: #1 Standard PREanalytical Code Version 4.0 - (version 3.0 is here: https://cdn.ymaws.com/www.isber.org/resource/resmgr/isber_2019/pdf/standard_preanalytical_code_.pdf) and also Robin for US

    Clinical Archtecture unmapped LOINCs:

    • Riki should check up with Charlie to see, if he knows where the LOINCs using the shorname in the description come from - as that is discouraged

  • Riki to set up her VSAC authoring log in

  • 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

Lab tests as procedures or orderables

Do we still need this?

Recommendation by SNOMED is that the Observable entity hierarchy be used for both ordering and resulting. 

As for the technique hierarchy, that in no way is intended to be used for either ordering or resulting laboratory tests.  Those concepts are used to model both observables and procedures.  

SNOMED LOINC extension: https://browser.loincsnomed.org/?perspective=full&conceptId1=363787002&edition=MAIN/LOINC/2025-09-21&release=&languages=en

The problem is that major EHR-s vendors have set up CPOE using Procedures for orders to initiate a workflow (that creates the triggering event in the system) - that’s where the push-back comes from.

There is a CPT to SNOMED CT mapping (as a paid mapping available from AMA), but no LOINC mapping.

Can we reach out to CAP Informatics, ADLM Informatics and ASCLS Informatics to get their take on where Lab tests should live

We had said we would work through the Colonoscopy example:

Reference links:

clinical guidelines: Official journal of the American College of Gastroenterology | ACG

Quality Indicators: Official journal of the American College of Gastroenterology | ACG

• For CAP cancer reporting is using SNOMED CT - would be good to look which they chose to represent the performed lab test

There is this question in the LOINC Community: https://forum.loinc.org/t/assistance-creating-a-value-set-for-all-loinc-procedure-concepts/2993

it is related to this US Core FHIR Change request: https://jira.hl7.org/browse/FHIR-54415

Answer to this one is that in USCDI Procedure (https://isp.healthit.gov/taxonomy/term/781/uscdi-v6) does not list LOINC as applicable Vocab standard in any verion, so remove it.

Often folks think of lab tests as procedures, because they can be ordered in CPOE (and outsidde the US, in the UK for example that’s how folks have modeled those, which is why LOINC was adding more of the high level order codes in 2.81 release, so we still should tackle the LOINC community question.

John was working on creatign an intesnional valueset definition based on class + type and maybe a few other attributes

European Semantic work

Link to the German FHIR IG around suceptibility testing:

https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsimplifier.net%2Fguide%2Fars-implementation-guide%3Fversion%3Dcurrent&data=05%7C02%7Criki.merrick%40aphl.org%7Ce11e8daf7f2d4827d07808ddcac8861c%7C434e0aedef824568a0493b17adc08ddd%7C1%7C0%7C638889684844672822%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=kZJRoBl2tMQzWQoYVkaRnEUaaBxepA9sAIu1myDQMyo%3D&reserved=0

Semantic Example section: https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsimplifier.net%2Fguide%2FARS-Implementation-Guide%2FHome%2FSemantics%3Fversion%3Dcurrent&data=05%7C02%7Criki.merrick%40aphl.org%7Ce11e8daf7f2d4827d07808ddcac8861c%7C434e0aedef824568a0493b17adc08ddd%7C1%7C0%7C638889684844702198%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=qQH%2Ff5xwG0O8DvNE4rbjZineXBhY%2BiOWmN047DRthNQ%3D&reserved=0

Confluence page:

Ask if Rob can keep us updated

Specimen CMT pilot implementers

• Review where we are: Vendor Connections

Specimen CMT - education

• Need education for providers and IT folks that helps with set up of the EHR-S / LIS configuration -this can be supported / accomplished? with the Implementaiton Guide we could write

• if we have a use case of how a patient is impacted on their journey through the healthcare system - CAP created a nice video that showed how patient care was affected by incorrect data https://infobeta.cap.org/shield/

Specimen CMT - tracking implementation impact

• Setting baseline

• Define metrics

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: Collection method is now USCDI element, review proposed value set: https://hackmd.io/38xa1BZ7TjaPMao6LJHuCA#Proposal