2023-11-02 LabMCoP Meeting Notes

X

Nancy Cornish

CDC

X

Manjula Gama-Ralalage

CDC

-

Riki Merrick

APHL

X

Christina Gallegos

APHL

-

Amy Liu

Inductive Health / APHL

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 Franklin

APHL

Pam Banning

 3M

Upcoming OOO

Y

• Riki OOO 10/6; 10/20-11/5

• SNOMED Business meeting 10/21-10/25 and Expo 10/26-10/27 = cancel call on 10/26 - leave on calendar for Amy and whoever can make it

• John OOO 10/12, 10/19 and 10/26

Previous Action Items

Y

• Modeling donor organs etc)

  • Have new contact at NMDP - Jane Pollack (Bob Milus retired)

  • Example modeling

  • 10/26: Bob Milus responded to email Nancy sent

    • He recommended we talk to Jane Pollack (jpollack@nmdp.org) at NMDP. She is the SME for standard vocabularies and terminologies for stem cell transplantation.

    • Nancy reached out to Jane Pollack - waiting for a response

      • Action item: Nancy to reach out Jane again

• Nancy Follow up

  • Serum separator tube:

    • Serum-separating tubes, also known as serum separator tubes or SSTs, are test tubes used in clinical chemistry tests requiring blood serum.

      SSTs are sometimes called "marble-top tubes", "tiger-tops", or "gold-topped tubes", referring to the stoppers which are either gold, red with a gold ring on top, or marbled red and grey. The stopper of SPS (sodium polyanethol sulfonate) tubes have a paler yellow colour, sometimes causing confusion; these are known as "yellow tops" not "gold". Trademarked versions of the SST include Covidien "Corvac" tubes.

      The tubes have micronized silica particles which help clot the blood before centrifugation, and a gel at the bottom which separates whole blood cells from serum.^[1]  Silica nanoparticles induce coagulation through contact activation of coagulation factor XII (Hageman factor).^[2] The silica particles are desiccants, which adsorb and hold water vapor.^[3]  This is used in the tubes so the blood adheres to the surface of the tiny silica particles and begins to clot. After the blood sample is centrifuged, the clear serum should be removed for testing.^[4][5]

      These tubes should be used with care when measuring drug or hormone levels because the drug or hormone may diffuse from the serum into the gel, causing a reduction in measured level. The gel in SST II tubes (which appears slightly less opaque) is supposed^{[weasel words]} to have less effect on drug levels in serum.^{[citation needed]}

  • ComboCytologicalMaterialfromEndocervixEctocervixVaginalFormix

  • ComboCytologicalMaterialfromEndocervixEctocervixVaginalFormixSlide

  • need reference to thin prep (request new term with parent cytology specimen container (physical object) for liquid-based cytology container)

  • More info on retracting pus:

    • reviewed several references:

      • Inflammatory responses and inflammation-associated diseases in organs - PMC (nih.gov)

      • Acute Inflammatory Response - StatPearls - NCBI Bookshelf (nih.gov)

      • Incision and Drainage - StatPearls - NCBI Bookshelf (nih.gov)

      • Abscess is the appropriate term for the disease process; The specimen type is abscess and the collection method is included such as Abscess drainage, abscess, aspiration, ( abscess, swab (not pus swab) )

        Swabs of wounds or tissues are not recommended, collect aspirates or biopsies of tissue or both. J. Michael Miller; A guide to Specimen Management in Clinical Microbiology, 3th ed. ASM Press 20217

    • Decision: recommend abscess specimen, instead of body fluid specimen to replace pus specimen

  • Scotchtape prep (scoth tape swab from Mike Miller’s book)

  • nasal sinus fluid definition

• Riki’s Follow up:

  • modeling exposure (wounds) - check when both Jim and John could join

  • need a new term for pacemaker insertion site sample - work with John

    • in SCT there are only swabs for insertion sites (line, drain, chest tube, vascular catherther) - 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

• Open homework EDTA Stopper top

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

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

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

    • Need to check on completeness against the Anne/Nancy list

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

    • K1 or K2 might be important to differentiate

USCDI v5 comments

 N

United States Core Data for Interoperability (USCDI)

• Had call with Maria Michaels, Nancy and Manjula - working on better coordination within CDC and with partners - will set up recurring calls well prior to next comment period

• Nancy talked to leadership and we have experienced scientist available (understands lab workflows and what issues exist with LIS and EHR-s)- may pull her into the Data Standardization Lab subgroup; USCDI is one of the topics; currently working on minimum data set for surveillance Desiree is running this there is also the CSTE work: (https://cste.sharepoint.com/:x:/g/EQdpo_BqId1Ih6EE0C1vKYIB0tkA4elCABwDA8Rn47xluQ?rtime=QO7JLK7F20g )

• this might re-org as part of the CDC re-organization - so might be a hiatus until all figured out

Reporting Biomarkers to Cancer registries

N

National Program of Cancer Registries (NPCR) | CDC

Sandy will put together a one-pager

Specimen CMT - review of terms with questions

 N

Specimen CMT pilot implementers

 N

• Review where we are: Vendor Connections

Specimen CMT - Hosting Options

 N

• 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.

Specimen CMT - education

 Y

• surgical insertion site peritonealDialysisTunnelSite

  • Nancy to review definitions

  • apply the modeling similar to the pacemaker insertion site

  • tunneling should help prevent infection

  • we do have concept for morphologic abnormality = 433861000124108 |Peritoneal dialysis catheter tunnel (morphologic abnormality, will use that

• surgical insertion site peritonealDialysisSite

  • Nancy to review definitions

  • apply the modeling similar to the pacemaker insertion site

• Aspirate_Tracheostomy

  • this would be an aspirate from the area around the opening

  • usually this will heal over, but fluid procution is often seen and misinterpreted asinfection and submit for culture, which they shouldn’t be sent, hence the designation of discouraged

  • added defintion - ready to publish

• Prostatic fluid for stamey test

  • use this SCT code, as it is speicfic for Stamey

  • difference between UTI, Cystitis, Prostatitis

• post prostatemassage urine

  • We have 2 Stamey procedures in SCT - 2 glass (midstream / post-massage = Diagnostic Prostatic Massage Technique: Approach Considerations, Four-Glass Test, Two-Glass Test ) and 4 glass (dirty catch = first void / mid-stream / prostate / post-prosthetic massage urine = Diagnostic Prostatic Massage Technique: Approach Considerations, Four-Glass Test, Two-Glass Test )

  • we can only link from the specimen to the procedure

  • we can add a new term for urine post-

  • SCT Modeling - do we want to have SCT codes that say ‘stamey’?

  • Need to follow up with Riki and John about this

• Stool_Formalin10_Isotone

  • Formalin and PVA - need additive for both - PVA SCT is added to SPM-6

  • will need to submit a code for formalin10

Specimen CMT - tracking implementation impact

• Setting baseline

• Define metrics

 N

Specimen CMT - Compare to NHS Medical Terminology testing

N

Future projects for this call after CMT

 N

• 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