2023-07-27 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

 X

Rob Hausam

Hausam Consulting

 X

Doug Franklin

APHL

Pam Banning

3M

Upcoming OOO

Nancy’s item

Y

• COPY of Nancy’s email: Hello Ms. Duncan, I am a long time member of CAP and I work at the CDC in the Division of Laboratory Systems. I recently got notification about half day summit at the CAP annual meeting and I wondered who was going to represent public health needs? We have a few groups working on this these issues here at CDC and are very interesting in the topics. Aligning our work may be very helpful. Thank you for your input.

  Riki, for discussion at the LabCoP today

  a. The Future of Cancer Data: Unlocking Insights with Pathology Reporting - Friday Only Oct 6^th 2023

  Join us for this half-day summit before CAP23, which will bring together thought leaders in the field, sharing their experiences, best practices, and novel uses of pathology data for research, public health, population science, and quality improvement. Together we can improve patient outcomes and make a real difference in the fight against cancer. Add your voice and experiences with synoptic reporting to the conversation and future direction of pathology data reporting.
  Note: Check-in and lunch will be available at 11:00 AM. The summit will start promptly at 12:00 PM and conclude at 4:30 PM.

  b. ONC Accepts CAP’s Suggestions for Next Version of Interoperability Data Standard

  On July 20, 2023, the Office of the National Coordinator for Health Information Technology (ONC) finalized version 4 of the United States Core Data for Interoperability (USCDI). The USCDI standard, which the ONC adopted in the 21st Century Cures Act defines how health care data must be formatted to be exchanged electronically nationwide. The USCDI standard enables the same health care data to be understood across different institutions. Data sharing through widely accepted standards is critical to ensure that health information is available and comprehensible across care settings for use in patient care, public health, and emergency (eg, pandemic) preparedness and response.

  On April 17, 2023, the CAP sent a comment letter on this issue to the ONC, which is tasked with promoting the use of the most advanced health information technology and the electronic exchange of health information. In its advocacy to the ONC, the CAP issued suggestions on how it could improve the fourth version of the USCDI standard. The CAP’s positioning on the USCDI is that the ONC should align the USCDI with the test reporting requirements in CLIA, and that the ONC should seek to achieve its goal with USCDI without overburdening pathologists and laboratories.

• CAP summit

  • Speakers are from NIH - one covers cancer registry data in research, PH and treatment

  • Cancer institute representation

  • Nancy to reach out to Helena Duncan to follow up

• CAP statement about lobbying ONC to include all CLIA requirements for pre-analytical data elements and those were accepted- see published verison 4: https://www.healthit.gov/isa/taxonomy/term/2481/uscdi-v4

Previous Action Items

 y

Riki’s SCT submissions - will work with John to get this done next week Mon or Wed

Nancy researched adverse events with incorrect specimen collection - online guidance for collecting nasal swabs were incorrect in about 50% of the time - <ADD LINK TO THE PAPER>

Riki to reach out to OpenELIS about implementing SpecimenCMT - no answer yet

Follow up (with John and Jim) around how to model exposure (bite wound / animal) - suggestion from Jim was to use SPM-5 and either use the event or organism hierarchy - see email: The event codes are what we used to define wounds DUE TO "Bite" events. If you are just trying to model the "source" of the bite as opposed to the bite event itself, then you would use the organism hierarchy to represent that (e.g. Dog bite would have a source of 106969009 |Family Canidae (organism)|).

Follow up email from Riki: we are struggling to figure out how/if we could do it in the constraints of the fields available in the SPM segment:

SPM-4 = specimen type (would have to be pre-coordinated for every type of bite)

SPM-5 = type modifier (maybe here, but which hierarchy to use)

Or … add OBX after SPM (or an observation on the specimen) to convey that information.

Response from Jim: What is the allowed range for the value of SPM-5? It would seem to me that either event or organism would work in that field if it was allowed. If you can only use qualifiers, then there is a problem.
Example
SPM-4 28971000087101 |Swab from bite wound (specimen)|
SPM-5 217697000 |Dog bite (event)|
OR
SPM-4 28971000087101 |Swab from bite wound (specimen)|
SPM-5 106969009 |Family Canidae (organism)|

This only decision is to be consistent is the assignment of the values for SPM-5 from only one of the hierarchies.

Last email from Riki: At this point we already allow several hierarchies – mostly qualifier and morphologic abnormality – the field does repeat, which is why we thought we could.

So need to reach out to Jim again and invite him to a future call!

Reporting Biomarkers to Cancer registries

 CHECK WHAT NEEDS TO BE DONE HERE _ who owns it?

Lab Test Naming Conventions

Andrea planning this

• SHIELD call topic (maybe for September)

  • TRUU Lab

  • LOINC

Specimen CMT - review of terms with questions

 y

•  Terms for Nancy to follow up on :

  • Postpone talking about wound

  • Defnition from Nancy

    • bloody liquid stool

    • Bronchial aspirate

    • BodyFluid

    • BronchusDonorSwab

  • BronchusDonorSwab

    • submit for new term for specimen from donor bronchus - Riki

      • John to review editorial guidance around that – so far have 4 other terms – need to decide how to model those (specimen source identity attribute that can be used)

      • Follow up email with Jim Case decided we submit for more terms

• Fluid_JacksonPrattDrainage

  • SPM-4 mapped to 309051001^body fluid sample (specimen)^SCT and suggestion of submitting a new term for SPM-7 (this is where we would indicate drainage via Jackson Pratt drain (a physical object))

  • 16210251000119108^Body fluid specimen obtained via Jackson-Pratt drain (specimen)^SCT is replacement for SPM-4

  • 705084002^Collection of fluid specimen via closed suction drain (procedure)^SCT (Syn: is Jackson Pratt Drain) for SPM-7

• BodyFluid_PenroseDrain
  o SNOMED has a physical object but not for specimen type
  o We would need to submit a term for this
  o Should not collect cultures from the penrose drain
  o Usage for the term is changed to “Do not use” to the database

• Blood_PotassiumEDTA

  • Need more info on the special stopper to submit for a new term – ask Riki for table on different tops (SPM-6)

• PericardialFluid
  o Nancy to review

• FungalIsolate
  o Partial-special or derived? – specimen coming from patient vs. specimen coming from plate in microbiology –
  o Full coordination

• Tissue_VascularGraftSitePopliteal → will review next meeting
  o Should it be mapped to Tissue_GraftSitePopliteal?
  o No specimen type listed

  • if you use a graft that you buy will come sterile vs. removing a vein to use as a graft (vein graft or man-made graft) -Want to take the tissue from graft site

  • May need a term for one for person’s vein and another term for the man-made graft and handle them the same way

  • some people may want to culture the sterile graft in case there is bacteria

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 Conceptmap-example-specimen-type - FHIR v6.0.0-ballot2 - based on this profile: ConceptMap - FHIR v6.0.0-ballot2

  • @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-ballot2 . 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

Specimen CMT - potential pilot sites

• 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

• Setting baseline

Specimen CMT - Compare to NHS Medical Terminology testing

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