Stream: genomics
Topic: DiagnosticReport categories
Bob Milius (Aug 27 2019 at 20:24):
I'm interested in the appropriate use of DiagnosticeReport.category. DR allows for multiple categories. Is it okay to use it to describe the gene family/group that the DG is about? eg. using HGNC gene group for HLA typing? Is this an appropriate use for category?
"category": [
{"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/v2-0074",
"code": "GE",
"display": "Genetics"
}
]},
{"coding": [
{
"system": "https://www.genenames.org/data/genegroup",
"code": "588",
"display": "Histocompatibility complex (HLA)"
}
]}
]
Bob Milius (Aug 28 2019 at 14:27):
I started a thread in OO around this -
https://chat.fhir.org/#narrow/stream/179256-Orders-and.20Observation.20WG/topic/DiagnosticReport.2Ecategory
Bret H (Sep 19 2019 at 14:30):
There is another thread that seems relevant as well on DiagnosticReport.code.coding. Is this thread related @ Bob Milius https://chat.fhir.org/#narrow/stream/179197-genomics/topic/DiagnosticReport.20codings.3F ?
Bob Milius (Sep 19 2019 at 15:47):
@Bret H Yes, I had started both threads and they are related (DR categories, and DR code). They merged into this OO thread https://chat.fhir.org/#narrow/stream/179256-Orders-and.20Observation.20WG/topic/DiagnosticReport.2Ecategory
Dora Walter (Sep 26 2019 at 09:17):
We discussed this at the WGM in Atlanta, didn't we?
Bob Milius (Sep 26 2019 at 16:05):
@Dora Finkeisen yes, we did. It was part of the genenames.org and gene-group ids discussion
Kevin Power (Sep 26 2019 at 17:40):
For those of us who didn't make the WGM - I did a search of the WGM notes and didn't see anything about this DR.code or DR.category. What was decided?
Bob Milius (Sep 26 2019 at 17:52):
@Kevin Power We didn't need to come to a decision about DR.category and DR.code because the pattern resolved in the OO thread I linked above. The issue we grappled with was focused on genenames.org and that gene names had a HGNC: prefix but gene groups do not. e.g., 588 - Histocompatibility complex, HLA) , vs HGNC:588 (ATG12, autophagy related 12). The issue that we recognized many systems don't capture the prefix, and may confuse the gene with gene group. The consensus, as I remember it, was to create two different namespace (e.g., https://www.genenames.org/hgnc vs https://www.genenames.org/genegroup). Until the namespaces are resolved, we continue to use genenames.org for both with clear wording about the differences between gene-names and gene-groups. I want to use a gene-group id as an additional coding for the master panel code we use in DR.code
Kevin Power (Sep 26 2019 at 17:54):
Got it, thanks for the info @ Bob Milius
Last updated: Apr 12 2022 at 19:14 UTC
