FHIR Chat · DiagnosticReport codings?

Stream: genomics

Topic: DiagnosticReport codings?

Bob Milius (Aug 27 2019 at 17:41):

Right now in the Genomics Reporting IG, DiagnosticReport profile requires a code for "Master HL7 genetic variant reporting panel". However,I'd like to see what kind of panel was done. One way is to look into the Observations the DG references, e.g.,

Look into each result observation, and/or...
Use Region Studied observation to list all the genes in the panel

But I'd really like to just look at the DR without having to look at other resources. The DR should effectively be a summary of the report. Here are the possibilities I see:

Use the text narrative of the DR to list separate tests or gene names
Have a set of other codings under the panel (eg one for each test)? E.g., is this appropriate? (The only thing is that this requires pre-coordinated codes, as components aren't available in DR.)

"code": {"coding": [
    {
        "system": "http://loinc.org",
        "code": "81247-9",
        "display": "Master HL7 genetic variant reporting panel"
    },
    {
        "system" : "http://loinc.org",
        "code" : "13298-5",
        "display" : "HLA-A [Type]"
    },
    {
        "system": "http://loinc.org",
        "code": "13299-3",
        "display": "HLA-B [Type]"
    },
    {
        "system": "http://loinc.org",
        "code": "13302-5",
        "display": "HLA-C [Type]"
    },
    {
        "system": "http://loinc.org",
        "code": "57298-2",
        "display": "HLA-DRB1 [Type]"
    },
    {
        "system": "http://loinc.org",
        "code": "53938-7",
        "display": "HLA-DQB1 [Type]"
    }
]},

Bob Milius (Aug 28 2019 at 14:27):

I started a thread in OO about this:
https://chat.fhir.org/#narrow/stream/179256-Orders-and.20Observation.20WG/topic/DiagnosticReport.2Ecategory

Bob Milius (Aug 29 2019 at 14:58):

After a bit of discussion in the OO stream, and thinking more about this, I think adding the individual gene codes in the diagnosticreport.code.coding is wrong, since although each of the genes may be subsumed by "Master HL7 genetic variant reporting panel," they are not semantically the same concept with each other. So I'm leaning towards this solution for diagnosticreport

"category": [
    {"coding": [
        {
            "system": "http://terminology.hl7.org/CodeSystem/v2-0074",
            "code": "GE",
            "display": "Genetics"
        }
    ]},
    {"coding": [
        {
            "system": "http://terminology.hl7.org/CodeSystem/v2-0074",
            "code": "LAB",
            "display": "Laboratory"
        }
    ]}
],
"code": {"coding": [
    {
        "system": "http://loinc.org",
        "code": "81247-9",
        "display": "Master HL7 genetic variant reporting panel"
    },
    {
        "system": "https://www.genenames.org/data/genegroup",
        "code": "588",
        "display": "Histocompatibility complex (HLA)"
    }
]}

Bret H (Sep 19 2019 at 14:29):

@ Bob Milius did you mean that you want to use code.coding instead of category.coding? or that you want to use a gene group identifier for your use case?

Bob Milius (Sep 19 2019 at 15:44):

@Bret H Originally, I wanted to use the HLA gene group as a DR.category.code, and individual genes as different DR.code.codings. Re the latter, I decided that was a bad idea because while each gene is conceptually subsumed by "Master HL7 genetic variant reporting panel," each gene is not conceptually equivalent with each other. So I leave out the individual genes in the DR.code.coding. Re the category, the general consensus in another thread is that HLA gene family shouldn't be in a DR.category, but should be in DR.code
see https://chat.fhir.org/#narrow/stream/179256-Orders-and.20Observation.20WG/topic/DiagnosticReport.2Ecategory

Last updated: Apr 12 2022 at 19:14 UTC

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