FHIR Chat · specimen.subject in IG · genomics

Stream: genomics

Topic: specimen.subject in IG

Bob Milius (Nov 15 2018 at 22:30):

Specimen.subject is no longer required in R4, but we still have it required in our IG. We should relax it to be consistent with Specimen. Use case for not having it required is an org sending out samples to testing lab that are de-identified, and only have a specimen.identifer.

Lloyd McKenzie (Nov 15 2018 at 22:38):

But our IG is about lab reporting - what's the use-case for having it missing there?

Bob Milius (Nov 15 2018 at 22:40):

The lab might not have the subject. Ours don't. We send a whole bunch of buccal swabs (hundreds at a time) to a contract lab that are only identified with an id. We have the person's name in another system (non-FHIR) that is cross-referenced to the specimen identifier.

Bob Milius (Nov 15 2018 at 22:47):

I suppose I can use the base Specimen resource that's not part of the IG.

Bob Milius (Nov 15 2018 at 22:50):

If I use the IG's specimen profile, then it looks like this:

<Specimen xmlns="http://hl7.org/fhir">
    <id value="specimen-hla-r4"/>
    <meta>
        <profile value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/specimen"/>
    </meta>
    <text>
        <status value="generated"/>
        <div xmlns="http://www.w3.org/1999/xhtml">
            <pre>buccal swab: 001-123456789 </pre>
        </div>
    </text>
    <identifier>
        <value value="001^123456789"/>
    </identifier>
    <type>
        <coding>
            <system value="http://snomed.info/sct"/>
            <code value="258564008"/>
            <display value="Buccal smear sample"/>
        </coding>
    </type>
    <!-- the IG currently requires subject, but in this use case the sample is deidentified, so we re-use the sample.identifer as the subject -->
    <subject>
        <identifier>
            <value value="001^123456789"/>
        </identifier>
    </subject>
    <receivedTime value="2018-05-01"/>
    <collection>
        <method>
            <coding>
                <system value="http://hl7.org/fhir/v2/0488"/>
                <code value="SWA"/>
                <display value="Swab"/>
            </coding>
        </method>
        <bodySite>
            <coding>
                <system value="http://snomed.info/sct"/>
                <code value="261063000"/>
                <display value="Buccal space"/>
            </coding>
        </bodySite>
    </collection>
</Specimen>

Lloyd McKenzie (Nov 15 2018 at 22:57):

Does the DiagnosticReport mandate the inclusion of the subject? Do the Observations? Because either all do or none do - the lab report is going to include all of those resources.

Bob Milius (Nov 15 2018 at 23:01):

DiagnosticReport, Haplotype, Genotype, ComplexVariant do NOT require subject.

Bob Milius (Nov 15 2018 at 23:02):

DG doesn't require specimen, but looks like the Observations do.

Bob Milius (Nov 15 2018 at 23:10):

"Request for Genetic Test" (ServiceRequest) requires subject. So does the ServiceRequest base resource, although I would argue against that as well, for the same use case I mentioned above. I would use ServiceRequest.specimen, and use that identifer value stubbed in for ServiceRequest.subject.

Lloyd McKenzie (Nov 16 2018 at 07:59):

We should never stub in the specimen id in subject. If the subject can be unknown, the model should allow for the subject to be absent. Anything else implies an improper design. If we need to support reports where the subject is unknown to the lab (including no knowledge of any subject demographic information), then subject should be optional (but mustSupport) in all of our profiles.

Last updated: Apr 12 2022 at 19:14 UTC