Genomics Reporting Implementation Guide
1.1.0 - Ballot
Genomics Reporting Implementation Guide
1.1.0 - Ballot
This page is part of the Genetic Reporting Implementation Guide (v1.1.0: STU 2 Ballot 1) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions 
<!--
Questions:
1. How does DNA range work if you're testing genes on different chromosomes?
2. Section 4 says it repeats for each gene tested, however the panel can point to multiple Genes. Should it not say it will repeat for each relevant gene or gene combination?
3. When capturing "effect on drug metabolism" and "effect on drug efficacy", should that not be drug-specific? If so, why is it not listed under the Medication Panel?
4. Section C has Allelic phase basis, but not the allelic phases. Why?
5. F.5 talks about F.1 being the medication assessed, but it's not. It's the Gene assessed.
New:
6. Do we need the "panel" notion for the pharmacogenomics panel bit?
-->
<Bundle xmlns="http://hl7.org/fhir">
<id value="diagnosticreport-cgexample"/>
<type value="collection"/>
<entry>
<fullUrl value="http://example.org/fhir/DiagnosticReport/report"/>
<resource>
<DiagnosticReport>
<id value="report"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-report"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml">TODO</div>
</text>
<!-- We don't expose A (81306-3) because the variables that apply to the study are captured a variety of places and there's no need to group them. Their applicability is clear based on where they're positioned. -->
<!-- <extension url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/draft-dr-haplotype-def">
<extension url="gene">
<valueCodeableConcept>
<coding>
H.1 Gene studied
<system value="http://example.org/hgnc-symb"/>
<code value="2623"/>
<display value="CYP2C9"/>
</coding>
</valueCodeableConcept>
</extension>
<extension url="name">
H.2 Haplotype name
<valueString value="*18"/>
</extension>
<extension url="variant">
<extension url="location">
<valueCodeableConcept>
<coding>
I.1 dbSNP ID
<system value="http://example.org/dbsnp"/>
<version value="137"/>
<code value="1057910"/>
<display value="rs1057910"/>
</coding>
</valueCodeableConcept>
</extension>
<extension url="allele">
I.2 Genomic alt allele
CLEM: Should this be coded?
<valueString value="C"/>
</extension>
</extension>
<extension url="variant">
<extension url="location">
<valueCodeableConcept>
<coding>
J.1 dbSNP ID
<system value="http://example.org/dbsnp"/>
<version value="137"/>
<code value="72558193"/>
<display value="rs72558193"/>
</coding>
</valueCodeableConcept>
</extension>
<extension url="allele">
J.2 Genomic alt allele
<valueString value="C"/>
</extension>
</extension>
</extension> -->
<basedOn>
<reference value="DiagnosticRequest/request"/>
</basedOn>
<status value="final"/>
<category>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
<code value="GE"/>
</coding>
</category>
<code>
<coding>
<!-- Top (same as diagnostic request -->
<system value="http://loinc.org"/>
<code value="81247-9"/>
</coding>
</code>
<subject>
<reference value="Patient/patient"/>
</subject>
<effectiveDateTime value="2016"/>
<issued value="2016-09-06T00:00:00-05:00"/>
<performer>
<reference value="Organization/lab"/>
</performer>
<result>
<reference value="Observation/overall-interp"/>
</result>
<!-- <result>
<reference value="Observation/negatives"/>
</result>
<result>
<reference value="Observation/iscn"/>
</result> -->
<result>
<reference value="Observation/discrete-variant"/>
</result>
<result>
<reference value="Observation/dis-path"/>
</result>
<result>
<reference value="Observation/complex-variant"/>
</result>
<result>
<reference value="Observation/complex-dis-path"/>
</result>
<result>
<reference value="Observation/pharmPanel"/>
</result>
<presentedForm>
<!-- A.10 Genetic analysis report -->
<!-- Can be included directly or referenced by URL -->
<contentType value="text/plain"/>
<data value="UHV0IHRoZSByZXBvcnQgdGV4dCBoZXJlIC0gbWltZS1lbmNvZGVk"/>
</presentedForm>
</DiagnosticReport>
</resource>
</entry>
<entry>
<fullUrl value="http://example.org/fhir/Patient/patient"/>
<resource>
<Patient>
<id value="patient"/>
<text>
<status value="additional"/>
<div xmlns="http://www.w3.org/1999/xhtml">This would contain patient identifiers, demographics, etc.</div>
</text>
</Patient>
</resource>
</entry>
<entry>
<fullUrl value="http://example.org/fhir/Specimen/specimen"/>
<resource>
<Specimen>
<!-- This would contain details about the type of specimen, processing, etc. -->
<id value="specimen"/>
<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">TODO</div>
</text>
<subject>
<reference value="Patient/patient"/>
</subject>
</Specimen>
</resource>
</entry>
<entry>
<fullUrl value="http://example.org/fhir/Organization/lab"/>
<resource>
<Organization>
<id value="lab"/>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml">TODO</div>
</text>
<name value="Some lab"/>
</Organization>
</resource>
</entry>
<entry>
<fullUrl value="http://example.org/fhir/DiagnosticRequest/request"/>
<resource>
<ServiceRequest>
<id value="request"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/servicerequest"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml">TODO</div>
</text>
<status value="active"/>
<intent value="original-order"/>
<code>
<coding>
<!-- Top -->
<system value="http://loinc.org"/>
<code value="81247-9"/>
</coding>
</code>
<subject>
<reference value="Patient/patient"/>
</subject>
<reasonCode>
<!-- A.1 Reason for Study -->
<text value="Worried about family planning"/>
</reasonCode>
</ServiceRequest>
</resource>
</entry>
<entry>
<fullUrl value="http://example.org/fhir/Observation/overall-interp"/>
<resource>
<Observation>
<id value="overall-interp"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/overall-interpretation"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml">TODO</div>
</text>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="51968-6"/>
</coding>
</code>
<subject>
<reference value="Patient/patient"/>
</subject>
<effectiveDateTime value="2016"/>
<issued value="2016-09-06T00:00:00-05:00"/>
<performer>
<reference value="Organization/lab"/>
</performer>
<valueCodeableConcept>
<!-- A.8 Overall Interpretation -->
<coding>
<system value="http://loinc.org"/>
<code value="LA6576-8"/>
<display value="Positive"/>
</coding>
<coding>
<system value="http://snomed.info/sct"/>
<code value="10828004"/>
<display value="Positive"/>
</coding>
</valueCodeableConcept>
<specimen>
<reference value="Specimen/specimen"/>
</specimen>
</Observation>
</resource>
</entry>
<!-- <entry>
<fullUrl value="http://example.org/fhir/Observation/negatives"/>
<resource>
<Observation>
<id value="negatives"/>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml">TODO</div>
</text>
<status value="final"/>
<category>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="51968-6"/>
<display value="Overall Interpretation"/>
</coding>
</code>
<subject>
<reference value="Patient/patient"/>
</subject>
<effectiveDateTime value="2016"/>
<issued value="2016-09-06T00:00:00-05:00"/>
<performer>
<reference value="Organization/lab"/>
</performer>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA6577-6"/>
<display value="Negative"/>
</coding>
</valueCodeableConcept>
<specimen>
<reference value="Specimen/specimen"/>
</specimen>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="51967-8"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://snomed.info/sct"/>
<code value="445274004"/>
<display value="Deficiency of isobutyryl-coenzyme A dehydrogenase (disorder)"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="51963-7"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.nlm.nih.gov/research/umls/rxnorm"/>
<code value="50005"/>
<display value="Fluoxetine"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="51963-7"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.nlm.nih.gov/research/umls/rxnorm"/>
<code value="84701"/>
<display value="Atorvastatin"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="51963-7"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.nlm.nih.gov/research/umls/rxnorm"/>
<code value="45000"/>
<display value="Naproxen"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="51963-7"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.nlm.nih.gov/research/umls/rxnorm"/>
<code value="11289"/>
<display value="Coumadin"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48018-6"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://example.org/hgnc-symb"/>
<code value="21497"/>
<display value="ACAD9"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="36908-2"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://example.org/clinvar"/>
<version value="???"/>
<code value="7129"/>
<display value="NM_000492.3(CFTR):c.3846G>A (p.Trp1282Ter)"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="51959-5"/>
</coding>
</code>
<valueRange>
<low>
<value value="2000753"/>
</low>
<high>
<value value="2234579"/>
</high>
</valueRange>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81293-3"/>
</coding>
</code>
<valueString value="All coding regions and appropriate flanking regions"/>
</component>
</Observation>
</resource>
</entry>
<entry>
<fullUrl value="http://example.org/fhir/Observation/iscn"/>
<resource>
<Observation>
<id value="iscn"/>
<meta>
<profile value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/obs-structural-genetic-finding"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml">TODO</div>
</text>
<status value="final"/>
<category>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81291-7"/>
</coding>
</code>
<subject>
<reference value="Patient/patient"/>
</subject>
<effectiveDateTime value="2016"/>
<issued value="2016-09-06T00:00:00-05:00"/>
<performer>
<reference value="Organization/lab"/>
</performer>
<valueCodeableConcept>
<coding>
<system value="http://example.org/icsn"/>
<code value="???"/>
</coding>
</valueCodeableConcept>
<specimen>
<reference value="Specimen/specimen"/>
</specimen>
</Observation>
</resource>
</entry>
-->
<entry>
<fullUrl value="http://example.org/fhir/Observation/discrete-variant"/>
<!-- This observation represents the sequence that was found (or not) -->
<!-- Panel B -->
<resource>
<Observation>
<id value="discrete-variant"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml">TODO</div>
</text>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69548-6"/>
<display value="Genetic variant assessment"/>
</coding>
</code>
<subject>
<reference value="Patient/patient"/>
</subject>
<effectiveDateTime value="2016"/>
<issued value="2016-09-06T00:00:00-05:00"/>
<performer>
<reference value="Organization/lab"/>
</performer>
<valueCodeableConcept>
<coding>
<!-- B.21 Genetic variant Assessment -->
<system value="http://loinc.org"/>
<code value="LA9633-4"/>
<display value="Present"/>
</coding>
</valueCodeableConcept>
<specimen>
<reference value="Specimen/specimen"/>
</specimen>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81252-9"/>
<display value="Discrete genetic variant"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<!-- B.2 Discrete genetic variant (ClinVar or COSMIC) -->
<system value="http://example.org/clinvar"/>
<version value="???"/>
<!-- A.16 ClinVar version -->
<code value="30880"/>
<display value="NM_014049.4(ACAD9):c.1249C>T (p.Arg417Cys)"/>
</coding>
<coding>
<!-- B.16 CIGAR-simple genetic variant -->
<system value="http://example.org/cigar"/>
<code value="tbd"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48018-6"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<!-- B.3 Gene studied -->
<system value="http://example.org/hgnc"/>
<code value="21497"/>
<display value="ACAD9"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="51958-7"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<!-- B.4 Transcript Reference MolecularSequence ID -->
<system value="http://www.ncbi.nlm.nih.gov/refseq"/>
<code value="NM_014049.4"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48013-7"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<!-- B.9 Genomic Reference MolecularSequence -->
<system value="http://www.ncbi.nlm.nih.gov/refseq"/>
<code value="NG_017064.1"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81290-9"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<!-- B.10 Genomic DNA change -->
<system value="http://varnomen.hgvs.org"/>
<!-- A.13 HGVS version -->
<code value="NC_000003.11:g.128625063C>T"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81255-2"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<!-- B.15 dbSNP ID -->
<system value="http://example.org/dbsnp"/>
<version value="137"/>
<!-- A.14 dbSNP version -->
<code value="rs368949613"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48004-6"/>
</coding>
</code>
<valueCodeableConcept>
<!-- No need to echo a display that's the same as the code - if there's no display and you
can't look up the display, default is to display the code -->
<coding>
<!-- B.5 DNA change cHGVS -->
<!-- Need to define a proper URL for this -->
<system value="http://varnomen.hgvs.org"/>
<version value="15.11"/>
<!-- A.13 HGVS version -->
<code value="c.1249C>T"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48005-3"/>
</coding>
</code>
<valueCodeableConcept>
<!-- No need to echo a display that's the same as the code - if there's no display and you
can't look up the display, default is to display the code -->
<coding>
<!-- B.6 Amino acid change pHGVS -->
<!-- Need to define a proper URL for this -->
<system value="http://varnomen.hgvs.org"/>
<version value="15.11"/>
<!-- A.13 HGVS version -->
<code value="p.Arg417Cys"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48019-4"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<!-- B.7 DNA change type -->
<system value="http://loinc.org"/>
<code value="LA6690-7"/>
<display value="Substitution"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48006-1"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<!-- B.8 Amino acid change type -->
<system value="http://loinc.org"/>
<code value="LA6698-0"/>
<display value="Missense"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69547-8"/>
</coding>
</code>
<!-- B.11 Genomic Ref allele -->
<valueString value="C"/>
</component>
<component>
<code>
<coding>
<system
value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes"/>
<code value="exact-start-end"/>
</coding>
</code>
<valueRange>
<!-- B.12 Genomic Allele start-end -->
<low>
<value value="31731"/>
</low>
<high>
<value value="31731"/>
</high>
</valueRange>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69551-0"/>
</coding>
</code>
<!-- B.13 Genomic Alt allele -->
<valueString value="T"/>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48001-2"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<!-- B.17 cytogenetic (chromosome) location -->
<system value="http://example.org/Chrom-Loc"/>
<code value="3q21"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48002-0"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<!-- B.18 Genomic source class -->
<system value="http://loinc.org"/>
<code value="LA6683-2"/>
<display value="Germline"/>
</coding>
</valueCodeableConcept>
</component>
<!-- The following components may get moved, depending on discussions w/ Eric H. as they aren't really
defining the sequence -->
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="53034-5"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<!-- B.23 Allelic state -->
<system value="http://loinc.org"/>
<code value="LA6706-1"/>
<display value="Heterozygous"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81258-6"/>
</coding>
</code>
<!-- B.24 Allelic Frequency -->
<valueQuantity>
<value value="47"/>
<system value="http://unitsofmeasure.org"/>
<code value="%"/>
</valueQuantity>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="82121-5"/>
</coding>
</code>
<!-- B.25 Allelic Read Depth -->
<valueQuantity>
<value value="208"/>
<system value="http://unitsofmeasure.org"/>
<code value="1"/>
</valueQuantity>
</component>
<!-- now observation.method for sequence-phase-rel
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="82309-6"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
B.27 Basis for allelic phase
<system value="http://loinc.org"/>
<code value="LA26429-3"/>
<display value="Inferred from population data"/>
</coding>
</valueCodeableConcept>
</component> -->
<!-- Structual variant-specific elements -->
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="82155-3"/>
</coding>
</code>
<valueQuantity>
<!-- B.28 Genomic structural variant copy number -->
<value value="1"/>
<system value="http://unitsofmeasure.org"/>
<code value="1"/>
</valueQuantity>
</component>
<component>
<code>
<!-- B.29 Genomic structural variant reported arrCGH ratio -->
<coding>
<system value="http://loinc.org"/>
<code value="81299-0"/>
</coding>
</code>
<valueQuantity>
<value value="0.48"/>
</valueQuantity>
</component>
<component>
<code>
<!-- CLEM: Can't this be calculated from start/end? -->
<coding>
<system value="http://loinc.org"/>
<code value="81300-6"/>
</coding>
</code>
<valueQuantity>
<!-- B.30 Structural variant length -->
<value value="1396929"/>
<system value="http://unitsofmeasure.org"/>
<code value="1"/>
</valueQuantity>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81301-4"/>
</coding>
</code>
<valueRange>
<!-- B.31 Structural variant outer start-end -->
<low>
<value value="13200589"/>
</low>
<high>
<value value="15592000"/>
</high>
</valueRange>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81302-2"/>
</coding>
</code>
<valueRange>
<!-- CLEM: this is the same as the actual start/end. In what cases would it be different? -->
<!-- B.32 Structural variant inner start-end -->
<low>
<value value="14184616"/>
</low>
<high>
<value value="15581544"/>
</high>
</valueRange>
</component>
</Observation>
</resource>
</entry>
<entry>
<fullUrl value="http://example.org/fhir/Observation/dis-path"/>
<resource>
<Observation>
<id value="dis-path"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml">TODO</div>
</text>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<code>
<coding>
<system
value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes"/>
<code value="diagnostic-implication"/>
</coding>
</code>
<subject>
<reference value="Patient/patient"/>
</subject>
<effectiveDateTime value="2016"/>
<issued value="2016-09-06T00:00:00-05:00"/>
<performer>
<reference value="Organization/lab"/>
</performer>
<derivedFrom>
<reference value="Observation/discrete-variant"/>
</derivedFrom>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="53037-8"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<!-- B.20 Genetic variation clinical significance -->
<system value="http://loinc.org"/>
<code value="LA6668-3"/>
<display value="Pathogenic"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81259-4"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<!-- B.22 Probable associated phenotype -->
<system value="http://example.org/MedGen-Dis"/>
<code value="C1970173"/>
<display
value="Acyl-CoA dehydrogenase family, member 9, deficiency of"/>
</coding>
</valueCodeableConcept>
</component>
</Observation>
</resource>
</entry>
<entry>
<fullUrl value="http://example.org/fhir/Observation/complex-variant"/>
<resource>
<Observation>
<id value="complex-variant"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml">TODO</div>
</text>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69548-6"/>
</coding>
</code>
<subject>
<reference value="Patient/patient"/>
</subject>
<effectiveDateTime value="2016"/>
<issued value="2016-09-06T00:00:00-05:00"/>
<performer>
<reference value="Organization/lab"/>
</performer>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA9633-4"/>
<display value="Present"/>
</coding>
</valueCodeableConcept>
<specimen>
<reference value="Specimen/specimen"/>
</specimen>
<hasMember>
<reference value="Observation/complex-component-D"/>
</hasMember>
<hasMember>
<reference value="Observation/complex-component-E"/>
</hasMember>
<!-- obs-complex-variant
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81260-2"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://example.org/clinvar"/>
<version value="???"/>
<code value="16895"/>
<display value="NM_000106.5(CYP2D):c.[886C>T;457G>C] – Haplotype"/>
</coding>
<coding>
<system value="http://varnomen.hgvs.org"/>
<code value="c.[886C>T;457G>C"/>
</coding>
</valueCodeableConcept>
</component>
-->
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81263-6"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA26218-0"/>
<display value="Haplotype"/>
</coding>
</valueCodeableConcept>
</component>
</Observation>
</resource>
</entry>
<entry>
<fullUrl value="http://example.org/fhir/Observation/complex-dis-path"/>
<resource>
<Observation>
<id value="complex-dis-path"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml">TODO</div>
</text>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<code>
<coding>
<system
value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes"/>
<code value="diagnostic-implication"/>
</coding>
</code>
<subject>
<reference value="Patient/patient"/>
</subject>
<effectiveDateTime value="2016"/>
<issued value="2016-09-06T00:00:00-05:00"/>
<performer>
<reference value="Organization/lab"/>
</performer>
<derivedFrom>
<reference value="Observation/complex-variant"/>
</derivedFrom>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="53037-8"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<!-- C.5 Complex variant type -->
<system value="http://loinc.org"/>
<code value="LA6668-3"/>
<display value="Pathogenic"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81259-4"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<!-- C.4 Associated phenotype -->
<system value="http://snomed.info/sct"/>
<code value="293498008"/>
<display value="Debrisoquine adverse reaction (disorder)"/>
</coding>
</valueCodeableConcept>
</component>
</Observation>
</resource>
</entry>
<entry>
<fullUrl value="http://example.org/fhir/Observation/complex-component-D"/>
<!-- Panel D -->
<resource>
<Observation>
<id value="complex-component-D"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml">TODO</div>
</text>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69548-6"/>
<display value="Genetic variant assessment"/>
</coding>
</code>
<subject>
<reference value="Patient/patient"/>
</subject>
<effectiveDateTime value="2016"/>
<issued value="2016-09-06T00:00:00-05:00"/>
<performer>
<reference value="Organization/lab"/>
</performer>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<!-- B.21 Genetic variation assessment -->
<code value="LA9633-4"/>
<display value="Present"/>
</coding>
</valueCodeableConcept>
<specimen>
<reference value="Specimen/specimen"/>
</specimen>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81252-9"/>
<display value="Discrete genetic variant"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<!-- D.1(B.2) Discrete genetic variant (ClinVar or COSMIC) -->
<system value="http://example.org/clinvar"/>
<version value="???"/>
<!-- A.16 ClinVar version -->
<code value="31934"/>
<display value="NM_000106.5(CYP2D6):c.886C>T (p.Arg296Cys)"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="51958-7"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<!-- D.2(B.4) Transcript Reference MolecularSequence ID -->
<!-- Need to define a proper URL for this -->
<system value="http://example.org/RefSeq-T"/>
<code value="NM_000106.5"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48004-6"/>
</coding>
</code>
<valueCodeableConcept>
<!-- No need to echo a display that's the same as the code - if there's no display and you
can't look up the display, default is to display the code -->
<coding>
<!-- D.3(B.5) DNA change cHGVS -->
<!-- Need to define a proper URL for this -->
<system value="http://varnomen.hgvs.org"/>
<version value="15.11"/>
<!-- A.13 HGVS version -->
<code value="c.886C>T"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48005-3"/>
</coding>
</code>
<valueCodeableConcept>
<!-- No need to echo a display that's the same as the code - if there's no display and you
can't look up the display, default is to display the code -->
<coding>
<!-- D.4(B.6) Amino acid change pHGVS -->
<!-- Need to define a proper URL for this -->
<system value="http://varnomen.hgvs.org"/>
<version value="15.11"/>
<!-- A.13 HGVS version -->
<code value="p.Arg296Cys"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48019-4"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<!-- D.5(B.7) DNA change type -->
<system value="http://loinc.org"/>
<code value="LA6690-7"/>
<display value="Substitution"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48006-1"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<!-- D.6(B.8) Amino acid change type -->
<system value="http://loinc.org"/>
<code value="LA6698-0"/>
<display value="Missense"/>
</coding>
</valueCodeableConcept>
</component>
</Observation>
</resource>
</entry>
<entry>
<fullUrl value="http://example.org/fhir/Observation/complex-component-E"/>
<!-- Panel E -->
<resource>
<Observation>
<id value="complex-component-E"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml">TODO</div>
</text>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69548-6"/>
<display value="Genetic variant assessment"/>
</coding>
</code>
<subject>
<reference value="Patient/patient"/>
</subject>
<effectiveDateTime value="2016"/>
<issued value="2016-09-06T00:00:00-05:00"/>
<performer>
<reference value="Organization/lab"/>
</performer>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<!-- B.21 Genetic variation assessment -->
<code value="LA9633-4"/>
<display value="Present"/>
</coding>
</valueCodeableConcept>
<specimen>
<reference value="Specimen/specimen"/>
</specimen>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81252-9"/>
<display value="Discrete genetic variant"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<!-- E.1(B.2) Discrete genetic variant (ClinVar or COSMIC) -->
<system value="http://example.org/clinvar"/>
<version value="???"/>
<!-- A.16 ClinVar version -->
<code value="38486"/>
<display value="NM_000106.5(CYP2D6):c.1457G>C (p.Ser486Thr)"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="51958-7"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<!-- E.2(B.4) Transcript Reference MolecularSequence ID -->
<!-- Need to define a proper URL for this -->
<system value="http://example.org/RefSeq-T"/>
<code value="NM_000106.5"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48004-6"/>
</coding>
</code>
<valueCodeableConcept>
<!-- No need to echo a display that's the same as the code - if there's no display and you
can't look up the display, default is to display the code -->
<coding>
<!-- E.3(B.5) DNA change cHGVS -->
<!-- Need to define a proper URL for this -->
<system value="http://varnomen.hgvs.org"/>
<version value="15.11"/>
<!-- A.13 HGVS version -->
<code value="c.1457G>C"/>
</coding>
</valueCodeableConcept>
</component>
</Observation>
</resource>
</entry>
<entry>
<fullUrl value="http://example.org/fhir/Observation/pharmPanel"/>
<resource>
<Observation>
<!-- D Pharmacogenomics results grouper -->
<id value="pharmPanel"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/grouper"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml">TODO</div>
</text>
<extension
url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/RecommendedAction">
<valueReference>
<reference value="Task/usage"/>
</valueReference>
</extension>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<code>
<coding>
<system
value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes"/>
<code value="grouper"/>
</coding>
</code>
<subject>
<reference value="Patient/patient"/>
</subject>
<effectiveDateTime value="2016"/>
<issued value="2016-09-06T00:00:00-05:00"/>
<performer>
<reference value="Organization/lab"/>
</performer>
<hasMember>
<reference value="Observation/haplotype"/>
</hasMember>
<hasMember>
<reference value="Observation/genotype"/>
</hasMember>
<hasMember>
<reference value="Observation/metab"/>
</hasMember>
<hasMember>
<reference value="Observation/efficacy"/>
</hasMember>
</Observation>
</resource>
</entry>
<entry>
<fullUrl value="http://example.org/fhir/Observation/haplotype"/>
<resource>
<Observation>
<id value="haplotype"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml">TODO</div>
</text>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="84414-2"/>
</coding>
</code>
<subject>
<reference value="Patient/patient"/>
</subject>
<effectiveDateTime value="2016"/>
<issued value="2016-09-06T00:00:00-05:00"/>
<performer>
<reference value="Organization/lab"/>
</performer>
<valueCodeableConcept>
<coding>
<!-- B.14 Haplotype name -->
<system value="http://example.org/???"/>
<code value="*2"/>
</coding>
</valueCodeableConcept>
<specimen>
<reference value="Specimen/specimen"/>
</specimen>
<derivedFrom>
<!-- D1.3 -->
<reference value="Observation/discrete-variant"/>
</derivedFrom>
</Observation>
</resource>
</entry>
<entry>
<fullUrl value="http://example.org/fhir/Observation/genotype"/>
<resource>
<Observation>
<id value="genotype"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml">TODO</div>
</text>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="84413-4"/>
</coding>
</code>
<subject>
<reference value="Patient/patient"/>
</subject>
<effectiveDateTime value="2016"/>
<issued value="2016-09-06T00:00:00-05:00"/>
<performer>
<reference value="Organization/lab"/>
</performer>
<!-- F.2.a, F.2.b Genotype display name -->
<!-- TODO: Figure out how to separate these -->
<!-- valueString value="*2/*5,*A/*A"/ -->
<!-- missing the VKORC1 valueCodeableConcept for now -->
<valueCodeableConcept>
<coding>
<system value="http://www.pharmvar.org"/>
<code value="CYP2C9 *2/*5"/>
<display value="CYP2C9 *2/*5"/>
</coding>
</valueCodeableConcept>
<specimen>
<reference value="Specimen/specimen"/>
</specimen>
<derivedFrom>
<!-- D1.3 -->
<reference value="Observation/haplotype"/>
</derivedFrom>
<component>
<!-- This isn't "what did we observe?", but rather a qualification on "what did we look at?" -->
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48018-6"/>
</coding>
</code>
<valueCodeableConcept>
<!-- CLEM: I believe this is just part of the genotype observation, right? -->
<!-- F.1.a Gene studied -->
<!-- lloyd: 1 gene per variation -->
<coding>
<system value="http://example.org/hgnc"/>
<code value="2623"/>
<display value="CYP2C9"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48018-6"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<!-- B.3 Gene studied -->
<system value="http://example.org/hgnc"/>
<code value="23663"/>
<display value="VKORC1"/>
</coding>
</valueCodeableConcept>
</component>
</Observation>
</resource>
</entry>
<entry>
<fullUrl value="http://example.org/fhir/Observation/metab"/>
<resource>
<Observation>
<id value="metab"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml">TODO</div>
</text>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<code>
<coding>
<system
value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes"/>
<code value="therapeutic-implication"/>
</coding>
</code>
<subject>
<reference value="Patient/patient"/>
</subject>
<effectiveDateTime value="2016"/>
<issued value="2016-09-06T00:00:00-05:00"/>
<performer>
<reference value="Organization/lab"/>
</performer>
<derivedFrom>
<reference value="Observation/genotype"/>
</derivedFrom>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="51963-7"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<!-- G.1 Medication assessed -->
<system value="http://www.nlm.nih.gov/research/umls/rxnorm"/>
<code value="11289"/>
<display value="Warfarin"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="53040-2"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<!-- F.3 Genetic variation's effect on drug metabolism -->
<system value="http://loinc.org"/>
<code value="LA25390-8"/>
<display value="Rapid metabolizer"/>
</coding>
</valueCodeableConcept>
</component>
</Observation>
</resource>
</entry>
<entry>
<fullUrl value="http://example.org/fhir/Observation/efficacy"/>
<resource>
<Observation>
<id value="efficacy"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml">TODO</div>
</text>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<code>
<coding>
<system
value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes"/>
<code value="therapeutic-implication"/>
</coding>
</code>
<subject>
<reference value="Patient/patient"/>
</subject>
<effectiveDateTime value="2016"/>
<issued value="2016-09-06T00:00:00-05:00"/>
<performer>
<reference value="Organization/lab"/>
</performer>
<derivedFrom>
<reference value="Observation/genotype"/>
</derivedFrom>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="51961-1"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<!-- F.4 Genetic variation's effect on drug efficacy -->
<system value="http://loinc.org"/>
<code value="LA6676-6"/>
<display value="Resistant"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="51963-7"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<!-- G.1 Medication assessed -->
<system value="http://www.nlm.nih.gov/research/umls/rxnorm"/>
<code value="11289"/>
<display value="Warfarin"/>
</coding>
</valueCodeableConcept>
</component>
</Observation>
</resource>
</entry>
<entry>
<fullUrl value="http://example.org/fhir/Observation/highrisk"/>
<resource>
<Observation>
<id value="highrisk"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml">TODO</div>
</text>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<code>
<coding>
<system
value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes"/>
<code value="therapeutic-implication"/>
</coding>
</code>
<subject>
<reference value="Patient/patient"/>
</subject>
<effectiveDateTime value="2016"/>
<issued value="2016-09-06T00:00:00-05:00"/>
<performer>
<reference value="Organization/lab"/>
</performer>
<derivedFrom>
<reference value="Observation/genotype"/>
</derivedFrom>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="83009-1"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<!-- F.5 Genetic variation’s effect on high-risk allele -->
<system value="http://loinc.org"/>
<code value="LA19542-2"/>
<display value="Low risk"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="51963-7"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<!-- G.1 Medication assessed -->
<system value="http://www.nlm.nih.gov/research/umls/rxnorm"/>
<code value="11289"/>
<display value="Warfarin"/>
</coding>
</valueCodeableConcept>
</component>
</Observation>
</resource>
</entry>
<entry>
<fullUrl value="http://example.org/fhir/Task/usage"/>
<resource>
<Task>
<!-- G1 -->
<id value="usage"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/task-med-chg"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml">TODO</div>
</text>
<contained>
<MedicationStatement>
<id value="med"/>
<status value="unknown"/>
<medicationCodeableConcept>
<coding>
<!-- G.1 Medication assessed -->
<system value="http://www.nlm.nih.gov/research/umls/rxnorm"/>
<code value="11289"/>
<display value="Warfarin"/>
</coding>
</medicationCodeableConcept>
<subject>
<reference value="Patient/patient"/>
</subject>
</MedicationStatement>
</contained>
<status value="requested"/>
<intent value="proposal"/>
<code>
<coding>
<!-- G.2 Medication usage suggestion -->
<system value="http://loinc.org"/>
<code value="LA26423-6"/>
<display value="Increase dose"/>
</coding>
<!-- G.3 Medication usage suggestion [narrative] -->
<text value="May need higher dosage than usual."/>
</code>
<focus>
<reference value="#med"/>
</focus>
<for>
<reference value="Patient/patient"/>
</for>
<requester>
<reference value="Organization/lab"/>
</requester>
<reasonReference>
<reference value="Observation/metab"/>
</reasonReference>
</Task>
</resource>
</entry>
</Bundle>
IG © 2019+ HL7 International Clinical Genomics Work Group. Package hl7.fhir.uv.genomics-reporting#1.1.0 based on FHIR 4.0.1. Generated 2021-04-13
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