<StructureDefinition xmlns="http://hl7.org/fhir">
  <id value="observation-genetics" />
  <text>
    <status value="generated" />
    <div xmlns="http://www.w3.org/1999/xhtml">to do</div>
  </text>
  <url value="http://hl7.org/fhir/StructureDefinition/observation-genetics" />
  <name value="Observation-genetics" />
  <status value="draft" />
  <experimental value="false" />
  <date value="2016-03-14" />
  <publisher value="Health Level Seven International (Clinical Genomics)" />
  <contact>
    <telecom>
      <system value="url" />
      <value value="http://www.hl7.org/Special/committees/clingenomics" />
    </telecom>
  </contact>
  <description value="Describes how the observation resource is used to report structured genetic test results" />
  <fhirVersion value="3.0.1" />
  <mapping>
    <identity value="workflow" />
    <uri value="http://hl7.org/fhir/workflow" />
    <name value="Workflow Mapping" />
  </mapping>
  <mapping>
    <identity value="sct-concept" />
    <uri value="http://snomed.info/conceptdomain" />
    <name value="SNOMED CT Concept Domain Binding" />
  </mapping>
  <mapping>
    <identity value="v2" />
    <uri value="http://hl7.org/v2" />
    <name value="HL7 v2 Mapping" />
  </mapping>
  <mapping>
    <identity value="rim" />
    <uri value="http://hl7.org/v3" />
    <name value="RIM Mapping" />
  </mapping>
  <mapping>
    <identity value="w5" />
    <uri value="http://hl7.org/fhir/w5" />
    <name value="W5 Mapping" />
  </mapping>
  <mapping>
    <identity value="sct-attr" />
    <uri value="http://snomed.info/sct" />
    <name value="SNOMED CT Attribute Binding" />
  </mapping>
  <kind value="resource" />
  <abstract value="false" />
  <type value="Observation" />
  <baseDefinition value="http://hl7.org/fhir/StructureDefinition/Observation" />
  <derivation value="constraint" />
  <differential>
    <element id="Observation">
      <path value="Observation" />
      <min value="0" />
      <max value="*" />
    </element>
    <element id="Observation.extension:dnasequencevariantname">
      <path value="Observation.extension" />
      <sliceName value="DNASequenceVariantName" />
      <short value="DNA sequence variant" />
      <definition value="A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)). This element is the Human Genome Variation Society ([HGVS](http://varnomen.hgvs.org/)) nomenclature for a single or set of DNA sequence variant(s) identified in testing. Reference sequence ID used for HGVS naming must be annotated." />
      <min value="0" />
      <max value="1" />
      <type>
        <code value="Extension" />
        <profile value="http://hl7.org/fhir/StructureDefinition/observation-geneticsDNASequenceVariantName" />
      </type>
    </element>
    <element id="Observation.extension:dnavariantid">
      <path value="Observation.extension" />
      <sliceName value="DNAVariantId" />
      <short value="DNA sequence variant ID" />
      <definition value="Identifier for DNA sequence variant.  If a germline variant, ClinVar or dbSNP identifier should be used.  If a somatic variant, COSMIC identifier should be used, unless in ClinVar then either maybe used. Need to provide the code system used (ClinVar, dbSNP, COSMIC)." />
      <min value="0" />
      <max value="1" />
      <type>
        <code value="Extension" />
        <profile value="http://hl7.org/fhir/StructureDefinition/observation-geneticsDNAVariantId" />
      </type>
    </element>
    <element id="Observation.extension:dnasequencevarianttype">
      <path value="Observation.extension" />
      <sliceName value="DNASequenceVariantType" />
      <short value="DNA sequence variant type" />
      <definition value="Codified type for associated DNA sequence variant. DNA sequence variants use the HGVS notation, which implies the DNA sequence variant type." />
      <min value="0" />
      <max value="1" />
      <type>
        <code value="Extension" />
        <profile value="http://hl7.org/fhir/StructureDefinition/observation-geneticsDNASequenceVariantType" />
      </type>
    </element>
    <element id="Observation.extension:aminoacidchangename">
      <path value="Observation.extension" />
      <sliceName value="AminoAcidChangeName" />
      <short value="Amino acid change" />
      <definition value="Human Genome Variation Society (HGVS) nomenclature for an amino acid change. Reference sequence ID used for HGVS naming must be annotated. An amino acid is a sequence feature that corresponds to a single amino acid residue in a polypeptide ([SO:0001237](http://www.sequenceontology.org/browser/current_svn/term/SO:0001237))." />
      <min value="0" />
      <max value="1" />
      <type>
        <code value="Extension" />
        <profile value="http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChangeName" />
      </type>
    </element>
    <element id="Observation.extension:aminoacidchangetype">
      <path value="Observation.extension" />
      <sliceName value="AminoAcidChangeType" />
      <short value="Amino Acid Change Type" />
      <definition value="Codified type for associated Amino Acid Change." />
      <min value="0" />
      <max value="1" />
      <type>
        <code value="Extension" />
        <profile value="http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChangeType" />
      </type>
    </element>
    <element id="Observation.extension:genesymbol">
      <path value="Observation.extension" />
      <sliceName value="GeneSymbol" />
      <short value="HGNC gene symbol" />
      <definition value="A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions ([SO:0000704](http://www.sequenceontology.org/browser/current_svn/term/SO:0000704)). This element is the official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name ([HGNC](http://www.genenames.org))." />
      <comment value="Other systems or genes not defined in HGNC (e.g., BCR-ABL fusion gene) can be added by using a local extension." />
      <min value="0" />
      <max value="1" />
      <type>
        <code value="Extension" />
        <profile value="http://hl7.org/fhir/StructureDefinition/observation-geneticsGene" />
      </type>
    </element>
    <element id="Observation.extension:dnaregionname">
      <path value="Observation.extension" />
      <sliceName value="DNARegionName" />
      <short value="DNA region name" />
      <definition value="A human readable name for the region of interest. Typically Exon #, Intron # or other. NOTE: This is not standardized and is mainly for convenience and display purposes." />
      <min value="0" />
      <max value="1" />
      <type>
        <code value="Extension" />
        <profile value="http://hl7.org/fhir/StructureDefinition/observation-geneticsDNARegionName" />
      </type>
    </element>
    <element id="Observation.extension:allelename">
      <path value="Observation.extension" />
      <sliceName value="AlleleName" />
      <short value="Name of allele" />
      <definition value="An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). This element is the common name for the allele." />
      <min value="0" />
      <max value="1" />
      <type>
        <code value="Extension" />
        <profile value="http://hl7.org/fhir/StructureDefinition/observation-geneticsAlleleName" />
      </type>
    </element>
    <element id="Observation.extension:allelicstate">
      <path value="Observation.extension" />
      <sliceName value="AllelicState" />
      <short value="The level of occurrence of a single DNA sequence variant within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous" />
      <definition value="The level of occurrence of a single DNA Sequence Variant within a set of chromosomes. Heterozygous indicates the DNA sequence variant is only present in one of the two genes contained in homologous chromosomes. Homozygous indicates the DNA Sequence Variant is present in both genes contained in homologous chromosomes. Hemizygous indicates the DNA Sequence Variant exists in the only single copy of a gene in a non-homologous chromosome (the male X and Y chromosome are non-homologous). Hemiplasmic indicates that the DNA Sequence Variant is present in some but not all of the copies of mitochondrial DNA. Homoplasmic indicates that the DNA Sequence Variant is present in all of the copies of mitochondrial DNA." />
      <min value="0" />
      <max value="1" />
      <type>
        <code value="Extension" />
        <profile value="http://hl7.org/fhir/StructureDefinition/observation-geneticsAllelicState" />
      </type>
    </element>
    <element id="Observation.extension:allelicfrequency">
      <path value="Observation.extension" />
      <sliceName value="AllelicFrequency" />
      <short value="Allele frequency" />
      <definition value="A physical quality which inheres to the allele by virtue of the number instances of the allele within a population." />
      <min value="0" />
      <max value="1" />
      <type>
        <code value="Extension" />
        <profile value="http://hl7.org/fhir/StructureDefinition/observation-geneticsAllelicFrequency" />
      </type>
    </element>
    <element id="Observation.extension:copynumberevent">
      <path value="Observation.extension" />
      <sliceName value="CopyNumberEvent" />
      <short value="Copy number variation" />
      <definition value="A variation that increases or decreases the copy number of a given region ([SO:0001019](http://www.sequenceontology.org/browser/current_svn/term/SO:0001019)). Values: amplification/deletion/LOH." />
      <comment value="Loss of heterozygosity (LOH) is a functional variant whereby the sequence alteration causes a loss of function of one allele of a gene ([SO:0001786](http://www.sequenceontology.org/browser/current_svn/term/SO:0001786))." />
      <min value="0" />
      <max value="1" />
      <type>
        <code value="Extension" />
        <profile value="http://hl7.org/fhir/StructureDefinition/observation-geneticsCopyNumberEvent" />
      </type>
    </element>
    <element id="Observation.extension:genomicsourceclass">
      <path value="Observation.extension" />
      <sliceName value="GenomicSourceClass" />
      <short value="Genomic source class" />
      <definition value="Source of sample used to determine the sequence in sequencing lab -- germline, somatic, prenatal." />
      <min value="0" />
      <max value="1" />
      <type>
        <code value="Extension" />
        <profile value="http://hl7.org/fhir/StructureDefinition/observation-geneticsGenomicSourceClass" />
      </type>
    </element>
    <element id="Observation.extension:phaseset">
      <path value="Observation.extension" />
      <sliceName value="PhaseSet" />
      <short value="Phase set identifier (UUID/OID)" />
      <definition value="Chromosomal phase set identifier (UUID/OID). All sequences with the same PhaseSet identifier are asserted to be on the same chromosome (cis)." />
      <min value="0" />
      <max value="1" />
      <type>
        <code value="Extension" />
        <profile value="http://hl7.org/fhir/StructureDefinition/observation-geneticsPhaseSet" />
      </type>
    </element>
    <element id="Observation.extension:sequence">
      <path value="Observation.extension" />
      <sliceName value="Sequence" />
      <short value="Sequence" />
      <definition value="Refers to the Sequence resource, representing raw genetics data." />
      <min value="0" />
      <max value="*" />
      <type>
        <code value="Extension" />
        <profile value="http://hl7.org/fhir/StructureDefinition/observation-geneticsSequence" />
      </type>
    </element>
    <element id="Observation.extension:interpretation">
      <path value="Observation.extension" />
      <sliceName value="Interpretation" />
      <short value="Clinical interpretations for variant" />
      <definition value="Clinical Interpretations for variant. It's a reference to an Observation resource." />
      <min value="0" />
      <max value="1" />
      <type>
        <code value="Extension" />
        <profile value="http://hl7.org/fhir/StructureDefinition/observation-geneticsInterpretation" />
      </type>
    </element>
  </differential>
</StructureDefinition>