<status value="draft" /> <experimental value="false" /> <date value="2017-05-20T00:00:00+00:00" /> <publisher value="HL7 Clinical Genomics WG" /> <description value="Observation-related profiles" /> <fhirVersion value="4.0.1" /> <mapping> <identity value="v2-cg-results" /> <uri value="http://unknown.org/V2-CG-Results" /> <name value="V2-CG-Results" /> </mapping> <mapping> <identity value="workflow" /> <uri value="http://hl7.org/fhir/workflow" /> <name value="Workflow Pattern" /> </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/fivews" /> <name value="FiveWs Pattern Mapping" /> </mapping> <mapping> <identity value="sct-attr" /> <uri value="http://snomed.org/attributebinding" /> <name value="SNOMED CT Attribute Binding" /> </mapping> <kind value="resource" /> <abstract value="false" /> <type value="Observation" /> <baseDefinition value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/implication" /> <derivation value="constraint" /> <snapshot /> <differential> <element id="Observation"> <path value="Observation" /> <short value="Inherited Disease Pathogenicity" /> <definition value="Provides an indication of whether there's a pathologic risk associated with a particular genotype, haplotype, variant or combination there-of, and if so, what the associated pathology is." /> <mustSupport value="false" /> </element> <element id="Observation.code"> <path value="Observation.code" /> <short value="Genetic variation clinical significance" /> <definition value="Single DNA marker or individual allele interpretation in the context of the assessed genetic disease. Prior to the LOINC release 2.56 (June 2016), the answer list was updated per the recommendations of the American College of Medical Genetics (ACMG). The previous answer list number was LL603-2, and two of the answer strings and LA codes are the same in the new list (pathogenic and benign). In the new answer list, the presumed pathogenic, unknown significance and presumed benign answers from LL603-2 have been replaced by likely pathogenic, uncertain significance and likely benign. The answer strings and their respective LA codes from LL603-2 remain valid." /> <min value="1" /> <max value="1" /> <type> <code value="CodeableConcept" /> </type> <patternCodeableConcept> <coding> <system value="http://loinc.org" /> <code value="53037-8" /> </coding> </patternCodeableConcept> <mustSupport value="false" /> </element> <element id="Observation.valueCodeableConcept"> <path value="Observation.valueCodeableConcept" /> <short value="Pathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign" /> <definition value="Clinical significance of genetic variation." /> <min value="1" /> <max value="1" /> <type> <code value="CodeableConcept" /> </type> <mustSupport value="false" /> <binding> <strength value="extensible" /> <description value="Genetic sequence variation clinical significance values" /> <valueSet value="http://loinc.org/vs/LL4034-6" /> </binding> <mapping> <identity value="v2-cg-results" /> <map value="A.8" /> </mapping> </element> <element id="Observation.component"> <path value="Observation.component" /> <slicing> <discriminator> <type value="pattern" /> <path value="code" /> </discriminator> <rules value="open" /> </slicing> <mustSupport value="false" /> </element> <element id="Observation.component:associated-phenotype"> <path value="Observation.component" /> <sliceName value="associated-phenotype" /> <short value="Associated phenotype" /> <definition value="The possible phenotype associated with the genetic variant found in this study." /> <comment value="If sending multiple phenotypes, break up the assertions based on the independently assessed conditions, whether they be a single term or a collection of co-occurring terms." /> <min value="0" /> <max value="*" /> <mustSupport value="false" /> </element> <element id="Observation.component:associated-phenotype.code"> <path value="Observation.component.code" /> <min value="1" /> <max value="1" /> <type> <code value="CodeableConcept" /> </type> <patternCodeableConcept> <coding> <system value="http://loinc.org" /> <code value="81259-4" /> </coding> </patternCodeableConcept> <mustSupport value="false" /> </element> <element id="Observation.component:associated-phenotype.value[x]"> <path value="Observation.component.value[x]" /> <min value="1" /> <max value="1" /> <type> <code value="CodeableConcept" /> </type> <mustSupport value="false" /> <binding> <strength value="example" /> <description value="Binding not yet defined" /> </binding> <mapping> <identity value="v2-cg-results" /> <map value="B.22, C.4" /> </mapping> </element> <element id="Observation.component:mode-of-inheritance"> <path value="Observation.component" /> <sliceName value="mode-of-inheritance" /> <short value="Mode of Inheritance" /> <min value="0" /> <max value="1" /> <mustSupport value="false" /> </element> <element id="Observation.component:mode-of-inheritance.code"> <path value="Observation.component.code" /> <min value="1" /> <max value="1" /> <type> <code value="CodeableConcept" /> </type> <patternCodeableConcept> <coding> <system value="http://loinc.org" /> <code value="79742-3" /> </coding> </patternCodeableConcept> <mustSupport value="false" /> </element> <element id="Observation.component:mode-of-inheritance.value[x]"> <path value="Observation.component.value[x]" /> <short value="Autosomal dominant|Autosomal recessive|X-linked dominant|X-linked recessive|Y-linked|Codominant|Mitochondrial" /> <definition value="Modes of Inheritance, values from https://ghr.nlm.nih.gov/primer/inheritance/inheritancepatterns." /> <min value="1" /> <max value="1" /> <type> <code value="CodeableConcept" /> </type> <mustSupport value="false" /> <binding> <strength value="preferred" /> <description value="Inheritance pattern from family history" /> <valueSet value="http://loinc.org/vs/LL3731-8" /> </binding> <mapping> <identity value="v2-cg-results" /> <map value="N/A" /> </mapping> </element> </differential> </StructureDefinition>

Name	Card.	Type	Description & Constraints
Observation	0 .. *		Inherited Disease Pathogenicity
code	1..1	CodeableConcept	Genetic variation clinical significance Required Pattern: At least the following
coding	1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system	1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
code	1..1	code	Symbol in syntax defined by the system Fixed Value: 53037-8
valueCodeableConcept	1..1	CodeableConcept	Pathogenic \| Likely pathogenic \| Uncertain significance \| Likely benign \| Benign Binding: LOINC Answer List LL4034-6 (extensible)
component	0 .. *	(Slice Definition)	Slice: Unordered, Open by pattern:code
component:associated-phenotype	0..*	BackboneElement	Associated phenotype
code	1..1	CodeableConcept	Required Pattern: At least the following
coding	1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system	1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
code	1..1	code	Symbol in syntax defined by the system Fixed Value: 81259-4
value[x]	1..1	CodeableConcept	Binding: (unbound) (example)
component:mode-of-inheritance	0..1	BackboneElement	Mode of Inheritance
code	1..1	CodeableConcept	Required Pattern: At least the following
coding	1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system	1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
code	1..1	code	Symbol in syntax defined by the system Fixed Value: 79742-3
value[x]	1..1	CodeableConcept	Autosomal dominant\|Autosomal recessive\|X-linked dominant\|X-linked recessive\|Y-linked\|Codominant\|Mitochondrial Binding: LOINC Answer List LL3731-8 (preferred)
Documentation for this format