Name Flags Card. Type Description & Constraints doco
. . Observation 0 .. * Region Studied
. . . code 1..1 CodeableConcept Region Studied
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: 53041-0
. . . valueCodeableConcept 0 .. 0
. . . component 0 .. * (Slice Definition) Slice: Unordered, Open by pattern:code
. . . . component:gene-studied 0..* BackboneElement Gene studied ID
. . . . . 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: 48018-6
. . . . . value[x] 1..1 CodeableConcept Binding: HGNC (extensible)
. . . . component:gene-mutations 0..* BackboneElement Gene Mutations ID
. . . . . 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: 36908-2
. . . . . value[x] 1..1 CodeableConcept Binding: HGVS (required)
. . . . component:region-description 0..* BackboneElement Region Description
. . . . . 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: 81293-3
. . . . . value[x] 1..1 string
. . . . component:region-coverage 0..1 BackboneElement Region Coverage
. . . . . 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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes
. . . . . . . code 1..1 code Symbol in syntax defined by the system
Fixed Value: region-coverage
. . . . . value[x] 1..1 Quantity
. . . . component:ranges-examined 0..* BackboneElement Range(s) of DNA sequence examined
. . . . . 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: 51959-5
. . . . . value[x] 1..1 Range
. . . . component:coordinate-system 0..1 BackboneElement Coordinate System
. . . . . 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: 92822-6
. . . . . value[x] 1..1 CodeableConcept 0-based interval | 0-based character | 1-based character
Binding: LOINC Answer List LL5323-2 (preferred)
. . . . component:genomic-ref-seq 0..1 BackboneElement Genomic reference sequence ID
. . . . . 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: 48013-7
. . . . . value[x] 1..1 CodeableConcept Binding: (unbound) (example)

doco Documentation for this format
<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/genomics-base" /> <derivation value="constraint" /> <snapshot /> <differential> <element id="Observation"> <path value="Observation" /> <short value="Region Studied" /> <definition value="The Region Studied profile is used to assert actual regions studied for the performed test(s). Intended coverage areas may differ from actual coverage areas (e.g. due to technical limitations during test performance)." /> <mustSupport value="false" /> <mapping> <identity value="v2-cg-results" /> <map value="C" /> </mapping> </element> <element id="Observation.code"> <path value="Observation.code" /> <short value="Region Studied" /> <definition value="The panel code that is used to contain the details about the region studied." /> <min value="1" /> <max value="1" /> <type> <code value="CodeableConcept" /> </type> <patternCodeableConcept> <coding> <system value="http://loinc.org" /> <code value="53041-0" /> </coding> </patternCodeableConcept> <mustSupport value="false" /> </element> <element id="Observation.valueCodeableConcept"> <path value="Observation.valueCodeableConcept" /> <min value="0" /> <max value="0" /> <type> <code value="CodeableConcept" /> </type> <mustSupport value="false" /> </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:gene-studied"> <path value="Observation.component" /> <sliceName value="gene-studied" /> <short value="Gene studied ID" /> <definition value="HUGO Gene Nomenclature Committee (HGNC) identifier for a gene. List the gene(s) examined in full or in part by the study. If the study addresses multiple genes, these can be recorded in multiple gene studied components . The required coding will use the HGNC gene symbol as the display text and HGNC gene ID as the code." /> <min value="0" /> <max value="*" /> <mustSupport value="false" /> </element> <element id="Observation.component:gene-studied.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="48018-6" /> </coding> </patternCodeableConcept> <mustSupport value="false" /> </element> <element id="Observation.component:gene-studied.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="extensible" /> <description value="HGNC: Human Gene Nomenclature Committee" /> <valueSet value="http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc" /> </binding> <mapping> <identity value="v2-cg-results" /> <map value="A.4" /> </mapping> </element> <element id="Observation.component:gene-mutations"> <path value="Observation.component" /> <sliceName value="gene-mutations" /> <short value="Gene Mutations ID" /> <definition value="Gene mutations that were tested for." /> <min value="0" /> <max value="*" /> <mustSupport value="false" /> </element> <element id="Observation.component:gene-mutations.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="36908-2" /> </coding> </patternCodeableConcept> <mustSupport value="false" /> </element> <element id="Observation.component:gene-mutations.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="required" /> <description value="HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society" /> <valueSet value="http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs" /> </binding> </element> <element id="Observation.component:region-description"> <path value="Observation.component" /> <sliceName value="region-description" /> <short value="Region Description" /> <definition value="Description of region examined." /> <min value="0" /> <max value="*" /> <mustSupport value="false" /> </element> <element id="Observation.component:region-description.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="81293-3" /> </coding> </patternCodeableConcept> <mustSupport value="false" /> </element> <element id="Observation.component:region-description.value[x]"> <path value="Observation.component.value[x]" /> <min value="1" /> <max value="1" /> <type> <code value="string" /> </type> <mustSupport value="false" /> </element> <element id="Observation.component:region-coverage"> <path value="Observation.component" /> <sliceName value="region-coverage" /> <short value="Region Coverage" /> <definition value="When sequencing, what % of the region was covered." /> <min value="0" /> <max value="1" /> <mustSupport value="false" /> </element> <element id="Observation.component:region-coverage.code"> <path value="Observation.component.code" /> <min value="1" /> <max value="1" /> <type> <code value="CodeableConcept" /> </type> <patternCodeableConcept> <coding> <system value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes" /> <code value="region-coverage" /> </coding> </patternCodeableConcept> <mustSupport value="false" /> </element> <element id="Observation.component:region-coverage.value[x]"> <path value="Observation.component.value[x]" /> <min value="1" /> <max value="1" /> <type> <code value="Quantity" /> </type> <mustSupport value="false" /> </element> <element id="Observation.component:ranges-examined"> <path value="Observation.component" /> <sliceName value="ranges-examined" /> <short value="Range(s) of DNA sequence examined" /> <definition value="This term is used to report the region(s) of interest for sequencing studies as one or more numeric ranges that identify the parts of the reference sequence that are sequenced. These can be recorded as one or more HL7 numeric ranges using repeat delimiters to seperate multiple such ranges." /> <min value="0" /> <max value="*" /> <mustSupport value="false" /> </element> <element id="Observation.component:ranges-examined.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="51959-5" /> </coding> </patternCodeableConcept> <mustSupport value="false" /> </element> <element id="Observation.component:ranges-examined.value[x]"> <path value="Observation.component.value[x]" /> <min value="1" /> <max value="1" /> <type> <code value="Range" /> </type> <mustSupport value="false" /> </element> <element id="Observation.component:coordinate-system"> <path value="Observation.component" /> <sliceName value="coordinate-system" /> <short value="Coordinate System" /> <definition value="Base number of coordinate system either 0-based, with inclusive start and exclusive end (called interval), or 1-based, with inclusive start and end. However, two versions of 1-based are in common use.These systems are HGVS 1-based (called variant method) and VCF 1-based (called alignment method). In general, HGVS recommends right-justification and VCF recommends left-justification. However, these systems further address questions such as wheather or not to place an insertion before or after the nucleotide, and, if always placed before the nucleotide, how to handle insertion after the end of the sequence. Additionally, the systems deal with handling boundary effects of numbers between features. For more details see the HGVS and VCF guides." /> <min value="0" /> <max value="1" /> <mustSupport value="false" /> </element> <element id="Observation.component:coordinate-system.code"> <path value="Observation.component.code" /> <definition value="This captures the base numbering used to calculate base positions in the reported sequence information." /> <min value="1" /> <max value="1" /> <type> <code value="CodeableConcept" /> </type> <patternCodeableConcept> <coding> <system value="http://loinc.org" /> <code value="92822-6" /> </coding> </patternCodeableConcept> <mustSupport value="false" /> </element> <element id="Observation.component:coordinate-system.value[x]"> <path value="Observation.component.value[x]" /> <short value="0-based interval | 0-based character | 1-based character" /> <min value="1" /> <max value="1" /> <type> <code value="CodeableConcept" /> </type> <mustSupport value="false" /> <binding> <strength value="preferred" /> <description value="Base coordinate systems start and end measurements for variants" /> <valueSet value="http://loinc.org/vs/LL5323-2" /> </binding> </element> <element id="Observation.component:genomic-ref-seq"> <path value="Observation.component" /> <sliceName value="genomic-ref-seq" /> <short value="Genomic reference sequence ID" /> <definition value="This field carries the ID for the genomic reference sequence. The genomic reference sequence is a contiguous stretch of chromosome DNA that spans all of the exons of the gene and includes transcribed and non transcribed stretches. For this ID use either the NCBI genomic nucleotide RefSeq IDs with their version number (see: NCBI.NLM.NIH.Gov/RefSeq) or use the LRG identifiers, without transcript (t or p) extensions -- when they become available. (See- Report sponsored by GEN2PHEN at the European Bioinformatics Institute at Hinxton UK April 24-25, 2008). The NCI RefSeq genomic IDs are distinguished by a prefix of"NG" for genes from the nuclear chromosomes and prefix of "NC" for genes from mitochondria. The LRG Identifiers have a prefix of "LRG_" Mitochondrial genes are not in the scope of LRG." /> <min value="0" /> <max value="1" /> <mustSupport value="false" /> </element> <element id="Observation.component:genomic-ref-seq.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="48013-7" /> </coding> </patternCodeableConcept> <mustSupport value="false" /> </element> <element id="Observation.component:genomic-ref-seq.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.9" /> </mapping> </element> </differential> </StructureDefinition>