description: Observation-related profiles
package_name: hl7.fhir.uv.genomics
derivation: constraint
name: Copy Number Change
type: Observation
elements:
  code:
    isModifier: false
    short: Copy Number Change
    type: CodeableConcept
    mustSupport: true
    pattern:
      type: CodeableConcept
      value:
        coding:
        - {code: 62377-7, system: 'http://loinc.org'}
    index: 0
  valueCodeableConcept: {isModifier: false, short: todo, type: CodeableConcept, mustSupport: true, index: 1}
  device:
    type: Reference
    isModifier: false
    mustSupport: true
    refers: ['http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/device-micro-plat']
    index: 2
  component:
    isModifier: false
    mustSupport: false
    index: 3
    slicing:
      rules: open
      discriminator:
      - {path: code, type: pattern}
      min: null
      slices:
        human-ref-seq-assembly-version:
          match:
            code:
              coding:
              - {code: 62373-6, system: 'http://loinc.org'}
          schema:
            isModifier: false
            short: Human reference assembly release, UCSC version
            mustSupport: true
            index: 31
            elements:
              code:
                type: CodeableConcept
                isModifier: false
                mustSupport: true
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 62373-6, system: 'http://loinc.org'}
                index: 32
              valueCodeableConcept:
                isModifier: false
                short: hg19 | hg18 | hg 17 | hg16
                type: CodeableConcept
                mustSupport: true
                binding: {strength: required, valueSet: 'http://loinc.org/vs/LL1039-8'}
                index: 33
            required: [valueCodeableConcept, code]
        flanking-normal-region-before-start:
          match:
            code:
              coding:
              - {code: 62383-5, system: 'http://loinc.org'}
          schema:
            isModifier: false
            short: Flanking normal region before start
            mustSupport: true
            index: 22
            elements:
              code:
                type: CodeableConcept
                isModifier: false
                mustSupport: true
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 62383-5, system: 'http://loinc.org'}
                index: 23
              valueCodeableConcept: {isModifier: false, type: CodeableConcept, mustSupport: true, index: 24}
            required: [valueCodeableConcept, code]
        base-pair-start-coordinate:
          match:
            code:
              coding:
              - {code: 62381-9, system: 'http://loinc.org'}
          schema:
            isModifier: false
            short: Base pair start coordinate
            mustSupport: true
            index: 16
            elements:
              code:
                type: CodeableConcept
                isModifier: false
                mustSupport: true
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 62381-9, system: 'http://loinc.org'}
                index: 17
              valueQuantity: {type: Quantity, isModifier: false, mustSupport: true, index: 18}
            required: [valueQuantity, code]
        chromosome-band-start:
          match:
            code:
              coding:
              - {code: 62379-3, system: 'http://loinc.org'}
          schema:
            isModifier: false
            short: Chromosome band involved start
            mustSupport: true
            index: 10
            elements:
              code:
                type: CodeableConcept
                isModifier: false
                mustSupport: true
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 62379-3, system: 'http://loinc.org'}
                index: 11
              valueCodeableConcept: {isModifier: false, type: CodeableConcept, mustSupport: true, index: 12}
            required: [valueCodeableConcept, code]
        chromosome-band-end:
          match:
            code:
              coding:
              - {code: 62380-1, system: 'http://loinc.org'}
          schema:
            isModifier: false
            short: Chromosome band involved end
            mustSupport: true
            index: 13
            elements:
              code:
                type: CodeableConcept
                isModifier: false
                mustSupport: true
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 62380-1, system: 'http://loinc.org'}
                index: 14
              valueCodeableConcept: {type: CodeableConcept, isModifier: false, mustSupport: true, index: 15}
            required: [valueCodeableConcept, code]
        copy-number:
          match:
            code:
              coding:
              - {code: 82155-3, system: 'http://loinc.org'}
          schema:
            isModifier: false
            short: Copy Number
            mustSupport: true
            index: 7
            elements:
              code:
                type: CodeableConcept
                isModifier: false
                mustSupport: true
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 82155-3, system: 'http://loinc.org'}
                index: 8
              valueQuantity: {type: Quantity, isModifier: false, mustSupport: true, index: 9}
            required: [valueQuantity, code]
        arrCGH-ratio:
          match:
            code:
              coding:
              - {code: 81299-0, system: 'http://loinc.org'}
          schema:
            isModifier: false
            short: Structural variant reported arrCGH [Ratio]
            mustSupport: true
            index: 34
            elements:
              code:
                type: CodeableConcept
                isModifier: false
                mustSupport: true
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 81299-0, system: 'http://loinc.org'}
                index: 35
              valueQuantity: {type: Quantity, isModifier: false, mustSupport: true, index: 36}
            required: [valueQuantity, code]
        flanking-normal-region-after-end:
          match:
            code:
              coding:
              - {code: 62384-3, system: 'http://loinc.org'}
          schema:
            isModifier: false
            short: Flanking normal region after end
            mustSupport: true
            index: 25
            elements:
              code:
                type: CodeableConcept
                isModifier: false
                mustSupport: true
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 62384-3, system: 'http://loinc.org'}
                index: 26
              valueCodeableConcept: {isModifier: false, type: CodeableConcept, mustSupport: true, index: 27}
            required: [valueCodeableConcept, code]
        chromosome-copy-number-change-type:
          match:
            code:
              coding:
              - {code: 62378-5, system: 'http://loinc.org'}
          schema:
            isModifier: false
            short: Chromosome copy number change type
            mustSupport: true
            index: 4
            elements:
              code:
                type: CodeableConcept
                isModifier: false
                mustSupport: true
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 62378-5, system: 'http://loinc.org'}
                index: 5
              valueCodeableConcept:
                isModifier: false
                short: Copy number gain | Copy number loss
                type: CodeableConcept
                mustSupport: true
                binding: {strength: required, valueSet: 'http://loinc.org/vs/LL1041-4'}
                index: 6
            required: [valueCodeableConcept, code]
        human-ref-seq-assembly-release:
          match:
            code:
              coding:
              - {code: 62374-4, system: 'http://loinc.org'}
          schema:
            isModifier: false
            short: Human reference sequence assembly version
            mustSupport: true
            index: 28
            elements:
              code:
                type: CodeableConcept
                isModifier: false
                mustSupport: true
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 62374-4, system: 'http://loinc.org'}
                index: 29
              valueCodeableConcept:
                isModifier: false
                short: NCBI Build 34 | GRCh37 | NCBI Build 36.1 | NCBI Build 35
                type: CodeableConcept
                mustSupport: true
                binding: {strength: preferred, valueSet: 'http://loinc.org/vs/LL1040-6'}
                index: 30
            required: [valueCodeableConcept, code]
        base-pair-end-coordinate:
          match:
            code:
              coding:
              - {code: 62382-7, system: 'http://loinc.org'}
          schema:
            isModifier: false
            short: Base pair end coordinate
            mustSupport: true
            index: 19
            elements:
              code:
                type: CodeableConcept
                isModifier: false
                mustSupport: true
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 62382-7, system: 'http://loinc.org'}
                index: 20
              valueQuantity: {type: Quantity, isModifier: false, mustSupport: true, index: 21}
            required: [valueQuantity, code]
package_version: reporting-0.3.0
class: profile
kind: resource
url: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/obs-copy-num-chg
base: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/obs-comp-gen-finding
version: 0.3.0
required: [valueCodeableConcept, code]