MII-Initiative

MII IG Molekulares Tumorboard DE v2025

Molekularer Biomarker: Observation


Inhalt

Dieses abstrakte Profil beschreibt einen Molekularen Biomarker im NGS-Bericht. Es basiert inhaltlich auf der Molekularen Biomarker-Definition des Clinical Genomic Reporting Implementation Guides STU3, ohne in der Kommentierungsversion davon direkt zu erben. Er ist Grundlage sowohl für die gen-übergreifenden Biomarker wie HRD, MSI, TMB und BRCAness, als auch für Immunhistochemie und In-Situ-Hybridisierung.


Verknüpfungen zu anderen Ressourcen


Zeitliche Zuordnung im Verlauf

NameStatusVersionCanonicalBasis
MII_PR_MTB_Molekularer_Biomarkerdraft2024.0.0-ballothttps://www.medizininformatik-initiative.de/fhir/ext/modul-mtb/StructureDefinition/mii-pr-mtb-molekularer-biomarkerhttp://hl7.org/fhir/StructureDefinition/Observation

Inhalt

idΣ0..1string
id0..1string
extensionI0..*Extension
versionIdΣ0..1id
lastUpdatedΣ0..1instant
sourceΣ0..1uri
profileS Σ0..*canonical(StructureDefinition)
securityΣ0..*CodingBinding
tagΣ0..*Coding
implicitRulesΣ ?!0..1uri
language0..1codeBinding
text0..1Narrative
contained0..*Resource
extensionI0..*Extension
modifierExtension?! I0..*Extension
identifierΣ0..*Identifier
basedOnΣ0..*Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)
partOfΣ0..*Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy)
statusΣ ?!1..1codeBinding
id0..1string
extensionI0..*Extension
codingΣ1..1CodingPattern
textΣ0..1string
id0..1string
extensionI0..*Extension
codingΣ1..1CodingPattern
textΣ0..1string
id0..1string
extensionI0..*Extension
codingΣ1..1CodingPattern
textΣ0..1string
codeΣ1..1CodeableConceptBinding
subjectΣ0..1Reference(Patient | Group | Device | Location)
focusS Σ0..*Reference(MII_PR_Onko_Diagnose_Primaertumor | MII_PR_MTB_Diagnose_Primaertumor)
encounterΣ0..1Reference(Encounter)
effectiveDateTimedateTime
effectivePeriodPeriod
effectiveTimingTiming
effectiveInstantinstant
issuedΣ0..1instant
performerΣ0..*Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson)
valueQuantityQuantity
valueCodeableConceptCodeableConcept
valueStringstring
valueBooleanboolean
valueIntegerinteger
valueRangeRange
valueRatioRatio
valueSampledDataSampledData
valueTimetime
valueDateTimedateTime
valuePeriodPeriod
dataAbsentReasonI0..1CodeableConceptBinding
interpretation0..*CodeableConceptBinding
note0..*Annotation
bodySite0..1CodeableConcept
method0..1CodeableConcept
specimen0..1Reference(Specimen)
device0..1Reference(Device | DeviceMetric)
id0..1string
extensionI0..*Extension
modifierExtensionΣ ?! I0..*Extension
lowI0..1SimpleQuantity
highI0..1SimpleQuantity
type0..1CodeableConceptBinding
appliesTo0..*CodeableConcept
age0..1Range
text0..1string
hasMemberΣ0..*Reference(Observation | QuestionnaireResponse | MolecularSequence)
variantΣ0..*Reference(Variant)
genotypeΣ0..*Reference(Genotype)
haplotypeΣ0..*Reference(Haplotype)
id0..1string
extensionI0..*Extension
modifierExtensionΣ ?! I0..*Extension
codeΣ1..1CodeableConcept
valueQuantityQuantity
valueCodeableConceptCodeableConcept
valueStringstring
valueBooleanboolean
valueIntegerinteger
valueRangeRange
valueRatioRatio
valueSampledDataSampledData
valueTimetime
valueDateTimedateTime
valuePeriodPeriod
dataAbsentReasonI0..1CodeableConceptBinding
interpretation0..*CodeableConceptBinding
referenceRange0..*see (referenceRange)
id0..1string
extensionI0..*Extension
modifierExtensionΣ ?! I0..*Extension
id0..1string
extensionI0..*Extension
codingΣ0..*CodingPattern
textΣ0..1string
valueQuantityQuantity
valueStringstring
valueBooleanboolean
valueIntegerinteger
valueRangeRange
valueRatioRatio
valueSampledDataSampledData
valueTimetime
valueDateTimedateTime
valuePeriodPeriod
valueCodeableConceptΣ0..1CodeableConceptBinding
dataAbsentReasonI0..1CodeableConceptBinding
interpretation0..*CodeableConceptBinding
referenceRange0..*see (referenceRange)
id0..1string
extensionI0..*Extension
modifierExtensionΣ ?! I0..*Extension
codeΣ1..1CodeableConceptPattern
valueCodeableConceptCodeableConcept
dataAbsentReasonI0..1CodeableConceptBinding
interpretation0..*CodeableConceptBinding
referenceRange0..*see (referenceRange)

Stellt einen gefundenden Biomarker dar. Das Profil ist auf Basis von https://build.fhir.org/ig/HL7/genomics-reporting/StructureDefinition-molecular-biomarker.html nachgebaut.

Feldname
Observation.meta
Observation.meta.profile
Observation.category:labCategory
Observation.focus
Observation.component:biomarker-category
<StructureDefinition xmlns="http://hl7.org/fhir">
    <id value="mii-pr-mtb-molekularer-biomarker" />
    <url value="https://www.medizininformatik-initiative.de/fhir/ext/modul-mtb/StructureDefinition/mii-pr-mtb-molekularer-biomarker" />
    <version value="2024.0.0-ballot" />
    <name value="MII_PR_MTB_Molekularer_Biomarker" />
    <title value="MII PR MTB Molekularer Biomarker" />
    <status value="draft" />
    <publisher value="Medizininformatik Initiative" />
    <contact>
        <telecom>
            <system value="url" />
            <value value="https://www.medizininformatik-initiative.de" />
        </telecom>
    </contact>
    <description value="Stellt einen gefundenden Biomarker dar. Das Profil ist auf Basis von https://build.fhir.org/ig/HL7/genomics-reporting/StructureDefinition-molecular-biomarker.html nachgebaut." />
    <fhirVersion value="4.0.1" />
    <kind value="resource" />
    <abstract value="false" />
    <type value="Observation" />
    <baseDefinition value="http://hl7.org/fhir/StructureDefinition/Observation" />
    <derivation value="constraint" />
    <differential>
        <element id="Observation.meta">
            <path value="Observation.meta" />
            <mustSupport value="true" />
        </element>
        <element id="Observation.meta.profile">
            <path value="Observation.meta.profile" />
            <mustSupport value="true" />
        </element>
        <element id="Observation.category">
            <path value="Observation.category" />
            <slicing>
                <discriminator>
                    <type value="value" />
                    <path value="coding" />
                </discriminator>
                <description value="Slices for category" />
                <ordered value="false" />
                <rules value="open" />
            </slicing>
            <min value="3" />
        </element>
        <element id="Observation.category:labCategory">
            <path value="Observation.category" />
            <sliceName value="labCategory" />
            <min value="1" />
            <max value="1" />
            <mustSupport value="true" />
        </element>
        <element id="Observation.category:labCategory.coding">
            <path value="Observation.category.coding" />
            <min value="1" />
            <max value="1" />
            <patternCoding>
                <system value="http://terminology.hl7.org/CodeSystem/observation-category" />
                <code value="laboratory" />
            </patternCoding>
        </element>
        <element id="Observation.category:geCategory">
            <path value="Observation.category" />
            <sliceName value="geCategory" />
            <min value="1" />
            <max value="1" />
        </element>
        <element id="Observation.category:geCategory.coding">
            <path value="Observation.category.coding" />
            <min value="1" />
            <max value="1" />
            <patternCoding>
                <system value="http://terminology.hl7.org/CodeSystem/v2-0074" />
                <code value="GE" />
            </patternCoding>
        </element>
        <element id="Observation.category:mbCategory">
            <path value="Observation.category" />
            <sliceName value="mbCategory" />
            <min value="1" />
            <max value="1" />
        </element>
        <element id="Observation.category:mbCategory.coding">
            <path value="Observation.category.coding" />
            <min value="1" />
            <max value="1" />
            <patternCoding>
                <system value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" />
                <code value="biomarker-category" />
            </patternCoding>
        </element>
        <element id="Observation.code">
            <path value="Observation.code" />
            <binding>
                <strength value="extensible" />
                <valueSet value="https://www.medizininformatik-initiative.de/fhir/ext/modul-mtb/ValueSet/mii-vs-mtb-molekulare-biomarker" />
            </binding>
        </element>
        <element id="Observation.focus">
            <path value="Observation.focus" />
            <type>
                <code value="Reference" />
                <targetProfile value="https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/StructureDefinition/mii-pr-onko-diagnose-primaertumor" />
                <targetProfile value="https://www.medizininformatik-initiative.de/fhir/ext/modul-mtb/StructureDefinition/mii-pr-mtb-diagnose-primaertumor" />
            </type>
            <mustSupport value="true" />
        </element>
        <element id="Observation.derivedFrom">
            <path value="Observation.derivedFrom" />
            <slicing>
                <discriminator>
                    <type value="profile" />
                    <path value="resolve()" />
                </discriminator>
                <description value="Slices for derivedFrom" />
                <ordered value="false" />
                <rules value="open" />
            </slicing>
        </element>
        <element id="Observation.derivedFrom:variant">
            <path value="Observation.derivedFrom" />
            <sliceName value="variant" />
            <min value="0" />
            <max value="*" />
            <type>
                <code value="Reference" />
                <targetProfile value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" />
            </type>
        </element>
        <element id="Observation.derivedFrom:genotype">
            <path value="Observation.derivedFrom" />
            <sliceName value="genotype" />
            <min value="0" />
            <max value="*" />
            <type>
                <code value="Reference" />
                <targetProfile value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype" />
            </type>
        </element>
        <element id="Observation.derivedFrom:haplotype">
            <path value="Observation.derivedFrom" />
            <sliceName value="haplotype" />
            <min value="0" />
            <max value="*" />
            <type>
                <code value="Reference" />
                <targetProfile value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype" />
            </type>
        </element>
        <element id="Observation.component">
            <path value="Observation.component" />
            <slicing>
                <discriminator>
                    <type value="value" />
                    <path value="code" />
                </discriminator>
                <description value="Slices for component" />
                <ordered value="false" />
                <rules value="open" />
            </slicing>
        </element>
        <element id="Observation.component:gene-studied">
            <path value="Observation.component" />
            <sliceName value="gene-studied" />
            <min value="0" />
            <max value="*" />
        </element>
        <element id="Observation.component:gene-studied.code.coding">
            <path value="Observation.component.code.coding" />
            <patternCoding>
                <system value="http://loinc.org" />
                <code value="48018-6" />
            </patternCoding>
        </element>
        <element id="Observation.component:gene-studied.value[x]">
            <path value="Observation.component.value[x]" />
            <slicing>
                <discriminator>
                    <type value="type" />
                    <path value="$this" />
                </discriminator>
                <ordered value="false" />
                <rules value="open" />
            </slicing>
        </element>
        <element id="Observation.component:gene-studied.value[x]:valueCodeableConcept">
            <path value="Observation.component.value[x]" />
            <sliceName value="valueCodeableConcept" />
            <short value="The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used." />
            <min value="0" />
            <max value="1" />
            <type>
                <code value="CodeableConcept" />
            </type>
            <binding>
                <strength value="extensible" />
                <valueSet value="http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs" />
            </binding>
        </element>
        <element id="Observation.component:biomarker-category">
            <path value="Observation.component" />
            <sliceName value="biomarker-category" />
            <min value="0" />
            <max value="*" />
            <mustSupport value="true" />
        </element>
        <element id="Observation.component:biomarker-category.code">
            <path value="Observation.component.code" />
            <patternCodeableConcept>
                <coding>
                    <system value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs" />
                    <code value="biomarker-category" />
                </coding>
            </patternCodeableConcept>
        </element>
        <element id="Observation.component:biomarker-category.value[x]">
            <path value="Observation.component.value[x]" />
            <type>
                <code value="CodeableConcept" />
            </type>
            <binding>
                <strength value="preferred" />
                <valueSet value="http://hl7.org/fhir/uv/genomics-reporting/ValueSet/molecular-biomarker-category-vs" />
            </binding>
        </element>
    </differential>
</StructureDefinition>
{
    "resourceType": "StructureDefinition",
    "id": "mii-pr-mtb-molekularer-biomarker",
    "url": "https://www.medizininformatik-initiative.de/fhir/ext/modul-mtb/StructureDefinition/mii-pr-mtb-molekularer-biomarker",
    "version": "2024.0.0-ballot",
    "name": "MII_PR_MTB_Molekularer_Biomarker",
    "title": "MII PR MTB Molekularer Biomarker",
    "status": "draft",
    "publisher": "Medizininformatik Initiative",
    "contact":  [
        {
            "telecom":  [
                {
                    "system": "url",
                    "value": "https://www.medizininformatik-initiative.de"
                }
            ]
        }
    ],
    "description": "Stellt einen gefundenden Biomarker dar. Das Profil ist auf Basis von https://build.fhir.org/ig/HL7/genomics-reporting/StructureDefinition-molecular-biomarker.html nachgebaut.",
    "fhirVersion": "4.0.1",
    "kind": "resource",
    "abstract": false,
    "type": "Observation",
    "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Observation",
    "derivation": "constraint",
    "differential": {
        "element":  [
            {
                "id": "Observation.meta",
                "path": "Observation.meta",
                "mustSupport": true
            },
            {
                "id": "Observation.meta.profile",
                "path": "Observation.meta.profile",
                "mustSupport": true
            },
            {
                "id": "Observation.category",
                "path": "Observation.category",
                "slicing": {
                    "discriminator":  [
                        {
                            "type": "value",
                            "path": "coding"
                        }
                    ],
                    "rules": "open",
                    "description": "Slices for category",
                    "ordered": false
                },
                "min": 3
            },
            {
                "id": "Observation.category:labCategory",
                "path": "Observation.category",
                "sliceName": "labCategory",
                "min": 1,
                "max": "1",
                "mustSupport": true
            },
            {
                "id": "Observation.category:labCategory.coding",
                "path": "Observation.category.coding",
                "min": 1,
                "max": "1",
                "patternCoding": {
                    "code": "laboratory",
                    "system": "http://terminology.hl7.org/CodeSystem/observation-category"
                }
            },
            {
                "id": "Observation.category:geCategory",
                "path": "Observation.category",
                "sliceName": "geCategory",
                "min": 1,
                "max": "1"
            },
            {
                "id": "Observation.category:geCategory.coding",
                "path": "Observation.category.coding",
                "min": 1,
                "max": "1",
                "patternCoding": {
                    "code": "GE",
                    "system": "http://terminology.hl7.org/CodeSystem/v2-0074"
                }
            },
            {
                "id": "Observation.category:mbCategory",
                "path": "Observation.category",
                "sliceName": "mbCategory",
                "min": 1,
                "max": "1"
            },
            {
                "id": "Observation.category:mbCategory.coding",
                "path": "Observation.category.coding",
                "min": 1,
                "max": "1",
                "patternCoding": {
                    "code": "biomarker-category",
                    "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"
                }
            },
            {
                "id": "Observation.code",
                "path": "Observation.code",
                "binding": {
                    "strength": "extensible",
                    "valueSet": "https://www.medizininformatik-initiative.de/fhir/ext/modul-mtb/ValueSet/mii-vs-mtb-molekulare-biomarker"
                }
            },
            {
                "id": "Observation.focus",
                "path": "Observation.focus",
                "type":  [
                    {
                        "code": "Reference",
                        "targetProfile":  [
                            "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/StructureDefinition/mii-pr-onko-diagnose-primaertumor",
                            "https://www.medizininformatik-initiative.de/fhir/ext/modul-mtb/StructureDefinition/mii-pr-mtb-diagnose-primaertumor"
                        ]
                    }
                ],
                "mustSupport": true
            },
            {
                "id": "Observation.derivedFrom",
                "path": "Observation.derivedFrom",
                "slicing": {
                    "discriminator":  [
                        {
                            "type": "profile",
                            "path": "resolve()"
                        }
                    ],
                    "rules": "open",
                    "description": "Slices for derivedFrom",
                    "ordered": false
                }
            },
            {
                "id": "Observation.derivedFrom:variant",
                "path": "Observation.derivedFrom",
                "sliceName": "variant",
                "min": 0,
                "max": "*",
                "type":  [
                    {
                        "code": "Reference",
                        "targetProfile":  [
                            "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
                        ]
                    }
                ]
            },
            {
                "id": "Observation.derivedFrom:genotype",
                "path": "Observation.derivedFrom",
                "sliceName": "genotype",
                "min": 0,
                "max": "*",
                "type":  [
                    {
                        "code": "Reference",
                        "targetProfile":  [
                            "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype"
                        ]
                    }
                ]
            },
            {
                "id": "Observation.derivedFrom:haplotype",
                "path": "Observation.derivedFrom",
                "sliceName": "haplotype",
                "min": 0,
                "max": "*",
                "type":  [
                    {
                        "code": "Reference",
                        "targetProfile":  [
                            "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype"
                        ]
                    }
                ]
            },
            {
                "id": "Observation.component",
                "path": "Observation.component",
                "slicing": {
                    "discriminator":  [
                        {
                            "type": "value",
                            "path": "code"
                        }
                    ],
                    "rules": "open",
                    "description": "Slices for component",
                    "ordered": false
                }
            },
            {
                "id": "Observation.component:gene-studied",
                "path": "Observation.component",
                "sliceName": "gene-studied",
                "min": 0,
                "max": "*"
            },
            {
                "id": "Observation.component:gene-studied.code.coding",
                "path": "Observation.component.code.coding",
                "patternCoding": {
                    "code": "48018-6",
                    "system": "http://loinc.org"
                }
            },
            {
                "id": "Observation.component:gene-studied.value[x]",
                "path": "Observation.component.value[x]",
                "slicing": {
                    "discriminator":  [
                        {
                            "type": "type",
                            "path": "$this"
                        }
                    ],
                    "ordered": false,
                    "rules": "open"
                }
            },
            {
                "id": "Observation.component:gene-studied.value[x]:valueCodeableConcept",
                "path": "Observation.component.value[x]",
                "sliceName": "valueCodeableConcept",
                "short": "The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.",
                "min": 0,
                "max": "1",
                "type":  [
                    {
                        "code": "CodeableConcept"
                    }
                ],
                "binding": {
                    "strength": "extensible",
                    "valueSet": "http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs"
                }
            },
            {
                "id": "Observation.component:biomarker-category",
                "path": "Observation.component",
                "sliceName": "biomarker-category",
                "min": 0,
                "max": "*",
                "mustSupport": true
            },
            {
                "id": "Observation.component:biomarker-category.code",
                "path": "Observation.component.code",
                "patternCodeableConcept": {
                    "coding":  [
                        {
                            "code": "biomarker-category",
                            "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"
                        }
                    ]
                }
            },
            {
                "id": "Observation.component:biomarker-category.value[x]",
                "path": "Observation.component.value[x]",
                "type":  [
                    {
                        "code": "CodeableConcept"
                    }
                ],
                "binding": {
                    "strength": "preferred",
                    "valueSet": "http://hl7.org/fhir/uv/genomics-reporting/ValueSet/molecular-biomarker-category-vs"
                }
            }
        ]
    }
}

Mapping Datensatz zu FHIR

DatensatzErklaerungFHIR
RNA Fusion

RNA Fusion

MII_PR_MTB_RNA_Seq
Varianten ID

Varianten ID

MII_PR_MTB_RNA_Seq.component[variation-code]
Entrez ID

Entrez ID

MII_PR_MTB_RNA_Seq.component[variation-code]
Ensemble ID

Ensemble ID

MII_PR_MTB_RNA_Seq.component[variation-code]
Gen

Gen

MII_PR_MTB_RNA_Seq.component[gene-studied]
Transcript ID

Transcript ID

MII_PR_MTB_RNA_Seq.component[transcript-id]
Transcripts Per Million

Transcripts Per Million

MII_PR_MTB_RNA_Seq.component[transcripts-per-million]
Tissue Corrected Expression

Tissue Corrected Expression

MII_PR_MTB_RNA_Seq.component[tissue-corrected-expression]
Raw counts

Raw counts

MII_PR_MTB_RNA_Seq.component[raw-counts]
Library size

Library size

MII_PR_MTB_RNA_Seq.component[library-size]
Cohort ranking

Cohort ranking

MII_PR_MTB_RNA_Seq.component[cohort-ranking]

Suchparameter

Folgende Suchparameter sind für das Modul Onkologie relevant, auch in Kombination:

  1. Der Suchparameter "_id" MUSS unterstützt werden:

    Beispiele:

    GET [base]/Observation?_id=12345

    Anwendungshinweise: Weitere Informationen zur Suche nach "_id" finden sich in der FHIR-Basisspezifikation - Abschnitt "Parameters for all resources".

  2. Der Suchparameter "_profile" MUSS unterstützt werden:

    Beispiele:

    GET [base]/Observation?_profile=https://www.medizininformatik-initiative.de/fhir/ext/modul-mtb/StructureDefinition/mii-pr-mtb-molekularer-biomarker

    Anwendungshinweise: Weitere Informationen zur Suche nach "_profile" finden sich in der FHIR-Basisspezifikation - Abschnitt "Parameters for all resources".

  3. Der Suchparameter "focus" MUSS unterstützt werden:

    Beispiele:

    GET [base]/Observation?focus=Condition/example-mii-mtb-diagnose

    Anwendungshinweise: Weitere Informationen zur Suche nach "focus" finden sich in der FHIR-Basisspezifikation - Abschnitt "reference".


Beispiele