MII Implementierungsleitfaden Kerndatensatz-Modul Molekulargenetischer Befundbericht
2027.0.0-ballot.1 -
Germany
This page is part of the MII IG Kerndatensatz-Modul Molekulargenetischer Befundbericht (v2027.0.0-ballot.1: Release) based on FHIR (HL7® FHIR® Standard) R4. This is the current published version in its permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions
{
"resourceType" : "Bundle",
"id" : "mii-exa-molgen-bundle-fam-his-breast-ovar-can",
"language" : "de",
"type" : "transaction",
"timestamp" : "2022-11-04T13:47:00+01:00",
"entry" : [
{
"fullUrl" : "https://www.medizininformatik-initiative.de/fhir/mii-exa-molgen-patient-brca1",
"resource" : {
"resourceType" : "Patient",
"id" : "mii-exa-molgen-patient-brca1",
"language" : "de",
"text" : {
"status" : "generated"
},
"identifier" : [
{
"use" : "usual",
"type" : {
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v2-0203",
"code" : "MR"
}
]
},
"system" : "https://www.charite.de/fhir/sid/patienten",
"value" : "9166147031",
"assigner" : {
"identifier" : {
"system" : "https://www.medizininformatik-initiative.de/fhir/core/CodeSystem/core-location-identifier",
"value" : "Charité"
},
"display" : "Charité - Universitätsmedizin Berlin"
}
},
{
"use" : "official",
"type" : {
"coding" : [
{
"system" : "http://fhir.de/CodeSystem/identifier-type-de-basis",
"code" : "GKV"
}
]
},
"system" : "http://fhir.de/sid/gkv/kvid-10",
"value" : "Z977188448",
"assigner" : {
"identifier" : {
"use" : "official",
"system" : "http://fhir.de/sid/arge-ik/iknr",
"value" : "109519005"
}
}
}
],
"name" : [
{
"use" : "official",
"family" : "Schmidt-Huber",
"_family" : {
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/humanname-own-name",
"valueString" : "Schmidt"
}
]
},
"given" : [
"Elisa"
]
}
],
"gender" : "female",
"birthDate" : "1973-03-12",
"deceasedBoolean" : false,
"address" : [
{
"type" : "both",
"line" : [
"Anna-Louisa-Karsch Str. 2"
],
"city" : "Berlin",
"state" : "DE-BE",
"postalCode" : "10178",
"country" : "DE"
}
]
},
"request" : {
"method" : "PUT",
"url" : "Patient/mii-exa-molgen-patient-brca1"
}
},
{
"fullUrl" : "https://www.medizininformatik-initiative.de/fhir/mii-exa-molgen-befundbericht-trurisk-panel",
"resource" : {
"resourceType" : "DiagnosticReport",
"id" : "mii-exa-molgen-befundbericht-trurisk-panel",
"meta" : {
"profile" : [
🔗 "https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/molekulargenetischer-befundbericht|2027.0.0-ballot.1"🔗 ,
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report|3.0.0"
]
},
"language" : "de",
"text" : {
"status" : "generated"
},
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact",
"valueRelatedArtifact" : {
"type" : "citation",
"citation" : "Plon SE, Eccles DM, Easton D, Foulkes WD, Genuardi M, Greenblatt MS, Hogervorst FB, Hoogerbrugge N, Spurdle AB, Tavtigian SV; IARC Unclassified Genetic Variants Working Group. Sequence variant classification and reporting: recommendations for improving the interpretation of cancer susceptibility genetic test results. Hum Mutat. 2008 Nov;29(11):1282-91. doi: 10.1002/humu.20880. PMID: 18951446; PMCID: PMC3075918.",
"url" : "https://doi.org/10.1002/humu.20880"
}
},
{
"url" : "http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact",
"valueRelatedArtifact" : {
"type" : "citation",
"citation" : "Rhiem K, Auber B, Briest S, Dikow N, Ditsch N, Dragicevic N, Grill S, Hahnen E, Horvath J, Jaeger B, Kast K, Kiechle M, Leinert E, Morlot S, Püsken M, Schäfer D, Schott S, Schroeder C, Siebers-Renelt U, Solbach C, Weber-Lassalle N, Witzel I, Zeder-Göß C, Schmutzler RK. Consensus Recommendations of the German Consortium for Hereditary Breast and Ovarian Cancer. Breast Care (Basel). 2022 Apr;17(2):199-207. doi: 10.1159/000516376. Epub 2021 Jul 19. PMID: 35702495; PMCID: PMC9149395.",
"url" : "https://doi.org/10.1159%2F000516376"
}
},
{
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-reference",
"valueReference" : {
🔗 "reference" : "Procedure/mii-exa-molgen-genomic-study-trurisk-panel"
}
},
{
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action",
"valueReference" : {
🔗 "reference" : "Task/mii-exa-molgen-folgemassnahme-brca1"
}
},
{
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-risk-assessment",
"valueReference" : {
🔗 "reference" : "RiskAssessment/mii-exa-molgen-prs-brca1"
}
}
],
"basedOn" : [
{
🔗 "reference" : "ServiceRequest/mii-exa-molgen-anforderung-trurisk-panel"
}
],
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
"code" : "GE",
"display" : "Genetics"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "51969-4",
"display" : "Genetic analysis report"
}
]
},
"subject" : {
🔗 "reference" : "Patient/mii-exa-molgen-patient-brca1"
},
"performer" : [
{
🔗 "reference" : "Practitioner/mii-exa-molgen-practitioner-lab"
}
],
"specimen" : [
{
🔗 "reference" : "Specimen/mii-exa-molgen-specimen-brca1"
}
],
"result" : [
{
🔗 "reference" : "Observation/mii-exa-molgen-variante-brca1"
},
{
🔗 "reference" : "Observation/mii-exa-molgen-diagnostische-implikation-brca1"
}
],
"conclusion" : "Nachweis heterozygoter Sequenzveränderung, die zum Funktionsverlust führt."
},
"request" : {
"method" : "PUT",
"url" : "DiagnosticReport/mii-exa-molgen-befundbericht-trurisk-panel"
}
},
{
"fullUrl" : "https://www.medizininformatik-initiative.de/fhir/mii-exa-molgen-folgemassnahme-brca1",
"resource" : {
"resourceType" : "Task",
"id" : "mii-exa-molgen-folgemassnahme-brca1",
"meta" : {
"profile" : [
🔗 "https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/empfohlene-folgemassnahme|2027.0.0-ballot.1"🔗 ,
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/followup-recommendation|3.0.0"
]
},
"language" : "de",
"text" : {
"status" : "generated"
},
"basedOn" : [
{
🔗 "reference" : "ServiceRequest/mii-exa-molgen-anforderung-trurisk-panel"
}
],
"status" : "requested",
"intent" : "proposal",
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA14020-4",
"display" : "Genetic counseling recommended"
}
]
},
"description" : "Eine genetische Beratung hinsichtlich einer gezielten Testung leiblicher Familienmitglieder wird empfohlen.",
"for" : {
🔗 "reference" : "Patient/mii-exa-molgen-patient-brca1"
}
},
"request" : {
"method" : "PUT",
"url" : "Task/mii-exa-molgen-folgemassnahme-brca1"
}
},
{
"fullUrl" : "https://www.medizininformatik-initiative.de/fhir/mii-exa-molgen-prs-brca1",
"resource" : {
"resourceType" : "RiskAssessment",
"id" : "mii-exa-molgen-prs-brca1",
"meta" : {
"profile" : [
🔗 "https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/polygener-risiko-score|2027.0.0-ballot.1"
]
},
"language" : "de",
"text" : {
"status" : "generated"
},
"status" : "final",
"subject" : {
🔗 "reference" : "Patient/mii-exa-molgen-patient-2"
},
"occurrenceDateTime" : "2022-11-01",
"basis" : [
{
🔗 "reference" : "Observation/mii-exa-molgen-variante-brca1"
}
],
"prediction" : [
{
"extension" : [
{
"url" : "https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/risk-assessment-einflussfaktor",
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://snomed.info/sct",
"code" : "414152003",
"display" : "European (ethnic group)"
}
],
"text" : "Der verwendete Polygene Risikoscore wurde bisher nur für die europäische Bevölkerung bei Brustkrebs validiert."
}
}
],
"outcome" : {
"coding" : [
{
"system" : "http://snomed.info/sct",
"code" : "718220008",
"display" : "Hereditary breast and ovarian cancer syndrome (disorder)"
}
]
},
"qualitativeRisk" : {
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/risk-probability",
"code" : "high",
"display" : "High likelihood"
}
]
}
}
]
},
"request" : {
"method" : "PUT",
"url" : "RiskAssessment/mii-exa-molgen-prs-brca1"
}
},
{
"fullUrl" : "https://www.medizininformatik-initiative.de/fhir/mii-exa-molgen-anforderung-trurisk-panel",
"resource" : {
"resourceType" : "ServiceRequest",
"id" : "mii-exa-molgen-anforderung-trurisk-panel",
"meta" : {
"profile" : [
🔗 "https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/anforderung-genetischer-test|2027.0.0-ballot.1"
]
},
"language" : "de",
"text" : {
"status" : "generated"
},
"identifier" : [
{
"system" : "https://www.charite.de/fhir/auftragsnummern",
"value" : "gen_test_03"
}
],
"status" : "active",
"intent" : "order",
"category" : [
{
"coding" : [
{
"system" : "http://snomed.info/sct",
"code" : "108252007",
"display" : "Laboratory procedure (procedure)"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://snomed.info/sct",
"code" : "405825005",
"display" : "Molecular genetic test (procedure)"
}
],
"text" : "Panelanalyse TruRisk®-V3 mit NGS basierter CNV-Analyse Bestimmung des Polygenen Risikoscores (PRS) für Brustkrebs"
},
"subject" : {
🔗 "reference" : "Patient/mii-exa-molgen-patient-brca1"
},
"authoredOn" : "2022-11-01",
"requester" : {
🔗 "reference" : "Practitioner/mii-exa-molgen-practitioner-physician"
},
"reasonCode" : [
{
"coding" : [
{
"system" : "http://snomed.info/sct",
"code" : "429740004",
"display" : "Family history of malignant neoplasm of breast (situation)"
}
]
},
{
"coding" : [
{
"system" : "http://snomed.info/sct",
"code" : "430705002",
"display" : "Family history of malignant neoplasm of ovary (situation)"
}
]
},
{
"coding" : [
{
"system" : "http://www.orpha.net",
"code" : "145",
"display" : "Hereditary breast and/or ovarian cancer syndrome"
}
]
},
{
"coding" : [
{
"system" : "http://www.omim.org",
"code" : "604370",
"display" : "BREAST-OVARIAN CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1; BROVCA1"
}
]
}
],
"specimen" : [
{
🔗 "reference" : "Specimen/mii-exa-molgen-specimen-brca1"
}
]
},
"request" : {
"method" : "PUT",
"url" : "ServiceRequest/mii-exa-molgen-anforderung-trurisk-panel"
}
},
{
"fullUrl" : "https://www.medizininformatik-initiative.de/fhir/mii-exa-molgen-practitioner-lab",
"resource" : {
"resourceType" : "Practitioner",
"id" : "mii-exa-molgen-practitioner-lab",
"language" : "de",
"text" : {
"status" : "generated"
},
"active" : true,
"name" : [
{
"use" : "official",
"text" : "Dr. Daniel Schmidt",
"family" : "Schmidt",
"given" : [
"Daniel"
],
"prefix" : [
"Dr."
]
}
]
},
"request" : {
"method" : "PUT",
"url" : "Practitioner/mii-exa-molgen-practitioner-lab"
}
},
{
"fullUrl" : "https://www.medizininformatik-initiative.de/fhir/mii-exa-molgen-practitioner-physician",
"resource" : {
"resourceType" : "Practitioner",
"id" : "mii-exa-molgen-practitioner-physician",
"language" : "de",
"text" : {
"status" : "generated"
},
"active" : true,
"name" : [
{
"use" : "official",
"text" : "Dr. Linda Rubens",
"family" : "Rubens",
"given" : [
"Linda"
],
"prefix" : [
"Dr."
]
}
]
},
"request" : {
"method" : "PUT",
"url" : "Practitioner/mii-exa-molgen-practitioner-physician"
}
},
{
"fullUrl" : "https://www.medizininformatik-initiative.de/fhir/mii-exa-molgen-specimen-brca1",
"resource" : {
"resourceType" : "Specimen",
"id" : "mii-exa-molgen-specimen-brca1",
"meta" : {
"profile" : [
🔗 "https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/SpecimenCore"
]
},
"language" : "de",
"text" : {
"status" : "generated"
},
"identifier" : [
{
"system" : "https://www.charite.de/fhir/sid/bioproben",
"value" : "specimen_03"
}
],
"status" : "available",
"type" : {
"coding" : [
{
"system" : "http://snomed.info/sct",
"code" : "127457009",
"display" : "Tissue specimen from breast (specimen)"
}
]
},
"subject" : {
🔗 "reference" : "Patient/mii-exa-molgen-patient-brca1"
},
"receivedTime" : "2022-11-01",
"collection" : {
"collectedDateTime" : "2022-11-01"
}
},
"request" : {
"method" : "PUT",
"url" : "Specimen/mii-exa-molgen-specimen-brca1"
}
},
{
"fullUrl" : "https://www.medizininformatik-initiative.de/fhir/mii-exa-molgen-device-sequencer-nextseq",
"resource" : {
"resourceType" : "Device",
"id" : "mii-exa-molgen-device-sequencer-nextseq",
"language" : "de",
"text" : {
"status" : "generated"
},
"status" : "active",
"manufacturer" : "Illumina",
"deviceName" : [
{
"name" : "NextSeq",
"type" : "manufacturer-name"
}
]
},
"request" : {
"method" : "PUT",
"url" : "Device/mii-exa-molgen-device-sequencer-nextseq"
}
},
{
"fullUrl" : "https://www.medizininformatik-initiative.de/fhir/mii-exa-molgen-variante-brca1",
"resource" : {
"resourceType" : "Observation",
"id" : "mii-exa-molgen-variante-brca1",
"meta" : {
"profile" : [
🔗 "https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/variante|2027.0.0-ballot.1"🔗 ,
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant|3.0.0"
]
},
"language" : "de",
"text" : {
"status" : "generated"
},
"basedOn" : [
{
🔗 "reference" : "ServiceRequest/mii-exa-molgen-anforderung-trurisk-panel"
}
],
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory",
"display" : "Laboratory"
}
]
},
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
"code" : "GE"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "69548-6",
"display" : "Genetic variant assessment"
}
]
},
"subject" : {
🔗 "reference" : "Patient/mii-exa-molgen-patient-brca1"
},
"effectiveDateTime" : "2022-11-01",
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA9633-4",
"display" : "Present"
}
]
},
"method" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA26398-0",
"display" : "Sequencing"
}
]
},
"specimen" : {
🔗 "reference" : "Specimen/mii-exa-molgen-specimen-brca1"
},
"device" : {
🔗 "reference" : "Device/mii-exa-molgen-device-sequencer-nextseq"
},
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48018-6",
"display" : "Gene studied [ID]"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.genenames.org/geneId",
"code" : "HGNC:1100",
"display" : "BRCA1"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48001-2"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "urn:oid:2.16.840.1.113883.6.335",
"code" : "17q21.31"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48004-6"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://varnomen.hgvs.org",
"code" : "NM_007294.3:c.5266dupC"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "51958-7"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.ncbi.nlm.nih.gov/refseq",
"code" : "NM_007294.3"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48019-4"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://sequenceontology.org",
"code" : "SO:1000035",
"display" : "Duplication"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "82121-5"
}
]
},
"valueQuantity" : {
"value" : 50,
"unit" : "Abdeckung der Fragmente",
"system" : "http://unitsofmeasure.org",
"code" : "1"
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81252-9"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.ncbi.nlm.nih.gov/projects/SNP",
"code" : "rs80357906"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48000-4"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA21270-6",
"display" : "Chromosome 17"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48005-3"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://varnomen.hgvs.org",
"code" : "p.Gln1756Profs"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "87706-8"
}
]
},
"valueQuantity" : {
"value" : 95,
"comparator" : ">",
"unit" : "%",
"system" : "http://unitsofmeasure.org",
"code" : "%"
}
}
]
},
"request" : {
"method" : "PUT",
"url" : "Observation/mii-exa-molgen-variante-brca1"
}
},
{
"fullUrl" : "https://www.medizininformatik-initiative.de/fhir/mii-exa-molgen-diagnostische-implikation-brca1",
"resource" : {
"resourceType" : "Observation",
"id" : "mii-exa-molgen-diagnostische-implikation-brca1",
"meta" : {
"profile" : [
🔗 "https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/diagnostische-implikation|2027.0.0-ballot.1"🔗 ,
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication|3.0.0"
]
},
"language" : "de",
"text" : {
"status" : "generated"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory",
"display" : "Laboratory"
}
]
},
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
"code" : "GE"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code" : "diagnostic-implication",
"display" : "Diagnostic Implication"
}
]
},
"subject" : {
🔗 "reference" : "Patient/mii-exa-molgen-patient-brca1"
},
"effectiveDateTime" : "2022-11-01",
"performer" : [
{
🔗 "reference" : "Practitioner/mii-exa-molgen-practitioner-lab"
}
],
"derivedFrom" : [
{
🔗 "reference" : "Observation/mii-exa-molgen-variante-brca1"
}
],
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code" : "conclusion-string"
}
]
},
"valueString" : "Nachweis heterozygoter Sequenzveränderung, die zum Funktionsverlust führt"
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "53037-8",
"display" : "Genetic variation clinical significance [Imp]"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA6668-3",
"display" : "Pathogenic"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81259-4"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://human-phenotype-ontology.org",
"code" : "HP:0003002",
"display" : "Breast carcinoma"
},
{
"system" : "http://human-phenotype-ontology.org",
"code" : "HP:0100615",
"display" : "Ovarian neoplasm"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "93044-6"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/clinvar-evidence-level-custom-cs",
"code" : "2-star",
"display" : "2 star"
}
]
}
}
]
},
"request" : {
"method" : "PUT",
"url" : "Observation/mii-exa-molgen-diagnostische-implikation-brca1"
}
}
]
}