MII Implementierungsleitfaden Kerndatensatz-Modul Molekulargenetischer Befundbericht
2027.0.0-ballot.1 -
Germany
MII Implementierungsleitfaden Kerndatensatz-Modul Molekulargenetischer Befundbericht
2027.0.0-ballot.1 -
Germany
MII IG Kerndatensatz-Modul Molekulargenetischer Befundbericht - Downloaded Version 2027.0.0-ballot.1 See the Directory of published versions
Language: de
Bundle mii-exa-molgen-bundle-comprehensive-wes of type transaction
Entry 1 - fullUrl = https://www.medizininformatik-initiative.de/fhir/Patient/mii-exa-molgen-patient-wes
Resource Patient:
Language: de
Max Mustermann Male, DoB: 1970-01-01 ( https://www.medizininformatik-initiative.de/fhir/patient-ids#WES2024001)
Request:
POST Patient
Entry 2 - fullUrl = https://www.medizininformatik-initiative.de/fhir/Device/mii-exa-molgen-device-illumina-novaseq
Resource Device:
Language: de
identifier:
https://www.medizininformatik-initiative.de/fhir/sid/lab-devices/NOVASEQ-6000-SN12345status: Active
manufacturer: Illumina Inc.
serialNumber: SN12345
modelNumber: NovaSeq 6000
type: Medical laboratory analyzer
Request:
POST Device
Entry 3 - fullUrl = https://www.medizininformatik-initiative.de/fhir/Device/mii-exa-molgen-device-thermofisher-ionchef
Resource Device:
Language: de
identifier:
https://www.medizininformatik-initiative.de/fhir/sid/lab-devices/IONCHEF-IC12345status: Active
manufacturer: Thermo Fisher Scientific
serialNumber: IC12345
modelNumber: Ion Chef
type: Template preparation system (Ion Chef)
Request:
POST Device
Entry 4 - fullUrl = https://www.medizininformatik-initiative.de/fhir/Specimen/mii-exa-molgen-specimen-blood-edta-bundle
Resource Specimen:
Language: de
identifier:
https://www.medizininformatik-initiative.de/fhir/sid/specimen-ids/EDTA-2024-001type: Plasma specimen
Collections
Collected[x] 2024-01-15 09:30:00+0100 container
Request:
POST Specimen
Entry 5 - fullUrl = https://www.medizininformatik-initiative.de/fhir/Specimen/mii-exa-molgen-specimen-dna-library-bundle
Resource Specimen:
Language: de
identifier:
https://www.medizininformatik-initiative.de/fhir/sid/specimen-ids/LIB-2024-001type: DNA Library
Processings
Description Time[x] DNA extraction and library preparation using Agilent SureSelect 2024-01-16 14:00:00+0100
Request:
POST Specimen
Entry 6 - fullUrl = https://www.medizininformatik-initiative.de/fhir/PlanDefinition/mii-exa-molgen-protocol-agilent-sureselect
Resource PlanDefinition:
Id: mii-exa-molgen-protocol-agilent-sureselect Title: Agilent SureSelect Human All Exon V7 Kit Protocol Type: system: http://terminology.hl7.org/CodeSystem/plan-definition-type
code: protocol
display: Protocol
Description: Target enrichment protocol for whole exome sequencing covering 35.8 Mb of the human exome Actions:
DNA Fragmentation: Fragment genomic DNA to 150-200bp using Covaris
Library Preparation: End repair, A-tailing, adapter ligation
Hybridization: Hybridize with SureSelect baits for 24 hours at 65°C
Capture: Streptavidin bead capture and washing
Amplification: PCR amplification of captured library
Request:
POST PlanDefinition
Entry 7 - fullUrl = https://www.medizininformatik-initiative.de/fhir/DocumentReference/mii-exa-molgen-documentreference-bed-file-bundle
Resource DocumentReference:
Language: de
status: Current
type: BED file - Agilent SureSelect V7 target regions
content
Attachments
ContentType Url Title text/plain https://www.medizininformatik-initiative.de/fhir/files/agilent_v7_targets.bed Agilent SureSelect Human All Exon V7 Target Regions
Request:
POST DocumentReference
Entry 8 - fullUrl = https://www.medizininformatik-initiative.de/fhir/DocumentReference/mii-exa-molgen-documentreference-fastq-bundle
Resource DocumentReference:
Language: de
status: Current
type: FASTQ files - paired-end sequencing data
content
Attachments
ContentType Url Title application/gzip https://www.medizininformatik-initiative.de/fhir/files/sample_R1.fastq.gz Forward reads content
Attachments
ContentType Url Title application/gzip https://www.medizininformatik-initiative.de/fhir/files/sample_R2.fastq.gz Reverse reads
Request:
POST DocumentReference
Entry 9 - fullUrl = https://www.medizininformatik-initiative.de/fhir/Procedure/mii-exa-molgen-genomic-study-comprehensive-wes-bundle
Resource Procedure:
Language: de
Profiles: MII PR MolGen Genomic Study, https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/genomic-study|2027.0.0-ballot.1
Genomic Study Analysis Extension: Procedure: extension = ->Specimen: identifier = https://www.medizininformatik-initiative.de/fhir/sid/specimen-ids#EDTA-2024-001; type = Plasma specimen,,DNA hybridization; status = completed; category = Laboratory
Genomic Study Analysis Extension: Procedure: extension = ->Specimen: identifier = https://www.medizininformatik-initiative.de/fhir/sid/specimen-ids#LIB-2024-001; type = Saliva specimen,,Sequencing,,; status = completed; category = Laboratory
Genomic Study Analysis Extension: Procedure: extension = ,Computational analysis,; status = completed; category = Laboratory
status: Completed
category: Laboratory
Request:
POST Procedure
Entry 10 - fullUrl = https://www.medizininformatik-initiative.de/fhir/Procedure/mii-exa-molgen-genomic-study-analysis-wes-library-prep-bundle
Resource Procedure:
Language: de
Profiles: MII PR MolGen Genomic Study Analysis, https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/genomic-study-analysis|2027.0.0-ballot.1
Genomic Study Analysis Specimen: Specimen: identifier = https://www.medizininformatik-initiative.de/fhir/sid/specimen-ids#EDTA-2024-001; type = Plasma specimen
Genomic Study Analysis Device
Genomic Study Analysis Method Type: DNA hybridization
status: Completed
category: Laboratory
Request:
POST Procedure
Entry 11 - fullUrl = https://www.medizininformatik-initiative.de/fhir/Procedure/mii-exa-molgen-genomic-study-analysis-wes-sequencing-bundle
Resource Procedure:
Language: de
Profiles: MII PR MolGen Genomic Study Analysis, https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/genomic-study-analysis|2027.0.0-ballot.1
Genomic Study Analysis Specimen: Specimen: identifier = https://www.medizininformatik-initiative.de/fhir/sid/specimen-ids#LIB-2024-001; type = Saliva specimen
Genomic Study Analysis Device
Genomic Study Analysis Method Type: Sequencing
status: Completed
category: Laboratory
Request:
POST Procedure
Entry 12 - fullUrl = https://www.medizininformatik-initiative.de/fhir/Procedure/mii-exa-molgen-genomic-study-analysis-wes-bioinformatics-bundle
Resource Procedure:
Language: de
Profiles: MII PR MolGen Genomic Study Analysis, https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/genomic-study-analysis|2027.0.0-ballot.1
Genomic Study Analysis Method Type: Computational analysis
status: Completed
category: Laboratory
Request:
POST Procedure
Entry 13 - fullUrl = https://www.medizininformatik-initiative.de/fhir/ServiceRequest/mii-exa-molgen-anforderung-wes-bundle
Resource ServiceRequest:
Language: de
Profile: MII PR MolGen Anforderung genetischer Test version: 2027.0.0-ballot.1
status: Completed
intent: Order
code: No display for ServiceRequest.code (concept: Whole exome sequence analysis in Blood or Tissue by Molecular genetics method)
authoredOn: 2024-01-10
requester: Practitioner Anna Schmidt
Request:
POST ServiceRequest
Entry 14 - fullUrl = https://www.medizininformatik-initiative.de/fhir/Observation/mii-exa-molgen-variante-comprehensive-pathogenic-bundle
Resource Observation:
Language: de
Profile: MII PR MolGen Variante version: 2027.0.0-ballot.1
status: Final
category: Laboratory, Genetics
code: Genetic variant assessment
effective: 2024-01-10
value: Present
component
code: Gene studied [ID]
value: KMT2A
component
code: DNA change (c.HGVS)
value: NM_005933.3:c.3463C>T
component
code: Amino acid change (pHGVS)
value: p.(Arg1155Ter)
Request:
POST Observation
Entry 15 - fullUrl = https://www.medizininformatik-initiative.de/fhir/Observation/mii-exa-molgen-diagnostische-implikation-comprehensive-bundle
Resource Observation:
Language: de
Profile: MII PR MolGen Diagnostische Implikation version: 2027.0.0-ballot.1
status: Final
category: Laboratory, Genetics
code: Diagnostic Implication
effective: 2024-01-10
derivedFrom: Observation Genetic variant assessment
Components
Code Value[x] Genetic variation clinical significance [Imp] Pathogenic
Request:
POST Observation
Entry 16 - fullUrl = https://www.medizininformatik-initiative.de/fhir/Media/mii-exa-molgen-media-coverage-plot
Resource DocumentReference:
Language: de
Request:
POST Media
Entry 17 - fullUrl = https://www.medizininformatik-initiative.de/fhir/DiagnosticReport/mii-exa-molgen-befundbericht-comprehensive-wes-bundle
Resource DiagnosticReport:
Language: de
Profiles: MII PR MolGen Molekulargenetischer Befundbericht version: 2027.0.0-ballot.1, Genomic Report version: 3.0.0
Genetic analysis report (Genetics)
Subject Max Mustermann Male, DoB: 1970-01-01 ( https://www.medizininformatik-initiative.de/fhir/patient-ids#WES2024001) Performer Practitioner Dr. Daniel Schmidt(official) Report Details
Code Value Flags Relevant Time Genetic variant assessment Present Final 2024-01-10 Diagnostic Implication Final 2024-01-10 Whole exome sequencing identified a pathogenic de novo variant in the KMT2A gene, consistent with Wiedemann-Steiner syndrome. Technical quality metrics met all acceptance criteria.
Coded Conclusions:
- Positive
Request:
POST DiagnosticReport
Entry 18 - fullUrl = https://www.medizininformatik-initiative.de/fhir/Practitioner/mii-exa-molgen-practitioner-bundle
Resource Practitioner:
Language: de
identifier:
https://www.medizininformatik-initiative.de/fhir/sid/practitioner-ids/12345name: Anna Schmidt
Request:
POST Practitioner
Entry 19 - fullUrl = https://www.medizininformatik-initiative.de/fhir/Practitioner/mii-exa-molgen-practitioner-lab-bundle
Resource Practitioner:
Language: de
identifier:
https://www.medizininformatik-initiative.de/fhir/sid/practitioner-ids/67890name: Thomas Weber
Request:
POST Practitioner