English

Generated Narrative: Patient mii-exa-molgen-patient-wes

Max Mustermann Male, DoB: 1970-01-01 ( https://www.medizininformatik-initiative.de/fhir/patient-ids#WES2024001)

English

Generated Narrative: Device mii-exa-molgen-device-illumina-novaseq

identifier: https://www.medizininformatik-initiative.de/fhir/sid/lab-devices/NOVASEQ-6000-SN12345

status: Active

manufacturer: Illumina Inc.

serialNumber: SN12345

DeviceNames

-NameType
*NovaSeq 6000 Sequencing SystemModel name

modelNumber: NovaSeq 6000

type: Medical laboratory analyzer

English

Generated Narrative: Device mii-exa-molgen-device-thermofisher-ionchef

identifier: https://www.medizininformatik-initiative.de/fhir/sid/lab-devices/IONCHEF-IC12345

status: Active

manufacturer: Thermo Fisher Scientific

serialNumber: IC12345

DeviceNames

-NameType
*Ion Chef SystemModel name

modelNumber: Ion Chef

type: Template preparation system (Ion Chef)

English

Generated Narrative: Specimen mii-exa-molgen-specimen-blood-edta-bundle

identifier: https://www.medizininformatik-initiative.de/fhir/sid/specimen-ids/EDTA-2024-001

type: Plasma specimen

subject: Max Mustermann Male, DoB: 1970-01-01 ( https://www.medizininformatik-initiative.de/fhir/patient-ids#WES2024001)

Collections

-Collected[x]
*2024-01-15 09:30:00+0100

Containers

-TypeCapacitySpecimenQuantity
*Evacuated blood collection tube with clot activator10 milliliter (Details: UCUM codemL = 'mL')10 milliliter (Details: UCUM codemL = 'mL')

English

Generated Narrative: Specimen mii-exa-molgen-specimen-dna-library-bundle

identifier: https://www.medizininformatik-initiative.de/fhir/sid/specimen-ids/LIB-2024-001

type: DNA Library

subject: Max Mustermann Male, DoB: 1970-01-01 ( https://www.medizininformatik-initiative.de/fhir/patient-ids#WES2024001)

parent: Specimen: identifier = https://www.medizininformatik-initiative.de/fhir/sid/specimen-ids#EDTA-2024-001; type = Plasma specimen

Processings

-DescriptionTime[x]
*DNA extraction and library preparation using Agilent SureSelect2024-01-16 14:00:00+0100

English

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
<type> <coding> <system value="http://terminology.hl7.org/CodeSystem/plan-definition-type"/> <code value="protocol"/> <display value="Protocol"/> </coding> </type> <status value="active"/> <description value="Target enrichment protocol for whole exome sequencing covering 35.8 Mb of the human exome"/> <action> <title value="DNA Fragmentation"/> <description value="Fragment genomic DNA to 150-200bp using Covaris"/> </action> <action> <title value="Library Preparation"/> <description value="End repair, A-tailing, adapter ligation"/> </action> <action> <title value="Hybridization"/> <description value="Hybridize with SureSelect baits for 24 hours at 65°C"/> </action> <action> <title value="Capture"/> <description value="Streptavidin bead capture and washing"/> </action> <action> <title value="Amplification"/> <description value="PCR amplification of captured library"/> </action> </PlanDefinition> </resource> <request> <method value="POST"/> <url value="PlanDefinition"/> </request> </entry> <entry> <fullUrl value="https://www.medizininformatik-initiative.de/fhir/DocumentReference/mii-exa-molgen-documentreference-bed-file-bundle"/> <resource> <DocumentReference> <id value="mii-exa-molgen-documentreference-bed-file-bundle"/> <text> <status value="generated"/><div xmlns="http://www.w3.org/1999/xhtml"><div xml:lang="en" lang="en"><hr/><p><b>English</b></p><hr/><a name="DocumentReference_mii-exa-molgen-documentreference-bed-file-bundle"> </a><p class="res-header-id"><b>Generated Narrative: DocumentReference mii-exa-molgen-documentreference-bed-file-bundle</b></p><a name="mii-exa-molgen-documentreference-bed-file-bundle"> </a><a name="hcmii-exa-molgen-documentreference-bed-file-bundle"> </a><p><b>status</b>: Current</p><p><b>type</b>: <span title="Codes:">BED file - Agilent SureSelect V7 target regions</span></p><p><b>subject</b>: <a href="Bundle-mii-exa-molgen-bundle-comprehensive-wes.html#Patient_mii-exa-molgen-patient-wes">Max Mustermann Male, DoB: 1970-01-01 ( https://www.medizininformatik-initiative.de/fhir/patient-ids#WES2024001)</a></p><blockquote><p><b>content</b></p><h3>Attachments</h3><table class="grid"><tr><td style="display: none">-</td><td><b>ContentType</b></td><td><b>Url</b></td><td><b>Title</b></td></tr><tr><td style="display: none">*</td><td>plain</td><td><a href="https://simplifier.net/resolve?scope=de.basisprofil.r4@1.6.0&canonical=https://www.medizininformatik-initiative.de/fhir/files/agilent_v7_targets.bed">https://www.medizininformatik-initiative.de/fhir/files/agilent_v7_targets.bed</a></td><td>Agilent SureSelect Human All Exon V7 Target Regions</td></tr></table></blockquote></div></div> </text> <status value="current"/> <type> <text value="BED file - Agilent SureSelect V7 target regions"/> </type> <subject> <reference value="Patient/mii-exa-molgen-patient-wes"/> </subject> <content> <attachment> <contentType value="text/plain"/> <url value="https://www.medizininformatik-initiative.de/fhir/files/agilent_v7_targets.bed"/> <title value="Agilent SureSelect Human All Exon V7 Target Regions"/> </attachment> </content> </DocumentReference> </resource> <request> <method value="POST"/> <url value="DocumentReference"/> </request> </entry> <entry> <fullUrl value="https://www.medizininformatik-initiative.de/fhir/DocumentReference/mii-exa-molgen-documentreference-fastq-bundle"/> <resource> <DocumentReference> <id value="mii-exa-molgen-documentreference-fastq-bundle"/> <text> <status value="generated"/><div xmlns="http://www.w3.org/1999/xhtml"><div xml:lang="en" lang="en"><hr/><p><b>English</b></p><hr/><a name="DocumentReference_mii-exa-molgen-documentreference-fastq-bundle"> </a><p class="res-header-id"><b>Generated Narrative: DocumentReference mii-exa-molgen-documentreference-fastq-bundle</b></p><a name="mii-exa-molgen-documentreference-fastq-bundle"> </a><a name="hcmii-exa-molgen-documentreference-fastq-bundle"> </a><p><b>status</b>: Current</p><p><b>type</b>: <span title="Codes:">FASTQ files - paired-end sequencing data</span></p><p><b>subject</b>: <a href="Bundle-mii-exa-molgen-bundle-comprehensive-wes.html#Patient_mii-exa-molgen-patient-wes">Max Mustermann Male, DoB: 1970-01-01 ( https://www.medizininformatik-initiative.de/fhir/patient-ids#WES2024001)</a></p><blockquote><p><b>content</b></p><h3>Attachments</h3><table class="grid"><tr><td style="display: none">-</td><td><b>ContentType</b></td><td><b>Url</b></td><td><b>Title</b></td></tr><tr><td style="display: none">*</td><td>gzip</td><td><a href="https://simplifier.net/resolve?scope=de.basisprofil.r4@1.6.0&canonical=https://www.medizininformatik-initiative.de/fhir/files/sample_R1.fastq.gz">https://www.medizininformatik-initiative.de/fhir/files/sample_R1.fastq.gz</a></td><td>Forward reads</td></tr></table></blockquote><blockquote><p><b>content</b></p><h3>Attachments</h3><table class="grid"><tr><td style="display: none">-</td><td><b>ContentType</b></td><td><b>Url</b></td><td><b>Title</b></td></tr><tr><td style="display: none">*</td><td>gzip</td><td><a href="https://simplifier.net/resolve?scope=de.basisprofil.r4@1.6.0&canonical=https://www.medizininformatik-initiative.de/fhir/files/sample_R2.fastq.gz">https://www.medizininformatik-initiative.de/fhir/files/sample_R2.fastq.gz</a></td><td>Reverse reads</td></tr></table></blockquote></div></div> </text> <status value="current"/> <type> <text value="FASTQ files - paired-end sequencing data"/> </type> <subject> <reference value="Patient/mii-exa-molgen-patient-wes"/> </subject> <content> <attachment> <contentType value="application/gzip"/> <url value="https://www.medizininformatik-initiative.de/fhir/files/sample_R1.fastq.gz"/> <title value="Forward reads"/> </attachment> </content> <content> <attachment> <contentType value="application/gzip"/> <url value="https://www.medizininformatik-initiative.de/fhir/files/sample_R2.fastq.gz"/> <title value="Reverse reads"/> </attachment> </content> </DocumentReference> </resource> <request> <method value="POST"/> <url value="DocumentReference"/> </request> </entry> <entry> <fullUrl value="https://www.medizininformatik-initiative.de/fhir/Procedure/mii-exa-molgen-genomic-study-comprehensive-wes-bundle"/> <resource> <Procedure> <id value="mii-exa-molgen-genomic-study-comprehensive-wes-bundle"/> <meta> <profile value="https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/mii-pr-molgen-genomic-study"/> <profile value="https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/genomic-study|2027.0.0-ballot.1"/> </meta> <text> <status value="extensions"/><div xmlns="http://www.w3.org/1999/xhtml"><div xml:lang="en" lang="en"><hr/><p><b>English</b></p><hr/><a name="Procedure_mii-exa-molgen-genomic-study-comprehensive-wes-bundle"> </a><p class="res-header-id"><b>Generated Narrative: Procedure mii-exa-molgen-genomic-study-comprehensive-wes-bundle</b></p><a name="mii-exa-molgen-genomic-study-comprehensive-wes-bundle"> </a><a name="hcmii-exa-molgen-genomic-study-comprehensive-wes-bundle"> </a><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px"/><p style="margin-bottom: 0px">Profiles: <a href="StructureDefinition-mii-pr-molgen-genomic-study.html">MII PR MolGen Genomic Study</a>, <a href="https://simplifier.net/resolve?scope=de.basisprofil.r4@1.6.0&canonical=https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/genomic-study|2027.0.0-ballot.1">https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/genomic-study|2027.0.0-ballot.1</a></p></div><p><b>Genomic Study Analysis Extension</b>: <a href="Procedure-mii-exa-molgen-genomic-study-analysis-wes-library-prep.html">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</a></p><p><b>Genomic Study Analysis Extension</b>: <a href="Procedure-mii-exa-molgen-genomic-study-analysis-wes-sequencing.html">Procedure: extension = ->Specimen: identifier = https://www.medizininformatik-initiative.de/fhir/sid/specimen-ids#LIB-2024-001; type = Saliva specimen,,Sequencing,,; status = completed; category = Laboratory</a></p><p><b>Genomic Study Analysis Extension</b>: <a href="Procedure-mii-exa-molgen-genomic-study-analysis-wes-bioinformatics.html">Procedure: extension = ,Computational analysis,; status = completed; category = Laboratory</a></p><p><b>status</b>: Completed</p><p><b>category</b>: <span title="Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span></p><p><b>subject</b>: <a href="Bundle-mii-exa-molgen-bundle-comprehensive-wes.html#Patient_mii-exa-molgen-patient-wes">Max Mustermann Male, DoB: 1970-01-01 ( https://www.medizininformatik-initiative.de/fhir/patient-ids#WES2024001)</a></p></div></div> </text> <extension url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-ext"> <valueReference> <reference value="Procedure/mii-exa-molgen-genomic-study-analysis-wes-library-prep"/> </valueReference> </extension> <extension url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-ext"> <valueReference> <reference value="Procedure/mii-exa-molgen-genomic-study-analysis-wes-sequencing"/> </valueReference> </extension> <extension url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-ext"> <valueReference> <reference value="Procedure/mii-exa-molgen-genomic-study-analysis-wes-bioinformatics"/> </valueReference> </extension> <status value="completed"/> <category> <coding> <system value="http://terminology.hl7.org/CodeSystem/observation-category"/> <code value="laboratory"/> </coding> </category> <subject> <reference value="Patient/mii-exa-molgen-patient-wes"/> </subject> </Procedure> </resource> <request> <method value="POST"/> <url value="Procedure"/> </request> </entry> <entry> <fullUrl value="https://www.medizininformatik-initiative.de/fhir/Procedure/mii-exa-molgen-genomic-study-analysis-wes-library-prep-bundle"/> <resource> <Procedure> <id value="mii-exa-molgen-genomic-study-analysis-wes-library-prep-bundle"/> <meta> <profile value="https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/mii-pr-molgen-genomic-study-analysis"/> <profile value="https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/genomic-study-analysis|2027.0.0-ballot.1"/> </meta> <text> <status value="extensions"/><div xmlns="http://www.w3.org/1999/xhtml"><div xml:lang="en" lang="en"><hr/><p><b>English</b></p><hr/><a name="Procedure_mii-exa-molgen-genomic-study-analysis-wes-library-prep-bundle"> </a><p class="res-header-id"><b>Generated Narrative: Procedure mii-exa-molgen-genomic-study-analysis-wes-library-prep-bundle</b></p><a name="mii-exa-molgen-genomic-study-analysis-wes-library-prep-bundle"> </a><a name="hcmii-exa-molgen-genomic-study-analysis-wes-library-prep-bundle"> </a><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px"/><p style="margin-bottom: 0px">Profiles: <a href="StructureDefinition-mii-pr-molgen-genomic-study-analysis.html">MII PR MolGen Genomic Study Analysis</a>, <a href="https://simplifier.net/resolve?scope=de.basisprofil.r4@1.6.0&canonical=https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/genomic-study-analysis|2027.0.0-ballot.1">https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/genomic-study-analysis|2027.0.0-ballot.1</a></p></div><p><b>Genomic Study Analysis Specimen</b>: <a href="Specimen-mii-exa-molgen-specimen-blood-edta.html">Specimen: identifier = https://www.medizininformatik-initiative.de/fhir/sid/specimen-ids#EDTA-2024-001; type = Plasma specimen</a></p><blockquote><p><b>Genomic Study Analysis Device</b></p><ul><li>device: <a href="Device-mii-exa-molgen-device-thermofisher-ionchef.html">Device: identifier = https://www.medizininformatik-initiative.de/fhir/sid/lab-devices#IONCHEF-IC12345; status = active; manufacturer = Thermo Fisher Scientific; serialNumber = IC12345; modelNumber = Ion Chef; type = </a></li></ul></blockquote><p><b>Genomic Study Analysis Method Type</b>: <span title="Codes:{http://loinc.org LA26810-4}">DNA hybridization</span></p><p><b>status</b>: Completed</p><p><b>category</b>: <span title="Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span></p><p><b>subject</b>: <a href="Bundle-mii-exa-molgen-bundle-comprehensive-wes.html#Patient_mii-exa-molgen-patient-wes">Max Mustermann Male, DoB: 1970-01-01 ( https://www.medizininformatik-initiative.de/fhir/patient-ids#WES2024001)</a></p></div></div> </text> <extension url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-specimen"> <valueReference> <reference value="Specimen/mii-exa-molgen-specimen-blood-edta"/> </valueReference> </extension> <extension url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-device"> <extension url="device"> <valueReference> <reference value="Device/mii-exa-molgen-device-thermofisher-ionchef"/> </valueReference> </extension> </extension> <extension url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-method-type"> <valueCodeableConcept> <coding> <system value="http://loinc.org"/> <code value="LA26810-4"/> <display value="DNA hybridization"/> </coding> </valueCodeableConcept> </extension> <status value="completed"/> <category> <coding> <system value="http://terminology.hl7.org/CodeSystem/observation-category"/> <code value="laboratory"/> </coding> </category> <subject> <reference value="Patient/mii-exa-molgen-patient-wes"/> </subject> </Procedure> </resource> <request> <method value="POST"/> <url value="Procedure"/> </request> </entry> <entry> <fullUrl value="https://www.medizininformatik-initiative.de/fhir/Procedure/mii-exa-molgen-genomic-study-analysis-wes-sequencing-bundle"/> <resource> <Procedure> <id value="mii-exa-molgen-genomic-study-analysis-wes-sequencing-bundle"/> <meta> <profile value="https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/mii-pr-molgen-genomic-study-analysis"/> <profile value="https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/genomic-study-analysis|2027.0.0-ballot.1"/> </meta> <text> <status value="extensions"/><div xmlns="http://www.w3.org/1999/xhtml"><div xml:lang="en" lang="en"><hr/><p><b>English</b></p><hr/><a name="Procedure_mii-exa-molgen-genomic-study-analysis-wes-sequencing-bundle"> </a><p class="res-header-id"><b>Generated Narrative: Procedure mii-exa-molgen-genomic-study-analysis-wes-sequencing-bundle</b></p><a name="mii-exa-molgen-genomic-study-analysis-wes-sequencing-bundle"> </a><a name="hcmii-exa-molgen-genomic-study-analysis-wes-sequencing-bundle"> </a><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px"/><p style="margin-bottom: 0px">Profiles: <a href="StructureDefinition-mii-pr-molgen-genomic-study-analysis.html">MII PR MolGen Genomic Study Analysis</a>, <a href="https://simplifier.net/resolve?scope=de.basisprofil.r4@1.6.0&canonical=https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/genomic-study-analysis|2027.0.0-ballot.1">https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/genomic-study-analysis|2027.0.0-ballot.1</a></p></div><p><b>Genomic Study Analysis Specimen</b>: <a href="Specimen-mii-exa-molgen-specimen-dna-library.html">Specimen: identifier = https://www.medizininformatik-initiative.de/fhir/sid/specimen-ids#LIB-2024-001; type = Saliva specimen</a></p><blockquote><p><b>Genomic Study Analysis Device</b></p><ul><li>device: <a href="Device-mii-exa-molgen-device-illumina-novaseq.html">Device: identifier = https://www.medizininformatik-initiative.de/fhir/sid/lab-devices#NOVASEQ-6000-SN12345; status = active; manufacturer = Illumina Inc.; serialNumber = SN12345; modelNumber = NovaSeq 6000; type = Medical laboratory analyzer</a></li></ul></blockquote><p><b>Genomic Study Analysis Method Type</b>: <span title="Codes:{http://loinc.org LA26398-0}">Sequencing</span></p><p><b>status</b>: Completed</p><p><b>category</b>: <span title="Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span></p><p><b>subject</b>: <a href="Bundle-mii-exa-molgen-bundle-comprehensive-wes.html#Patient_mii-exa-molgen-patient-wes">Max Mustermann Male, DoB: 1970-01-01 ( https://www.medizininformatik-initiative.de/fhir/patient-ids#WES2024001)</a></p></div></div> </text> <extension url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-specimen"> <valueReference> <reference value="Specimen/mii-exa-molgen-specimen-dna-library"/> </valueReference> </extension> <extension url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-device"> <extension url="device"> <valueReference> <reference value="Device/mii-exa-molgen-device-illumina-novaseq"/> </valueReference> </extension> </extension> <extension url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-method-type"> <valueCodeableConcept> <coding> <system value="http://loinc.org"/> <code value="LA26398-0"/> <display value="Sequencing"/> </coding> </valueCodeableConcept> </extension> <status value="completed"/> <category> <coding> <system value="http://terminology.hl7.org/CodeSystem/observation-category"/> <code value="laboratory"/> </coding> </category> <subject> <reference value="Patient/mii-exa-molgen-patient-wes"/> </subject> </Procedure> </resource> <request> <method value="POST"/> <url value="Procedure"/> </request> </entry> <entry> <fullUrl value="https://www.medizininformatik-initiative.de/fhir/Procedure/mii-exa-molgen-genomic-study-analysis-wes-bioinformatics-bundle"/> <resource> <Procedure> <id value="mii-exa-molgen-genomic-study-analysis-wes-bioinformatics-bundle"/> <meta> <profile value="https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/mii-pr-molgen-genomic-study-analysis"/> <profile value="https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/genomic-study-analysis|2027.0.0-ballot.1"/> </meta> <text> <status value="extensions"/><div xmlns="http://www.w3.org/1999/xhtml"><div xml:lang="en" lang="en"><hr/><p><b>English</b></p><hr/><a name="Procedure_mii-exa-molgen-genomic-study-analysis-wes-bioinformatics-bundle"> </a><p class="res-header-id"><b>Generated Narrative: Procedure mii-exa-molgen-genomic-study-analysis-wes-bioinformatics-bundle</b></p><a name="mii-exa-molgen-genomic-study-analysis-wes-bioinformatics-bundle"> </a><a name="hcmii-exa-molgen-genomic-study-analysis-wes-bioinformatics-bundle"> </a><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px"/><p style="margin-bottom: 0px">Profiles: <a href="StructureDefinition-mii-pr-molgen-genomic-study-analysis.html">MII PR MolGen Genomic Study Analysis</a>, <a href="https://simplifier.net/resolve?scope=de.basisprofil.r4@1.6.0&canonical=https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/genomic-study-analysis|2027.0.0-ballot.1">https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/genomic-study-analysis|2027.0.0-ballot.1</a></p></div><p><b>Genomic Study Analysis Method Type</b>: <span title="Codes:{http://loinc.org LA26811-2}">Computational analysis</span></p><p><b>status</b>: Completed</p><p><b>category</b>: <span title="Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span></p><p><b>subject</b>: <a href="Bundle-mii-exa-molgen-bundle-comprehensive-wes.html#Patient_mii-exa-molgen-patient-wes">Max Mustermann Male, DoB: 1970-01-01 ( https://www.medizininformatik-initiative.de/fhir/patient-ids#WES2024001)</a></p></div></div> </text> <extension url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-method-type"> <valueCodeableConcept> <coding> <system value="http://loinc.org"/> <code value="LA26811-2"/> <display value="Computational analysis"/> </coding> </valueCodeableConcept> </extension> <status value="completed"/> <category> <coding> <system value="http://terminology.hl7.org/CodeSystem/observation-category"/> <code value="laboratory"/> </coding> </category> <subject> <reference value="Patient/mii-exa-molgen-patient-wes"/> </subject> </Procedure> </resource> <request> <method value="POST"/> <url value="Procedure"/> </request> </entry> <entry> <fullUrl value="https://www.medizininformatik-initiative.de/fhir/ServiceRequest/mii-exa-molgen-anforderung-wes-bundle"/> <resource> <ServiceRequest> <id value="mii-exa-molgen-anforderung-wes-bundle"/> <meta> <profile value="https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/anforderung-genetischer-test|2027.0.0-ballot.1"/> </meta> <text> <status value="generated"/><div xmlns="http://www.w3.org/1999/xhtml"><div xml:lang="en" lang="en"><hr/><p><b>English</b></p><hr/><a name="ServiceRequest_mii-exa-molgen-anforderung-wes-bundle"> </a><p class="res-header-id"><b>Generated Narrative: ServiceRequest mii-exa-molgen-anforderung-wes-bundle</b></p><a name="mii-exa-molgen-anforderung-wes-bundle"> </a><a name="hcmii-exa-molgen-anforderung-wes-bundle"> </a><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px"/><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-mii-pr-molgen-anforderung-genetischer-test.html">MII PR MolGen Anforderung genetischer Test</a> version: 2027.0.0-ballot.1</p></div><p><b>status</b>: Completed</p><p><b>intent</b>: Order</p><p><b>code</b>: <span title="Codes:{http://loinc.org 86205-2}">Whole exome sequence analysis in Blood or Tissue by Molecular genetics method</span></p><p><b>subject</b>: <a href="Bundle-mii-exa-molgen-bundle-comprehensive-wes.html#Patient_mii-exa-molgen-patient-wes">Max Mustermann Male, DoB: 1970-01-01 ( https://www.medizininformatik-initiative.de/fhir/patient-ids#WES2024001)</a></p><p><b>authoredOn</b>: 2024-01-10</p><p><b>requester</b>: <a href="Bundle-mii-exa-molgen-bundle-comprehensive-wes.html#Practitioner_mii-exa-molgen-practitioner-bundle">Practitioner Anna Schmidt </a></p><p><b>reasonCode</b>: <span title="Codes:{http://snomed.info/sct 110359009}">Intellectual disability (disorder)</span></p></div></div> </text> <status value="completed"/> <intent value="order"/> <code> <coding> <system value="http://loinc.org"/> <code value="86205-2"/> <display value="Whole exome sequence analysis in Blood or Tissue by Molecular genetics method"/> </coding> </code> <subject> <reference value="Patient/mii-exa-molgen-patient-wes"/> </subject> <authoredOn value="2024-01-10"/> <requester> <reference value="Practitioner/mii-exa-molgen-practitioner-bundle"/> </requester> <reasonCode> <coding> <system value="http://snomed.info/sct"/> <code value="110359009"/> <display value="Intellectual disability (disorder)"/> </coding> </reasonCode> </ServiceRequest> </resource> <request> <method value="POST"/> <url value="ServiceRequest"/> </request> </entry> <entry> <fullUrl value="https://www.medizininformatik-initiative.de/fhir/Observation/mii-exa-molgen-variante-comprehensive-pathogenic-bundle"/> <resource> <Observation> <id value="mii-exa-molgen-variante-comprehensive-pathogenic-bundle"/> <meta> <profile value="https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/variante|2027.0.0-ballot.1"/> </meta> <text> <status value="generated"/><div xmlns="http://www.w3.org/1999/xhtml"><div xml:lang="en" lang="en"><hr/><p><b>English</b></p><hr/><a name="Observation_mii-exa-molgen-variante-comprehensive-pathogenic-bundle"> </a><p class="res-header-id"><b>Generated Narrative: Observation mii-exa-molgen-variante-comprehensive-pathogenic-bundle</b></p><a name="mii-exa-molgen-variante-comprehensive-pathogenic-bundle"> </a><a name="hcmii-exa-molgen-variante-comprehensive-pathogenic-bundle"> </a><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px"/><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-mii-pr-molgen-variante.html">MII PR MolGen Variante</a> version: 2027.0.0-ballot.1</p></div><p><b>status</b>: Final</p><p><b>category</b>: <span title="Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span>, <span title="Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}">Genetics</span></p><p><b>code</b>: <span title="Codes:{http://loinc.org 69548-6}">Genetic variant assessment</span></p><p><b>subject</b>: <a href="Bundle-mii-exa-molgen-bundle-comprehensive-wes.html#Patient_mii-exa-molgen-patient-wes">Max Mustermann Male, DoB: 1970-01-01 ( https://www.medizininformatik-initiative.de/fhir/patient-ids#WES2024001)</a></p><p><b>effective</b>: 2024-01-10</p><p><b>value</b>: <span title="Codes:{http://loinc.org LA9633-4}">Present</span></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48018-6}">Gene studied [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.genenames.org/geneId HGNC:7132}">KMT2A</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48004-6}">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NM_005933.3:c.3463C>T}">NM_005933.3:c.3463C>T</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48005-3}">Amino acid change (pHGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org p.(Arg1155Ter)}">p.(Arg1155Ter)</span></p></blockquote></div></div> </text> <status value="final"/> <category> <coding> <system value="http://terminology.hl7.org/CodeSystem/observation-category"/> <code value="laboratory"/> <display value="Laboratory"/> </coding> </category> <category> <coding> <system value="http://terminology.hl7.org/CodeSystem/v2-0074"/> <code value="GE"/> </coding> </category> <code> <coding> <system value="http://loinc.org"/> <code value="69548-6"/> <display value="Genetic variant assessment"/> </coding> </code> <subject> <reference value="Patient/mii-exa-molgen-patient-wes"/> </subject> <effectiveDateTime value="2024-01-10"/> <valueCodeableConcept> <coding> <system value="http://loinc.org"/> <code value="LA9633-4"/> <display value="Present"/> </coding> </valueCodeableConcept> <component> <code> <coding> <system value="http://loinc.org"/> <code value="48018-6"/> <display value="Gene studied [ID]"/> </coding> </code> <valueCodeableConcept> <coding> <system value="http://www.genenames.org/geneId"/> <code value="HGNC:7132"/> <display value="KMT2A"/> </coding> </valueCodeableConcept> </component> <component> <code> <coding> <system value="http://loinc.org"/> <code value="48004-6"/> <display value="DNA change (c.HGVS)"/> </coding> </code> <valueCodeableConcept> <coding> <system value="http://varnomen.hgvs.org"/> <code value="NM_005933.3:c.3463C>T"/> <display value="NM_005933.3:c.3463C>T"/> </coding> </valueCodeableConcept> </component> <component> <code> <coding> <system value="http://loinc.org"/> <code value="48005-3"/> <display value="Amino acid change (pHGVS)"/> </coding> </code> <valueCodeableConcept> <coding> <system value="http://varnomen.hgvs.org"/> <code value="p.(Arg1155Ter)"/> <display value="p.(Arg1155Ter)"/> </coding> </valueCodeableConcept> </component> </Observation> </resource> <request> <method value="POST"/> <url value="Observation"/> </request> </entry> <entry> <fullUrl value="https://www.medizininformatik-initiative.de/fhir/Observation/mii-exa-molgen-diagnostische-implikation-comprehensive-bundle"/> <resource> <Observation> <id value="mii-exa-molgen-diagnostische-implikation-comprehensive-bundle"/> <meta> <profile value="https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/diagnostische-implikation|2027.0.0-ballot.1"/> </meta> <text> <status value="generated"/><div xmlns="http://www.w3.org/1999/xhtml"><div xml:lang="en" lang="en"><hr/><p><b>English</b></p><hr/><a name="Observation_mii-exa-molgen-diagnostische-implikation-comprehensive-bundle"> </a><p class="res-header-id"><b>Generated Narrative: Observation mii-exa-molgen-diagnostische-implikation-comprehensive-bundle</b></p><a name="mii-exa-molgen-diagnostische-implikation-comprehensive-bundle"> </a><a name="hcmii-exa-molgen-diagnostische-implikation-comprehensive-bundle"> </a><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px"/><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-mii-pr-molgen-diagnostische-implikation.html">MII PR MolGen Diagnostische Implikation</a> version: 2027.0.0-ballot.1</p></div><p><b>status</b>: Final</p><p><b>category</b>: <span title="Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}">Laboratory</span>, <span title="Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}">Genetics</span></p><p><b>code</b>: <span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}">Diagnostic Implication</span></p><p><b>subject</b>: <a href="Bundle-mii-exa-molgen-bundle-comprehensive-wes.html#Patient_mii-exa-molgen-patient-wes">Max Mustermann Male, DoB: 1970-01-01 ( https://www.medizininformatik-initiative.de/fhir/patient-ids#WES2024001)</a></p><p><b>effective</b>: 2024-01-10</p><p><b>derivedFrom</b>: <a href="Observation-mii-exa-molgen-variante-comprehensive-pathogenic.html">Observation Genetic variant assessment</a></p><h3>Components</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td style="display: none">*</td><td><span title="Codes:{http://loinc.org 53037-8}">Genetic variation clinical significance [Imp]</span></td><td><span title="Codes:{http://loinc.org LA6668-3}">Pathogenic</span></td></tr></table></div></div> </text> <status value="final"/> <category> <coding> <system value="http://terminology.hl7.org/CodeSystem/observation-category"/> <code value="laboratory"/> <display value="Laboratory"/> </coding> </category> <category> <coding> <system value="http://terminology.hl7.org/CodeSystem/v2-0074"/> <code value="GE"/> </coding> </category> <code> <coding> <system value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/> <code value="diagnostic-implication"/> <display value="Diagnostic Implication"/> </coding> </code> <subject> <reference value="Patient/mii-exa-molgen-patient-wes"/> </subject> <effectiveDateTime value="2024-01-10"/> <derivedFrom> <reference value="Observation/mii-exa-molgen-variante-comprehensive-pathogenic"/> </derivedFrom> <component> <code> <coding> <system value="http://loinc.org"/> <code value="53037-8"/> </coding> </code> <valueCodeableConcept> <coding> <system value="http://loinc.org"/> <code value="LA6668-3"/> <display value="Pathogenic"/> </coding> </valueCodeableConcept> </component> </Observation> </resource> <request> <method value="POST"/> <url value="Observation"/> </request> </entry> <entry> <fullUrl value="https://www.medizininformatik-initiative.de/fhir/Media/mii-exa-molgen-media-coverage-plot"/> <resource> <Media> <id value="mii-exa-molgen-media-coverage-plot"/> <text> <status value="generated"/><div xmlns="http://www.w3.org/1999/xhtml"><div xml:lang="en" lang="en"><hr/><p><b>English</b></p><hr/><a name="Media_mii-exa-molgen-media-coverage-plot"> </a><p class="res-header-id"><b>Generated Narrative: Media mii-exa-molgen-media-coverage-plot</b></p><a name="mii-exa-molgen-media-coverage-plot"> </a><a name="hcmii-exa-molgen-media-coverage-plot"> </a><p><b>status</b>: Completed</p><p><b>type</b>: <span title="Codes:{http://terminology.hl7.org/CodeSystem/media-type image}">Image</span></p><p><b>subject</b>: <a href="Patient-mii-exa-molgen-patient.html">Maja Julia Van-der-Dussen (official) Female, DoB: 1968-09-19 ( Medical record number (use: usual, ))</a></p><p><b>created</b>: 2024-01-20 10:00:00+0100</p><h3>Contents</h3><table class="grid"><tr><td style="display: none">-</td><td><b>ContentType</b></td><td><b>Url</b></td><td><b>Title</b></td></tr><tr><td style="display: none">*</td><td>png</td><td><a href="https://simplifier.net/resolve?scope=de.basisprofil.r4@1.6.0&canonical=https://www.medizininformatik-initiative.de/fhir/plots/coverage_wes_2024001.png">https://www.medizininformatik-initiative.de/fhir/plots/coverage_wes_2024001.png</a></td><td>Exome Coverage Distribution Plot</td></tr></table></div></div> </text> <status value="completed"/> <type> <coding> <system value="http://terminology.hl7.org/CodeSystem/media-type"/> <code value="image"/> <display value="Image"/> </coding> </type> <subject> <reference value="Patient/mii-exa-molgen-patient"/> </subject> <createdDateTime value="2024-01-20T10:00:00+01:00"/> <content> <contentType value="image/png"/> <url value="https://www.medizininformatik-initiative.de/fhir/plots/coverage_wes_2024001.png"/> <title value="Exome Coverage Distribution Plot"/> </content> </Media> </resource> <request> <method value="POST"/> <url value="Media"/> </request> </entry> <entry> <fullUrl value="https://www.medizininformatik-initiative.de/fhir/DiagnosticReport/mii-exa-molgen-befundbericht-comprehensive-wes-bundle"/> <resource> <DiagnosticReport> <id value="mii-exa-molgen-befundbericht-comprehensive-wes-bundle"/> <meta> <profile value="https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/molekulargenetischer-befundbericht|2027.0.0-ballot.1"/> <profile value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report|3.0.0"/> </meta> <text> <status value="generated"/><div xmlns="http://www.w3.org/1999/xhtml"><div xml:lang="en" lang="en"><hr/><p><b>English</b></p><hr/><a name="DiagnosticReport_mii-exa-molgen-befundbericht-comprehensive-wes-bundle"> </a><p class="res-header-id"><b>Generated Narrative: DiagnosticReport mii-exa-molgen-befundbericht-comprehensive-wes-bundle</b></p><a name="mii-exa-molgen-befundbericht-comprehensive-wes-bundle"> </a><a name="hcmii-exa-molgen-befundbericht-comprehensive-wes-bundle"> </a><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px"/><p style="margin-bottom: 0px">Profiles: <a href="StructureDefinition-mii-pr-molgen-molekulargenetischer-befundbericht.html">MII PR MolGen Molekulargenetischer Befundbericht</a> version: 2027.0.0-ballot.1, <a href="http://hl7.org/fhir/uv/genomics-reporting/STU3/StructureDefinition-genomic-report.html">Genomic Report</a> version: 3.0.0</p></div><h2><span title="Codes:{http://loinc.org 51969-4}">Genetic analysis report</span> (<span title="Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}">Genetics</span>) </h2><table class="grid"><tr><td>Subject</td><td>Max Mustermann Male, DoB: 1970-01-01 ( https://www.medizininformatik-initiative.de/fhir/patient-ids#WES2024001)</td></tr><tr><td>Performer</td><td> <a href="Practitioner-mii-exa-molgen-practitioner-lab.html">Practitioner Dr. Daniel Schmidt(official)</a></td></tr></table><p><b>Report Details</b></p><table class="grid"><tr><td><b>Code</b></td><td><b>Value</b></td><td><b>Flags</b></td><td><b>Relevant Time</b></td></tr><tr><td><a href="Observation-mii-exa-molgen-variante-comprehensive-pathogenic.html"><span title="Codes:{http://loinc.org 69548-6}">Genetic variant assessment</span></a></td><td><span title="Codes:{http://loinc.org LA9633-4}">Present</span></td><td>Final</td><td>2024-01-10</td></tr><tr><td><a href="Observation-mii-exa-molgen-diagnostische-implikation-comprehensive.html"><span title="Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}">Diagnostic Implication</span></a></td><td/><td>Final</td><td>2024-01-10</td></tr></table><p>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.</p><p><b>Coded Conclusions:</b></p><ul><li><span title="Codes:{http://loinc.org LA6576-8}">Positive</span></li></ul></div></div> </text> <extension url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-reference"> <valueReference> <reference value="Procedure/mii-exa-molgen-genomic-study-comprehensive-wes"/> </valueReference> </extension> <basedOn> <reference value="ServiceRequest/mii-exa-molgen-anforderung-wes"/> </basedOn> <status value="final"/> <category> <coding> <system value="http://terminology.hl7.org/CodeSystem/v2-0074"/> <code value="GE"/> <display value="Genetics"/> </coding> </category> <code> <coding> <system value="http://loinc.org"/> <code value="51969-4"/> <display value="Genetic analysis report"/> </coding> </code> <subject> <reference value="Patient/mii-exa-molgen-patient-wes"/> </subject> <performer> <reference value="Practitioner/mii-exa-molgen-practitioner-lab"/> </performer> <specimen> <reference value="Specimen/mii-exa-molgen-specimen-blood-edta"/> </specimen> <result> <reference value="Observation/mii-exa-molgen-variante-comprehensive-pathogenic"/> </result> <result> <reference value="Observation/mii-exa-molgen-diagnostische-implikation-comprehensive"/> </result> <media> <comment value="Coverage plot showing uniform coverage across all exons"/> <link> <reference value="Media/mii-exa-molgen-media-coverage-plot"/> </link> </media> <conclusion value="Whole exome sequencing identified a pathogenic de novo variant in the KMT2A gene, consistent with Wiedemann-Steiner syndrome. 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