MII Implementierungsleitfaden Kerndatensatz-Modul Molekulargenetischer Befundbericht
2027.0.0-ballot.1 -
Germany
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. For a full list of available versions, see the Directory of published versions
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<id value="mii-exa-molgen-bundle-comprehensive-wes"/>
<language value="de"/>
<type value="transaction"/>
<timestamp value="2024-01-20T10:00:00+01:00"/>
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<fullUrl
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<resource>
<Patient>
<id value="mii-exa-molgen-patient-wes"/>
<language value="de"/>
<text>
<status value="generated"/>
</text>
<identifier>
<system
value="https://www.medizininformatik-initiative.de/fhir/patient-ids"/>
<value value="WES2024001"/>
</identifier>
<name>
<family value="Mustermann"/>
<given value="Max"/>
</name>
<gender value="male"/>
<birthDate value="1970-01-01"/>
</Patient>
</resource>
<request>
<method value="POST"/>
<url value="Patient"/>
</request>
</entry>
<entry>
<fullUrl
value="https://www.medizininformatik-initiative.de/fhir/Device/mii-exa-molgen-device-illumina-novaseq"/>
<resource>
<Device>
<id value="mii-exa-molgen-device-illumina-novaseq"/>
<language value="de"/>
<text>
<status value="generated"/>
</text>
<identifier>
<system
value="https://www.medizininformatik-initiative.de/fhir/sid/lab-devices"/>
<value value="NOVASEQ-6000-SN12345"/>
</identifier>
<status value="active"/>
<manufacturer value="Illumina Inc."/>
<serialNumber value="SN12345"/>
<deviceName>
<name value="NovaSeq 6000 Sequencing System"/>
<type value="model-name"/>
</deviceName>
<modelNumber value="NovaSeq 6000"/>
<type>
<coding>
<system value="http://snomed.info/sct"/>
<code value="30234008"/>
<display value="Medical laboratory analyzer"/>
</coding>
</type>
</Device>
</resource>
<request>
<method value="POST"/>
<url value="Device"/>
</request>
</entry>
<entry>
<fullUrl
value="https://www.medizininformatik-initiative.de/fhir/Device/mii-exa-molgen-device-thermofisher-ionchef"/>
<resource>
<Device>
<id value="mii-exa-molgen-device-thermofisher-ionchef"/>
<language value="de"/>
<text>
<status value="generated"/>
</text>
<identifier>
<system
value="https://www.medizininformatik-initiative.de/fhir/sid/lab-devices"/>
<value value="IONCHEF-IC12345"/>
</identifier>
<status value="active"/>
<manufacturer value="Thermo Fisher Scientific"/>
<serialNumber value="IC12345"/>
<deviceName>
<name value="Ion Chef System"/>
<type value="model-name"/>
</deviceName>
<modelNumber value="Ion Chef"/>
<type>
<text value="Template preparation system (Ion Chef)"/>
</type>
</Device>
</resource>
<request>
<method value="POST"/>
<url value="Device"/>
</request>
</entry>
<entry>
<fullUrl
value="https://www.medizininformatik-initiative.de/fhir/Specimen/mii-exa-molgen-specimen-blood-edta-bundle"/>
<resource>
<Specimen>
<id value="mii-exa-molgen-specimen-blood-edta-bundle"/>
<language value="de"/>
<text>
<status value="generated"/>
</text>
<identifier>
<system
value="https://www.medizininformatik-initiative.de/fhir/sid/specimen-ids"/>
<value value="EDTA-2024-001"/>
</identifier>
<type>
<coding>
<system value="http://snomed.info/sct"/>
<code value="119361006"/>
<display value="Plasma specimen"/>
</coding>
</type>
<subject>
<reference value="Patient/mii-exa-molgen-patient-wes"/>
</subject>
<collection>
<collectedDateTime value="2024-01-15T09:30:00+01:00"/>
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<container>
<type>
<coding>
<system value="http://snomed.info/sct"/>
<code value="767384004"/>
<display
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</coding>
</type>
<capacity>
<value value="10"/>
<unit value="milliliter"/>
<system value="http://unitsofmeasure.org"/>
<code value="mL"/>
</capacity>
<specimenQuantity>
<value value="10"/>
<unit value="milliliter"/>
<system value="http://unitsofmeasure.org"/>
<code value="mL"/>
</specimenQuantity>
</container>
</Specimen>
</resource>
<request>
<method value="POST"/>
<url value="Specimen"/>
</request>
</entry>
<entry>
<fullUrl
value="https://www.medizininformatik-initiative.de/fhir/Specimen/mii-exa-molgen-specimen-dna-library-bundle"/>
<resource>
<Specimen>
<id value="mii-exa-molgen-specimen-dna-library-bundle"/>
<language value="de"/>
<text>
<status value="generated"/>
</text>
<identifier>
<system
value="https://www.medizininformatik-initiative.de/fhir/sid/specimen-ids"/>
<value value="LIB-2024-001"/>
</identifier>
<type>
<coding>
<system value="http://snomed.info/sct"/>
<code value="119342007"/>
<display value="Saliva specimen"/>
</coding>
<text value="DNA Library"/>
</type>
<subject>
<reference value="Patient/mii-exa-molgen-patient-wes"/>
</subject>
<parent>🔗
<reference value="Specimen/mii-exa-molgen-specimen-blood-edta"/>
</parent>
<processing>
<description
value="DNA extraction and library preparation using Agilent SureSelect"/>
<timeDateTime value="2024-01-16T14:00:00+01:00"/>
</processing>
</Specimen>
</resource>
<request>
<method value="POST"/>
<url value="Specimen"/>
</request>
</entry>
<entry>
<fullUrl
value="https://www.medizininformatik-initiative.de/fhir/PlanDefinition/mii-exa-molgen-protocol-agilent-sureselect"/>
<resource>
<PlanDefinition>
<id value="mii-exa-molgen-protocol-agilent-sureselect"/>
<language value="de"/>
<text>
<status value="extensions"/>
<div xml:lang="en" lang="en"><hr/><p><b>English</b></p><hr/><a name="PlanDefinition_mii-exa-molgen-protocol-agilent-sureselect"> </a>
<div>
<table class="grid dict">
<tr>
<th scope="row"><b>Id: </b></th>
<td style="padding-left: 4px;">mii-exa-molgen-protocol-agilent-sureselect</td>
</tr>
<tr>
<th scope="row"><b>Title: </b></th>
<td style="padding-left: 4px;">Agilent SureSelect Human All Exon V7 Kit Protocol</td>
</tr>
<tr>
<th scope="row"><b>Type: </b></th>
<td style="padding-left: 4px;">
<p style="margin-bottom: 5px;">
<b>system: </b> <span><a href="http://terminology.hl7.org/7.3.0/CodeSystem-plan-definition-type.html">http://terminology.hl7.org/CodeSystem/plan-definition-type</a></span>
</p>
<p style="margin-bottom: 5px;">
<b>code: </b> <span>protocol</span>
</p>
<p style="margin-bottom: 5px;">
<b>display: </b> <span>Protocol</span>
</p>
</td>
</tr>
<tr>
<th scope="row"><b>Description: </b></th>
<td style="padding-left: 4px;"><div><p>Target enrichment protocol for whole exome sequencing covering 35.8 Mb of the human exome</p>
</div></td>
</tr>
<tr>
<th scope="row"><b>Actions: </b></th>
<td style="padding-left: 4px;">
<table class="grid-dict">
<tr>
<td>
<b> DNA Fragmentation:</b> Fragment genomic DNA to 150-200bp using Covaris
<br/>
</td>
</tr>
<tr>
<td>
<b> Library Preparation:</b> End repair, A-tailing, adapter ligation
<br/>
</td>
</tr>
<tr>
<td>
<b> Hybridization:</b> Hybridize with SureSelect baits for 24 hours at 65°C
<br/>
</td>
</tr>
<tr>
<td>
<b> Capture:</b> Streptavidin bead capture and washing
<br/>
</td>
</tr>
<tr>
<td>
<b> Amplification:</b> PCR amplification of captured library
<br/>
</td>
</tr>
</table>
</td>
</tr>
</table>
</div>
</div>
</text>
<name value="AgilentSureSelectV7"/>
<title value="Agilent SureSelect Human All Exon V7 Kit Protocol"/>
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<display value="Protocol"/>
</coding>
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<status value="active"/>
<description
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<action>
<title value="DNA Fragmentation"/>
<description
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</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"/>
<language value="de"/>
<text>
<status value="generated"/>
</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"/>
<language value="de"/>
<text>
<status value="generated"/>
</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>
<language value="de"/>
<text>
<status value="extensions"/>
</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
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<profile
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</meta>
<language value="de"/>
<text>
<status value="extensions"/>
</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
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<profile
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</meta>
<language value="de"/>
<text>
<status value="extensions"/>
</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>
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<status value="completed"/>
<category>
<coding>
<system
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<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
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<Procedure>
<id
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<meta>
<profile
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</meta>
<language value="de"/>
<text>
<status value="extensions"/>
</text>
<extension
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<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA26811-2"/>
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<category>
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<subject>
<reference value="Patient/mii-exa-molgen-patient-wes"/>
</subject>
</Procedure>
</resource>
<request>
<method value="POST"/>
<url value="Procedure"/>
</request>
</entry>
<entry>
<fullUrl
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<resource>
<ServiceRequest>
<id value="mii-exa-molgen-anforderung-wes-bundle"/>
<meta>
<profile
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</meta>
<language value="de"/>
<text>
<status value="generated"/>
</text>
<status value="completed"/>
<intent value="order"/>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="86205-2"/>
<display
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</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
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</meta>
<language value="de"/>
<text>
<status value="generated"/>
</text>
<status value="final"/>
<category>
<coding>
<system
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<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)"/>
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<valueCodeableConcept>
<coding>
<system value="http://varnomen.hgvs.org"/>
<code value="NM_005933.3:c.3463C>T"/>
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<component>
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<system value="http://loinc.org"/>
<code value="48005-3"/>
<display value="Amino acid change (pHGVS)"/>
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<coding>
<system value="http://varnomen.hgvs.org"/>
<code value="p.(Arg1155Ter)"/>
<display value="p.(Arg1155Ter)"/>
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</Observation>
</resource>
<request>
<method value="POST"/>
<url value="Observation"/>
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</entry>
<entry>
<fullUrl
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<resource>
<Observation>
<id
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<meta>
<profile
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<code value="GE"/>
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<code>
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<system
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<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"/>
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<component>
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<system value="http://loinc.org"/>
<code value="53037-8"/>
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<coding>
<system value="http://loinc.org"/>
<code value="LA6668-3"/>
<display value="Pathogenic"/>
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</Observation>
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<method value="POST"/>
<url value="Observation"/>
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</entry>
<entry>
<fullUrl
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<id value="mii-exa-molgen-media-coverage-plot"/>
<language value="de"/>
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<status value="completed"/>
<type>
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<system value="http://terminology.hl7.org/CodeSystem/media-type"/>
<code value="image"/>
<display value="Image"/>
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<subject>🔗
<reference value="Patient/mii-exa-molgen-patient"/>
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<createdDateTime value="2024-01-20T10:00:00+01:00"/>
<content>
<contentType value="image/png"/>
<url
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<title value="Exome Coverage Distribution Plot"/>
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</Media>
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<request>
<method value="POST"/>
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<fullUrl
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<meta>
<profile
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<language value="de"/>
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<valueReference>🔗
<reference
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<basedOn>🔗
<reference value="ServiceRequest/mii-exa-molgen-anforderung-wes"/>
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<status value="final"/>
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<performer>🔗
<reference value="Practitioner/mii-exa-molgen-practitioner-lab"/>
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<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
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<conclusionCode>
<coding>
<system value="http://loinc.org"/>
<code value="LA6576-8"/>
<display value="Positive"/>
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</DiagnosticReport>
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<method value="POST"/>
<url value="DiagnosticReport"/>
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</entry>
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<language value="de"/>
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<identifier>
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<value value="12345"/>
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<name>
<family value="Schmidt"/>
<given value="Anna"/>
<prefix value="Dr."/>
</name>
</Practitioner>
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<entry>
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<language value="de"/>
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<value value="67890"/>
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<name>
<family value="Weber"/>
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<prefix value="Dr."/>
</name>
</Practitioner>
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<request>
<method value="POST"/>
<url value="Practitioner"/>
</request>
</entry>
</Bundle>