<specimen><reference value="Specimen/denovo-1"/></specimen><date value="2021-01-01T01:01:10-06:00"/> <note><text value="This is a next generation sequencing analysis of a proband."/></note>   <input> <file><reference value="DocumentReference/genomicFile1"/></file><type><coding><code value="vcf"/><display value="VCF"/></coding></type></input><performer> <actor><reference value="Practitioner/practitioner02"/></actor><role><coding><system value="http://terminology.hl7.org/3.1.0/CodeSystem-v3-ParticipationType.html"/><code value="PRF"/><display value="Performer"/></coding></role></performer><device> <device><reference value="Device/NGS-device"/></device><function><coding><display value="Next Generation Sequencing"/></coding></function></device></analysis><analysis> <identifier><use value="temp"/><system value="http://www.somesystemabc.net/identifiers/genomicAnalyses"/><value value="urn:uuid:1111-1111-1111-1112"/></identifier> <instantiatesUri value="https://pubmed.ncbi.nlm.nih.gov/33927380/"/><title value="Maternal Sequence Variation Detection Using Next Generation Sequencing"/> <focus><reference value="Patient/denovoMother"/></focus><specimen><reference value="Specimen/denovo-2"/></specimen><date value="2021-01-01T01:01:10-06:00"/> <note><text value="This is a next generation sequencing analysis of a mother of a proband."/></note> <input> <file><reference value="DocumentReference/genomicFile2"/></file><type><coding><code value="vcf"/><display value="VCF"/></coding></type></input><performer> <actor><reference value="Practitioner/practitioner02"/></actor><role><coding><system value="http://terminology.hl7.org/3.1.0/CodeSystem-v3-ParticipationType.html"/><code value="PRF"/><display value="Performer"/></coding></role></performer> <device> <device><reference value="Device/NGS-device"/></device></device></analysis><analysis> <identifier><use value="temp"/><system value="http://www.somesystemabc.net/identifiers/genomicAnalyses"/><value value="urn:uuid:1111-1111-1111-1113"/></identifier> <instantiatesUri value="https://pubmed.ncbi.nlm.nih.gov/33927380/"/><title value="Paternal Sequence Variation Detection Using Next Generation Sequencing"/><focus><reference value="Patient/denovoFather"/></focus><specimen><reference value="Specimen/denovo-3"/></specimen><date value="2021-01-01T01:01:10-06:00"/> <note><text value="This is a next generation sequencing analysis of a father of a proband."/></note> <input> <file><reference value="DocumentReference/genomicFile3"/></file><type><coding><code value="vcf"/><display value="VCF"/></coding></type></input><performer> <actor><reference value="Practitioner/practitioner02"/></actor><role><coding><system value="http://terminology.hl7.org/3.1.0/CodeSystem-v3-ParticipationType.html"/><code value="PRF"/><display value="Performer"/></coding></role></performer> <device> <device><reference value="Device/NGS-device"/></device></device></analysis><analysis> <identifier><use value="temp"/><system value="http://www.somesystemabc.net/identifiers/genomicAnalyses"/><value value="urn:uuid:1111-1111-1111-1114"/></identifier> <instantiatesUri value="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6885382/"/><title value="De Novo Mutation Detection and Interpretation"/> <date value="2021-01-01T03:01:10-06:00"/> <note><text value="This is a next generation sequencing analysis of the comparison analysis of proband and parents sequences."/></note> <input> <file><reference value="DocumentReference/genomicFile1"/></file><type><coding><code value="vcf"/><display value="VCF"/></coding></type></input> <input> <file><reference value="DocumentReference/genomicFile2"/></file><type><coding><code value="vcf"/><display value="VCF"/></coding></type></input> <input> <file><reference value="DocumentReference/genomicFile3"/></file><type><coding><code value="vcf"/><display value="VCF"/></coding></type></input><performer> <actor><reference value="Practitioner/practitioner02"/></actor><role><coding><system value="http://terminology.hl7.org/3.1.0/CodeSystem-v3-ParticipationType.html"/><code value="PRF"/><display value="Performer"/></coding></role></performer> <device> <device><reference value="Device/Triodenovo-SW"/></device></device></analysis></GenomicStudy>

This is a genomic study that involves a de novo mutation analysis of a proband, mother, and father. The analysis involves the use use of NGS device and a specilized analysis platform.

    <specimen><reference value="Specimen/denovo-1"/></specimen><date value="2021-01-01T01:01:10-06:00"/>  <!--   0..1 The date of the analysis event   --><note><text value="This is a next generation sequencing analysis of a proband."/></note>  <!--   <protocolPerformed>0..1 Reference(Procedure|Task) The protocol that was performed for the analysis event</protocolPerformed>   -->  <!--   <regionsCalled>0..1 Reference(DocumentReference) Genomic regions actually called in the analysis event (BED file)</regionsCalled>   -->  <!--   <generatedBy[x]>0..1 Identifier|Reference(GenomicStudy) The analysis event or other GenomicStudy that generated this input file</generatedBy[x]>   --><input>  <!--   0..* Inputs for the analysis event of Child  --><file><reference value="DocumentReference/genomicFile1"/></file><type><coding><code value="vcf"/><display value="VCF"/></coding></type></input><performer>  <!--   0..* Performer for the analysis event   --><actor><reference value="Practitioner/practitioner02"/></actor><role><coding><system value="http://terminology.hl7.org/3.1.0/CodeSystem-v3-ParticipationType.html"/><code value="PRF"/><display value="Performer"/></coding></role></performer><device>  <!--   0..* Devices used for the analysis (e.g., instruments, software), with settings and parameters   --><device><reference value="Device/NGS-device"/></device><function><coding><display value="Next Generation Sequencing"/></coding></function></device></analysis><analysis>  <!--   0..* Genomic Analysis Event of mother   --><identifier><use value="temp"/><system value="http://www.somesystemabc.net/identifiers/genomicAnalyses"/><value value="urn:uuid:1111-1111-1111-1112"/></identifier>  <!--   <instantiatesCanonical>0..1 canonical(PlanDefinition) The defined protocol that describes the analysis</instantiatesCanonical>   --><instantiatesUri value="https://pubmed.ncbi.nlm.nih.gov/33927380/"/><title value="Maternal Sequence Variation Detection Using Next Generation Sequencing"/>  <!--   0..1 Name of the analysis event (human friendly)   --><focus><reference value="Patient/denovoMother"/></focus><specimen><reference value="Specimen/denovo-2"/></specimen><date value="2021-01-01T01:01:10-06:00"/>  <!--   0..1 The date of the analysis event   --><note><text value="This is a next generation sequencing analysis of a mother of a proband."/></note>  <!--   <generatedBy[x]>0..1 Identifier|Reference(GenomicStudy) The analysis event or other GenomicStudy that generated this input file</generatedBy[x]>   --><input>  <!--   0..* Inputs for the analysis event of Mother  --><file><reference value="DocumentReference/genomicFile2"/></file><type><coding><code value="vcf"/><display value="VCF"/></coding></type></input><performer>  <!--   0..* Performer for the analysis event   --><actor><reference value="Practitioner/practitioner02"/></actor><role><coding><system value="http://terminology.hl7.org/3.1.0/CodeSystem-v3-ParticipationType.html"/><code value="PRF"/><display value="Performer"/></coding></role></performer>  <!--   <function>0..1 CodeableConcept Specific function for the device used for the analysis</function>   --><device>  <!--   0..* Devices used for the analysis (e.g., instruments, software), with settings and parameters   --><device><reference value="Device/NGS-device"/></device></device></analysis><analysis>  <!--   0..* Genomic Analysis Event of father   --><identifier><use value="temp"/><system value="http://www.somesystemabc.net/identifiers/genomicAnalyses"/><value value="urn:uuid:1111-1111-1111-1113"/></identifier>  <!--   <instantiatesCanonical>0..1 canonical(PlanDefinition) The defined protocol that describes the analysis</instantiatesCanonical>   --><instantiatesUri value="https://pubmed.ncbi.nlm.nih.gov/33927380/"/><title value="Paternal Sequence Variation Detection Using Next Generation Sequencing"/><focus><reference value="Patient/denovoFather"/></focus><specimen><reference value="Specimen/denovo-3"/></specimen><date value="2021-01-01T01:01:10-06:00"/>  <!--   0..1 The date of the analysis event   --><note><text value="This is a next generation sequencing analysis of a father of a proband."/></note>  <!--   <generatedBy[x]>0..1 Identifier|Reference(GenomicStudy) The analysis event or other GenomicStudy that generated this input file</generatedBy[x]>   --><input>  <!--   0..* Inputs for the analysis event   --><file><reference value="DocumentReference/genomicFile3"/></file><type><coding><code value="vcf"/><display value="VCF"/></coding></type></input><performer>  <!--   0..* Performer for the analysis event   --><actor><reference value="Practitioner/practitioner02"/></actor><role><coding><system value="http://terminology.hl7.org/3.1.0/CodeSystem-v3-ParticipationType.html"/><code value="PRF"/><display value="Performer"/></coding></role></performer>  <!--   <function>0..1 CodeableConcept Specific function for the device used for the analysis</function>   --><device>  <!--   0..* Devices used for the analysis (e.g., instruments, software), with settings and parameters   --><device><reference value="Device/NGS-device"/></device></device></analysis><analysis>  <!--   0..* De Novo Mutation Analysis   --><identifier><use value="temp"/><system value="http://www.somesystemabc.net/identifiers/genomicAnalyses"/><value value="urn:uuid:1111-1111-1111-1114"/></identifier>  <!--   <instantiatesCanonical>0..1 canonical(PlanDefinition) The defined protocol that describes the analysis</instantiatesCanonical>   --><instantiatesUri value="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6885382/"/><title value="De Novo Mutation Detection and Interpretation"/>  <!--   <specimen> 0..1 Reference(Specimen) The specimen used in the analysis event</specimen>   --><date value="2021-01-01T03:01:10-06:00"/>  <!--   0..1 The date of the analysis event   --><note><text value="This is a next generation sequencing analysis of the comparison analysis of proband and parents sequences."/></note>  <!--   <generatedBy[x]>0..1 Identifier|Reference(GenomicStudy) The analysis event or other GenomicStudy that generated this input file</generatedBy[x]>   --><input>  <!--   0..* Inputs for the analysis event of Child  --><file><reference value="DocumentReference/genomicFile1"/></file><type><coding><code value="vcf"/><display value="VCF"/></coding></type></input>  <!--   <generatedBy[x]>0..1 Identifier|Reference(GenomicStudy) The analysis event or other GenomicStudy that generated this input file</generatedBy[x]>   --><input>  <!--   0..* Inputs for the analysis event of Mother  --><file><reference value="DocumentReference/genomicFile2"/></file><type><coding><code value="vcf"/><display value="VCF"/></coding></type></input>  <!--   <generatedBy[x]>0..1 Identifier|Reference(GenomicStudy) The analysis event or other GenomicStudy that generated this input file</generatedBy[x]>   --><input>  <!--   0..* Inputs for the analysis event of Father   --><file><reference value="DocumentReference/genomicFile3"/></file><type><coding><code value="vcf"/><display value="VCF"/></coding></type></input><performer>  <!--   0..* Performer for the analysis event   --><actor><reference value="Practitioner/practitioner02"/></actor><role><coding><system value="http://terminology.hl7.org/3.1.0/CodeSystem-v3-ParticipationType.html"/><code value="PRF"/><display value="Performer"/></coding></role></performer>  <!--   <function>0..1 CodeableConcept Specific function for the device used for the analysis</function>   --><device>  <!--   0..* Devices used for the analysis (e.g., instruments, software), with settings and parameters   --><device><reference value="Device/Triodenovo-SW"/></device></device></analysis></GenomicStudy>