{"resourceType":"GenomicStudy","id":"example","text":{"status":"additional","div":"\u003cdiv xmlns\u003d\"http://www.w3.org/1999/xhtml\"\u003eThis 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.\u003c/div\u003e"},"identifier":[{"use":"temp","system":"http://www.somesystemabc.net/identifiers/genomicstudies","value":"urn:uuid:1111-1111-1111-1111"}],"status":"unknown","type":[{"coding":[{"system":"http://hl7.org/fhir/genomicstudy-type","code":"fam-var-segr","display":"Familial variant segregation"}]}],"subject":{"reference":"Patient/denovoChild"},"encounter":{"reference":"Encounter/denovoEncounter"},"startDate":"2021-01-01","basedOn":[{"reference":"ServiceRequest/genomicServiceRequest"}],"referrer":{"reference":"Practitioner/practitioner01"},"interpreter":[{"reference":"Practitioner/practitioner02"}],"reason":[{"concept":{"coding":[{"system":"http://snomed.info/sct","code":"267431006","display":"Disorder of lipid metabolism (disorder)"}]}}],"note":[{"text":"This de novo mutation is urgent and important for establishing the treatment plan."}],"description":"De novo mutation study of the patient.","analysis":[{"identifier":[{"use":"temp","system":"http://www.somesystemabc.net/identifiers/genomicAnalyses","value":"urn:uuid:1111-1111-1111-1111"}],"instantiatesUri":"https://pubmed.ncbi.nlm.nih.gov/33927380/","title":"Proband Sequence Variation Detection Using Next Generation Sequencing","specimen":[{"reference":"Specimen/denovo-1"}],"date":"2021-01-01T01:01:10-06:00","note":[{"text":"This is a next generation sequencing analysis of a proband."}],"input":[{"file":{"reference":"DocumentReference/genomicFile1"},"type":{"coding":[{"code":"vcf","display":"VCF"}]}}],"performer":[{"actor":{"reference":"Practitioner/practitioner02"},"role":{"coding":[{"system":"http://terminology.hl7.org/3.1.0/CodeSystem-v3-ParticipationType.html","code":"PRF","display":"Performer"}]}}],"device":[{"device":{"reference":"Device/NGS-device"},"function":{"coding":[{"display":"Next Generation Sequencing"}]}}]},{"identifier":[{"use":"temp","system":"http://www.somesystemabc.net/identifiers/genomicAnalyses","value":"urn:uuid:1111-1111-1111-1112"}],"instantiatesUri":"https://pubmed.ncbi.nlm.nih.gov/33927380/","title":"Maternal Sequence Variation Detection Using Next Generation Sequencing","focus":[{"reference":"Patient/denovoMother"}],"specimen":[{"reference":"Specimen/denovo-2"}],"date":"2021-01-01T01:01:10-06:00","note":[{"text":"This is a next generation sequencing analysis of a mother of a proband."}],"input":[{"file":{"reference":"DocumentReference/genomicFile2"},"type":{"coding":[{"code":"vcf","display":"VCF"}]}}],"performer":[{"actor":{"reference":"Practitioner/practitioner02"},"role":{"coding":[{"system":"http://terminology.hl7.org/3.1.0/CodeSystem-v3-ParticipationType.html","code":"PRF","display":"Performer"}]}}],"device":[{"device":{"reference":"Device/NGS-device"}}]},{"identifier":[{"use":"temp","system":"http://www.somesystemabc.net/identifiers/genomicAnalyses","value":"urn:uuid:1111-1111-1111-1113"}],"instantiatesUri":"https://pubmed.ncbi.nlm.nih.gov/33927380/","title":"Paternal Sequence Variation Detection Using Next Generation Sequencing","focus":[{"reference":"Patient/denovoFather"}],"specimen":[{"reference":"Specimen/denovo-3"}],"date":"2021-01-01T01:01:10-06:00","note":[{"text":"This is a next generation sequencing analysis of a father of a proband."}],"input":[{"file":{"reference":"DocumentReference/genomicFile3"},"type":{"coding":[{"code":"vcf","display":"VCF"}]}}],"performer":[{"actor":{"reference":"Practitioner/practitioner02"},"role":{"coding":[{"system":"http://terminology.hl7.org/3.1.0/CodeSystem-v3-ParticipationType.html","code":"PRF","display":"Performer"}]}}],"device":[{"device":{"reference":"Device/NGS-device"}}]},{"identifier":[{"use":"temp","system":"http://www.somesystemabc.net/identifiers/genomicAnalyses","value":"urn:uuid:1111-1111-1111-1114"}],"instantiatesUri":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6885382/","title":"De Novo Mutation Detection and Interpretation","date":"2021-01-01T03:01:10-06:00","note":[{"text":"This is a next generation sequencing analysis of the comparison analysis of proband and parents sequences."}],"input":[{"file":{"reference":"DocumentReference/genomicFile1"},"type":{"coding":[{"code":"vcf","display":"VCF"}]}},{"file":{"reference":"DocumentReference/genomicFile2"},"type":{"coding":[{"code":"vcf","display":"VCF"}]}},{"file":{"reference":"DocumentReference/genomicFile3"},"type":{"coding":[{"code":"vcf","display":"VCF"}]}}],"performer":[{"actor":{"reference":"Practitioner/practitioner02"},"role":{"coding":[{"system":"http://terminology.hl7.org/3.1.0/CodeSystem-v3-ParticipationType.html","code":"PRF","display":"Performer"}]}}],"device":[{"device":{"reference":"Device/Triodenovo-SW"}}]}]}
{"resourceType":"GenomicStudy","id":"example-trio2","text":{"status":"additional","div":"\u003cdiv xmlns\u003d\"http://www.w3.org/1999/xhtml\"\u003ePrenatal Trio Whole Exome Sequencing testing to identify causal mutations of inherited diseases. Test order was for trio testing with three specimens i.e., proband, mother, father included. A comparator analysis-based trio report was to be generated for the proband; both parents had consented to receive reports on secondary findings.\u003c/div\u003e"},"identifier":[{"use":"temp","system":"http://www.somesystemabc.net/identifiers/genomicstudies","value":"urn:uuid:1111-1111-1111-1113"}],"status":"available","type":[{"coding":[{"code":"trio","display":"Trio-analysis"}]}],"subject":{"reference":"Patient/proband"},"encounter":{"reference":"Encounter/denovoEncounter"},"startDate":"2022-05-01","basedOn":[{"reference":"ServiceRequest/genomicSRProband"},{"reference":"ServiceRequest/genomicSRMother"},{"reference":"ServiceRequest/genomicSRFather"}],"referrer":{"reference":"Practitioner/practitioner01"},"interpreter":[{"reference":"Practitioner/practitioner02"}],"reason":[{"concept":{"coding":[{"system":"http://snomed.info/sct","code":"67799006","display":"Cystic fibrosis, prenatal detection (procedure) |"}]}}],"note":[{"text":"This de novo mutation is urgent and important for establishing the treatment plan."}],"description":"De novo mutation study of the patient. The Prenatal Trio Whole Exome Sequencing (Prenatal Trio WES) test is ordered by a physician and must be accompanied with a consent form and detailed clinical information. In general, the test is used when prenatal imaging detects an anomaly that strongly suggests that there is an underlying genetic etiology. Prenatal Trio WES is often considered only after fetal chromosome microarray analysis has been non-diagnostic.","analysis":[{"identifier":[{"use":"temp","system":"http://www.somesystemabc.net/identifiers/genomicAnalyses","value":"urn:uuid:1111-1111-1111-1112"}],"instantiatesUri":"https://pubmed.ncbi.nlm.nih.gov/33927380/","title":"Maternal Sequence Variation Detection Using Next Generation Sequencing","focus":[{"reference":"Patient/mother"}],"specimen":[{"reference":"Specimen/specimenMother"}],"date":"2022-07-01T01:01:10-06:00","note":[{"text":"This is a next generation sequencing analysis of a mother of a proband."}],"performer":[{"actor":{"reference":"Practitioner/practitioner02"},"role":{"coding":[{"system":"http://terminology.hl7.org/3.1.0/CodeSystem-v3-ParticipationType.html","code":"PRF","display":"Performer"}]}}],"device":[{"device":{"reference":"Device/NGS-device"}}]},{"identifier":[{"use":"temp","system":"http://www.somesystemabc.net/identifiers/genomicAnalyses","value":"urn:uuid:1111-1111-1111-1113"}],"instantiatesUri":"https://pubmed.ncbi.nlm.nih.gov/33927380/","title":"Paternal Sequence Variation Detection Using Next Generation Sequencing","focus":[{"reference":"Patient/father"}],"specimen":[{"reference":"Specimen/specimenFather"}],"date":"2022-07-01T01:01:10-06:00","note":[{"text":"This is a next generation sequencing analysis of a father of a proband."}],"performer":[{"actor":{"reference":"Practitioner/practitioner02"},"role":{"coding":[{"system":"http://terminology.hl7.org/3.1.0/CodeSystem-v3-ParticipationType.html","code":"PRF","display":"Performer"}]}}],"device":[{"device":{"reference":"Device/NGS-device"}}]},{"identifier":[{"use":"temp","system":"http://www.somesystemabc.net/identifiers/genomicAnalyses","value":"urn:uuid:1111-1111-1111-1114"}],"instantiatesUri":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6885382/","title":"De Novo Mutation Detection and Interpretation","focus":[{"reference":"Patient/denovoChild"},{"reference":"RelatedPerson/relatedPersonDenovoFather"},{"reference":"RelatedPerson/relatedPersonDenovoMother"}],"date":"2022-07-01T03:01:10-06:00","note":[{"text":"This is a next generation sequencing analysis of the comparison analysis of proband and parents sequences."}],"input":[{"file":{"reference":"DocumentReference/genomicFileProband"},"type":{"coding":[{"system":"http://hl7.org/fhir/genomicstudy-dataformat","code":"bam","display":"BAM"}]}},{"file":{"reference":"DocumentReference/genomicFileMother"},"type":{"coding":[{"system":"http://hl7.org/fhir/genomicstudy-dataformat","code":"bam","display":"BAM"}]}},{"file":{"reference":"DocumentReference/genomicFileFather"},"type":{"coding":[{"system":"http://hl7.org/fhir/genomicstudy-dataformat","code":"bam","display":"BAM"}]}}],"output":[{"file":{"reference":"DocumentReference/genomicFileGroupAsSubject"},"type":{"coding":[{"system":"http://hl7.org/fhir/genomicstudy-dataformat","code":"vcf","display":"VCF"}]}}],"performer":[{"actor":{"reference":"Practitioner/practitioner02"},"role":{"coding":[{"system":"http://terminology.hl7.org/3.1.0/CodeSystem-v3-ParticipationType.html","code":"PRF","display":"Performer"}]}}],"device":[{"device":{"reference":"Device/Triodenovo-SW"}}]}]}
{"resourceType":"GenomicStudy","id":"example-lungMass","text":{"status":"additional","div":"\u003cdiv xmlns\u003d\"http://www.w3.org/1999/xhtml\"\u003eWhole exome sequencing of lung biopsy. 300 genes are examined for simple variants (SNV, MNV, InDel), and 170 genes are also examined for CNVs. For technical reasons, PIK3CB was deemed uncallable.\u003c/div\u003e"},"identifier":[{"use":"temp","system":"http://www.somesystemabc.net/identifiers/genomicstudies","value":"urn:uuid:1111-1111-1111-1112"}],"status":"registered","type":[{"coding":[{"system":"http://snomed.info/sct","code":"443968007","display":"Whole Exome Sequencing - Sequencing of entire coding region of gene (procedure)"}]}],"subject":{"reference":"Patient/genomicPatient"},"encounter":{"reference":"Encounter/genomicEncounter"},"startDate":"2019-03-01","basedOn":[{"reference":"ServiceRequest/genomicServiceRequest2"}],"referrer":{"reference":"Practitioner/practitioner01"},"interpreter":[{"reference":"Practitioner/practitioner02"}],"reason":[{"concept":{"coding":[{"system":"http://snomed.info/sct","code":"309529002","display":"Lung mass (finding) "}]}}],"note":[{"text":"For technical reasons, PIK3CB was deemed uncallable."}],"description":"Whole exome sequencing of lung biopsy. 300 genes are examined for simple variants (SNV, MNV, InDel), and 170 genes are also examined for CNVs. For technical reasons, PIK3CB was deemed uncallable.","analysis":[{"identifier":[{"use":"official","system":"http://www.somesystemabc.net/identifiers/genomicAnalyses","value":"urn:uuid:1111-1111-1111-1112"}],"methodType":[{"coding":[{"system":"http://snomed.info/sct","code":"117040002","display":"Nucleic acid sequencing (procedure)"}]}],"changeType":[{"coding":[{"system":"http://sequenceontology.org","code":"SO:0001483","display":"SNV"}]},{"coding":[{"system":"http://sequenceontology.org","code":"SO:0002007","display":"MNV"}]},{"coding":[{"system":"http://sequenceontology.org","code":"SO:1000032","display":"delins"}]}],"genomeBuild":{"coding":[{"system":"http://loinc.org","code":"LA26806-2","display":"GRCh38"}]},"title":"Simple variant analysis","specimen":[{"reference":"Specimen/genomicSpecimen"}],"date":"2019-03-01T01:01:10-06:00","note":[{"text":"For technical reasons, PIK3CB was deemed uncallable using this method."}],"regionsStudied":[{"reference":"DocumentReference/WES_FullSequencedRegion_GRCh38"}],"regionsCalled":[{"reference":"DocumentReference/SimpleVariantAnalysis_called"}],"output":[{"file":{"reference":"DocumentReference/genomicVCFfile_simple"},"type":{"coding":[{"code":"vcf","display":"VCF"}]}}],"performer":[{"actor":{"reference":"Practitioner/practitioner02"},"role":{"coding":[{"system":"http://terminology.hl7.org/3.1.0/CodeSystem-v3-ParticipationType.html","code":"PRF","display":"Performer"}]}}],"device":[{"device":{"reference":"Device/NGS-device"},"function":{"coding":[{"display":"Next Generation Sequencing"}]}}]},{"identifier":[{"use":"official","system":"http://www.somesystemabc.net/identifiers/genomicAnalyses","value":"urn:uuid:1111-1111-1111-1115"}],"methodType":[{"coding":[{"system":"http://snomed.info/sct","code":"117040002","display":"Nucleic acid sequencing (procedure)"}]}],"changeType":[{"coding":[{"system":"http://sequenceontology.org","code":"SO:0001019","display":"CNV"}]}],"genomeBuild":{"coding":[{"system":"http://loinc.org","code":"LA26806-2","display":"GRCh38"}]},"title":"CNV analysis","specimen":[{"reference":"Specimen/genomicSpecimen"}],"date":"2019-03-01T01:01:10-06:00","note":[{"text":"For technical reasons, PIK3CB was deemed uncallable using this method."}],"regionsStudied":[{"reference":"DocumentReference/WES_FullSequencedRegion_GRCh38"}],"regionsCalled":[{"reference":"DocumentReference/CNVAnalysis_called"}],"output":[{"file":{"reference":"DocumentReference/genomicVCFfile_cnv"},"type":{"coding":[{"code":"vcf","display":"VCF"}]}}],"performer":[{"actor":{"reference":"Practitioner/practitioner02"},"role":{"coding":[{"system":"http://terminology.hl7.org/3.1.0/CodeSystem-v3-ParticipationType.html","code":"PRF","display":"Performer"}]}}]}]}