GenomicStudy - Trio study - De novo mutation 2

{
  "resourceType" : "GenomicStudy",
  "id" : "example-trio2",
  "text" : {
    "status" : "additional",
    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">Prenatal 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.</div>"
  },
  "identifier" : [{
    "use" : "temp",
    "system" : "http://www.somesystemabc.net/identifiers/genomicstudies",
    "value" : "urn:uuid:1111-1111-1111-1113"
  }],
  "status" : {
    "coding" : [{
      "system" : "http://hl7.org/fhir/genomicstudy-status",
      "code" : "available",
      "display" : "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",
    "subject" : {
      "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",
    "subject" : {
      "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",
    "subject" : {
      "reference" : "Patient/proband"
    },
    "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" : {
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          "display" : "Performer"
        }]
      }
    }],
    "device" : [{
      "device" : {
        "reference" : "Device/Triodenovo-SW"
      }
    }]
  }]
}