GenomicStudy - Trio study - De novo mutation 1

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