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"
          }
        }
      ]
    }
  ]
}