Release 5 Ballot

This page is part of the FHIR Specification (v5.0.0-ballot: FHIR R5 Ballot Preview). The current version which supercedes this version is 5.0.0. For a full list of available versions, see the Directory of published versions

Example GenomicStudy/example-lungMass (JSON)

Clinical Genomics Work GroupMaturity Level: N/AStandards Status: InformativeCompartments: Patient

Raw JSON (canonical form + also see JSON Format Specification)

GenomicStudy - Lung mass - sequencing analysis

{
  "resourceType": "GenomicStudy",
  "id": "example-lungMass",
  "text": {
    "status": "additional",
    "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\">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.</div>"
  },
  "identifier": [
    {
      "use": "temp",
      "system": "http://www.somesystemabc.net/identifiers/genomicstudies",
      "value": "urn:uuid:1111-1111-1111-1112"
    }
  ],
  "status": {
    "coding": [
      {
        "system": "http://hl7.org/fhir/genomicstudy-status",
        "code": "registered",
        "display": "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",
      "subject": {
        "reference": "Patient/genomicPatient"
      },
      "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",
      "subject": {
        "reference": "Patient/genomicPatient"
      },
      "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"
              }
            ]
          }
        }
      ]
    }
  ]
}

Usage note: every effort has been made to ensure that the examples are correct and useful, but they are not a normative part of the specification.