FHIR IG analytics

Resources that use this resource

No resources found

Resources that this resource uses

No resources found

Narrative

Note: links and images are rebased to the (stated) source

Source1

{
  "resourceType": "GenomicStudy",
  "resourceDefinition": "http://hl7.org/fhir/StructureDefinition/GenomicStudy|0.1.0-ci-build",
  "id": "example-pgx",
  "language": "en",
  "text": {
    "status": "generated",
    "div": "<!-- snip (see above) -->"
  },
  "identifier": [
    {
      "use": "temp",
      "system": "http://example.org/identifiers/genomicstudies",
      "value": "urn:uuid:pgx-study-0001"
    }
  ],
  "status": "available",
  "type": [
    {
      "coding": [
        {
          "system": "http://snomed.info/sct",
          "code": "405825005",
          "display": "Molecular genetic test (procedure)"
        }
      ]
    }
  ],
  "subject": {
    "reference": "Patient/pgxPatient"
  },
  "startDate": "2021-01-01",
  "basedOn": [
    {
      "reference": "ServiceRequest/pgxServiceRequest"
    }
  ],
  "interpreter": [
    {
      "reference": "Practitioner/practitioner02"
    }
  ],
  "reason": [
    {
      "concept": {
        "coding": [
          {
            "system": "http://snomed.info/sct",
            "code": "182992009",
            "display": "Treatment completed (situation)"
          }
        ]
      }
    }
  ],
  "note": [
    {
      "text": "PGX panel ordered prior to initiating warfarin therapy to guide dosing based on CYP2C9 and VKORC1 genotype."
    }
  ],
  "description": "Pharmacogenomics sequencing panel targeting protein-coding and exon-splicing regions of CYP2C19, CYP2C9, and VKORC1 to inform drug selection and dosing.",
  "analysis": [
    {
      "identifier": [
        {
          "use": "temp",
          "system": "http://example.org/identifiers/genomicAnalyses",
          "value": "urn:uuid:pgx-analysis-0001"
        }
      ],
      "methodType": [
        {
          "coding": [
            {
              "system": "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-methodtype",
              "code": "sequence-analysis-of-the-entire-coding-region",
              "display": "Sequence analysis of the entire coding region"
            }
          ]
        }
      ],
      "changeType": [
        {
          "coding": [
            {
              "system": "http://www.sequenceontology.org",
              "code": "SO:0001483",
              "display": "SNV"
            }
          ]
        },
        {
          "coding": [
            {
              "system": "http://www.sequenceontology.org",
              "code": "SO:0001019",
              "display": "copy_number_variation"
            }
          ]
        }
      ],
      "genomeBuild": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "LA26806-2",
            "display": "GRCh38"
          }
        ]
      },
      "genomicSourceClass": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "LA6683-2",
            "display": "Germline"
          }
        ]
      },
      "title": "PGX Targeted Gene Panel - Sequencing Analysis",
      "specimen": [
        {
          "reference": "Specimen/pgxSpecimen"
        }
      ],
      "date": "2021-01-01T01:01:10-06:00",
      "note": [
        {
          "text": "Sequencing coverage of 100% achieved across all targeted regions."
        }
      ],
      "metrics": {
        "sequencingCoverage": {
          "value": 100,
          "unit": "%",
          "system": "http://unitsofmeasure.org",
          "code": "%"
        },
        "description": "100% coverage of protein-coding and exon-splicing regions for all three genes."
      },
      "genomicRegion": [
        {
          "type": {
            "coding": [
              {
                "system": "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype",
                "code": "studied",
                "display": "Studied"
              }
            ]
          },
          "locus": [
            {
              "concept": {
                "coding": [
                  {
                    "system": "http://www.genenames.org",
                    "code": "HGNC:2621",
                    "display": "CYP2C19"
                  }
                ],
                "text": "protein-coding and exon-splicing regions of CYP2C19"
              }
            },
            {
              "concept": {
                "coding": [
                  {
                    "system": "http://www.genenames.org",
                    "code": "HGNC:2623",
                    "display": "CYP2C9"
                  }
                ],
                "text": "protein-coding and exon-splicing regions of CYP2C9"
              }
            },
            {
              "concept": {
                "coding": [
                  {
                    "system": "http://www.genenames.org",
                    "code": "HGNC:23663",
                    "display": "VKORC1"
                  }
                ],
                "text": "protein-coding and exon-splicing regions of VKORC1"
              }
            }
          ]
        },
        {
          "type": {
            "coding": [
              {
                "system": "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype",
                "code": "called",
                "display": "Called"
              }
            ]
          },
          "locus": [
            {
              "concept": {
                "coding": [
                  {
                    "system": "http://www.genenames.org",
                    "code": "HGNC:2621",
                    "display": "CYP2C19"
                  }
                ]
              }
            },
            {
              "concept": {
                "coding": [
                  {
                    "system": "http://www.genenames.org",
                    "code": "HGNC:2623",
                    "display": "CYP2C9"
                  }
                ]
              }
            },
            {
              "concept": {
                "coding": [
                  {
                    "system": "http://www.genenames.org",
                    "code": "HGNC:23663",
                    "display": "VKORC1"
                  }
                ]
              }
            }
          ]
        }
      ],
      "output": [
        {
          "file": {
            "reference": "DocumentReference/pgxVCFfile"
          },
          "type": {
            "coding": [
              {
                "system": "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat",
                "code": "vcf",
                "display": "VCF"
              }
            ]
          }
        }
      ],
      "performer": [
        {
          "actor": {
            "reference": "Practitioner/practitioner02"
          },
          "role": {
            "coding": [
              {
                "system": "http://terminology.hl7.org/CodeSystem/v3-ParticipationType",
                "code": "PRF",
                "display": "Performer"
              }
            ]
          }
        }
      ],
      "device": [
        {
          "device": {
            "reference": "Device/NGS-device"
          },
          "function": {
            "coding": [
              {
                "system": "http://loinc.org",
                "code": "LA26398-0",
                "display": "Sequencing"
              }
            ]
          }
        }
      ]
    }
  ]
}