FHIRsmith: Observation/Observation-EGFR-L858R-var.json

FHIR IG analytics

Package	hl7.fhir.uv.genomics-reporting.r4b
Resource Type	Observation
Id	Observation-EGFR-L858R-var.json
FHIR Version	R4B

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Narrative

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

Generated Narrative: Observation EGFR-L858R-var

status: Final

category: Laboratory, Genetics

code: Genetic variant assessment

subject: Substance Junior Hamsburg (official) Male, DoB: 1987-09-01 ( Medical record number: 1234567 (use: temp, period: 2021-01-01 --> (ongoing)))

effective: 2023-02-01

performer: Practitioner Test Dolin

value: Present

method: Sequencing

component
code: Discrete genetic variant
value: EGFR L858R

component
code: Amino acid change (pHGVS)
value: NP_005219.2:p.Leu858Arg

component
code: DNA change type
value: SNV

component
code: DNA change (c.HGVS)
value: NM_005228.4:c.2573T>G

component
code: Gene studied [ID]
value: EGFR

component
code: Genomic DNA change (gHGVS)
value: NC_000007.13:g.55259515T>G

component
code: Genomic source class [Type]
value: Somatic

component
code: Sample variant allelic frequency [NFr]
value: 0.066 decimal

Source1

{
  "resourceType": "Observation",
  "id": "EGFR-L858R-var",
  "meta": {
    "profile": [
      "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
    ]
  },
  "text": {
    "status": "generated",
    "div": "<!-- snip (see above) -->"
  },
  "status": "final",
  "category": [
    {
      "coding": [
        {
          "system": "http://terminology.hl7.org/CodeSystem/observation-category",
          "code": "laboratory"
        }
      ]
    },
    {
      "coding": [
        {
          "system": "http://terminology.hl7.org/CodeSystem/v2-0074",
          "code": "GE"
        }
      ]
    }
  ],
  "code": {
    "coding": [
      {
        "system": "http://loinc.org",
        "code": "69548-6"
      }
    ]
  },
  "subject": {
    "reference": "Patient/somaticPatient"
  },
  "effectiveDateTime": "2023-02-01",
  "performer": [
    {
      "reference": "Practitioner/pathologistPractitioner"
    }
  ],
  "valueCodeableConcept": {
    "coding": [
      {
        "system": "http://loinc.org",
        "code": "LA9633-4",
        "display": "Present"
      }
    ]
  },
  "method": {
    "coding": [
      {
        "system": "http://loinc.org",
        "code": "LA26398-0",
        "display": "Sequencing"
      }
    ]
  },
  "component": [
    {
      "code": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "81252-9"
          }
        ]
      },
      "valueCodeableConcept": {
        "text": "EGFR L858R"
      }
    },
    {
      "code": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "48005-3"
          }
        ]
      },
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://varnomen.hgvs.org",
            "code": "NP_005219.2:p.Leu858Arg"
          }
        ]
      }
    },
    {
      "code": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "48019-4"
          }
        ]
      },
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://www.sequenceontology.org",
            "code": "SO:0001483",
            "display": "SNV"
          }
        ]
      }
    },
    {
      "code": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "48004-6"
          }
        ]
      },
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://varnomen.hgvs.org",
            "code": "NM_005228.4:c.2573T>G"
          }
        ]
      }
    },
    {
      "code": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "48018-6"
          }
        ]
      },
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://www.genenames.org",
            "code": "HGNC:3236",
            "display": "EGFR"
          }
        ]
      }
    },
    {
      "code": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "81290-9"
          }
        ]
      },
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://varnomen.hgvs.org",
            "code": "NC_000007.13:g.55259515T>G"
          }
        ]
      }
    },
    {
      "code": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "48002-0"
          }
        ]
      },
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "LA6684-0",
            "display": "Somatic"
          }
        ]
      }
    },
    {
      "code": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "81258-6"
          }
        ]
      },
      "valueQuantity": {
        "value": 0.066,
        "unit": "decimal",
        "system": "http://unitsofmeasure.org"
      }
    }
  ]
}