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FHIR IG analytics

Packagehl7.fhir.uv.genomics-reporting.r4
Resource TypeProcedure
IdProcedure-lungMass-analysis2.json
FHIR VersionR4

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Narrative

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

Generated Narrative: Procedure lungMass-analysis2

Genomic Study Analysis Method Type: Deletion/duplication analysis

Genomic Study Analysis Source Class: Somatic

Genomic Study Analysis Change Type: CNV

Genomic Study Analysis Genome Build: GRCh38

Genomic Study Analysis Specimen: Specimen: identifier = http://www.somesystemabc.net/identifiers/specimens#4; status = available; type = Specimen from lung obtained by biopsy (specimen); receivedTime = 2019-03-01 01:01:01+0000

Genomic Study Analysis Focus: John Junior Doe (official) Unknown, DoB: 2001-01-01 ( Medical record number: 11117 (use: temp, period: 2021-01-01 --> (ongoing)))

Genomic Study Analysis Regions

Genomic Study Analysis Output

instantiatesUri: https://pubmed.ncbi.nlm.nih.gov/33927380/

status: Completed

category: Laboratory

subject: John Junior Doe (official) Unknown, DoB: 2001-01-01 ( Medical record number: 11117 (use: temp, period: 2021-01-01 --> (ongoing)))

performed: 2019-03-01 01:01:10-0600

Performers

-FunctionActor
*PerformerPractitioner Jane Doel

note: For technical reasons, PIK3CB was deemed uncallable using this method.

Source1

{
  "resourceType": "Procedure",
  "id": "lungMass-analysis2",
  "meta": {
    "profile": [
      "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis"
    ]
  },
  "text": {
    "status": "extensions",
    "div": "<!-- snip (see above) -->"
  },
  "extension": [
    {
      "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-method-type",
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-method-type-cs",
            "code": "deletion-duplication-analysis",
            "display": "Deletion/duplication analysis"
          }
        ]
      }
    },
    {
      "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-genomic-source-class",
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "LA6684-0",
            "display": "Somatic"
          }
        ]
      }
    },
    {
      "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-change-type",
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://www.sequenceontology.org",
            "code": "SO:0001019",
            "display": "CNV"
          }
        ]
      }
    },
    {
      "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-genome-build",
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "LA26806-2",
            "display": "GRCh38"
          }
        ]
      }
    },
    {
      "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-specimen",
      "valueReference": {
        "reference": "Specimen/genomicSpecimen"
      }
    },
    {
      "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-focus",
      "valueReference": {
        "reference": "Patient/genomicPatient"
      }
    },
    {
      "extension": [
        {
          "url": "studied",
          "valueReference": {
            "reference": "DocumentReference/WES-FullSequencedRegion-GRCh38"
          }
        },
        {
          "url": "called",
          "valueReference": {
            "reference": "DocumentReference/CNVAnalysis-called"
          }
        }
      ],
      "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-regions"
    },
    {
      "extension": [
        {
          "url": "type",
          "valueCodeableConcept": {
            "coding": [
              {
                "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs",
                "code": "vcf",
                "display": "VCF"
              }
            ]
          }
        },
        {
          "url": "file",
          "valueReference": {
            "reference": "DocumentReference/genomicVCFfile-cnv"
          }
        }
      ],
      "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-output"
    }
  ],
  "instantiatesUri": [
    "https://pubmed.ncbi.nlm.nih.gov/33927380/"
  ],
  "status": "completed",
  "category": {
    "coding": [
      {
        "system": "http://terminology.hl7.org/CodeSystem/observation-category",
        "code": "laboratory"
      }
    ]
  },
  "subject": {
    "reference": "Patient/genomicPatient"
  },
  "performedDateTime": "2019-03-01T01:01:10-06:00",
  "performer": [
    {
      "function": {
        "coding": [
          {
            "system": "http://terminology.hl7.org/CodeSystem/v3-ParticipationType",
            "code": "PRF",
            "display": "Performer"
          }
        ]
      },
      "actor": {
        "reference": "Practitioner/practitioner02"
      }
    }
  ],
  "note": [
    {
      "text": "For technical reasons, PIK3CB was deemed uncallable using this method."
    }
  ]
}