FHIR IG analytics

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Narrative

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Source1

{
  "resourceType": "Procedure",
  "id": "mii-exa-molgen-genomic-study-analysis-wes-sequencing",
  "meta": {
    "profile": [
      "https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/mii-pr-molgen-genomic-study-analysis",
      "https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/StructureDefinition/genomic-study-analysis|2027.0.0-ballot.1"
    ]
  },
  "text": {
    "status": "extensions",
    "div": "<!-- snip (see above) -->"
  },
  "extension": [
    {
      "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-specimen",
      "valueReference": {
        "reference": "Specimen/mii-exa-molgen-specimen-dna-library"
      }
    },
    {
      "extension": [
        {
          "url": "device",
          "valueReference": {
            "reference": "Device/mii-exa-molgen-device-illumina-novaseq"
          }
        }
      ],
      "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-device"
    },
    {
      "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-method-type",
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "LA26398-0",
            "display": "Sequencing"
          }
        ]
      }
    },
    {
      "extension": [
        {
          "url": "read-depth",
          "valueQuantity": {
            "value": 120,
            "unit": "reads",
            "system": "http://unitsofmeasure.org",
            "code": "1"
          }
        },
        {
          "url": "sequencing-coverage",
          "valueQuantity": {
            "value": 98.5,
            "unit": "percent",
            "system": "http://unitsofmeasure.org",
            "code": "%"
          }
        },
        {
          "url": "metrics-description",
          "valueString": "High-quality sequencing run with mean coverage of 120X. 98.5% of target regions achieved >20X coverage. Q30 bases: 92%. Contamination estimate: <1%. Sample identity confirmed by SNP fingerprinting."
        }
      ],
      "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-metrics"
    },
    {
      "extension": [
        {
          "url": "description",
          "valueString": "Whole Exome - Agilent SureSelect Human All Exon V7"
        }
      ],
      "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-regions"
    }
  ],
  "status": "completed",
  "category": {
    "coding": [
      {
        "system": "http://terminology.hl7.org/CodeSystem/observation-category",
        "code": "laboratory"
      }
    ]
  },
  "subject": {
    "reference": "Patient/mii-exa-molgen-patient"
  }
}