Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.1-SNAPSHOT built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions

: somaticReport - JSON Representation

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{
  "resourceType" : "DiagnosticReport",
  "id" : "somaticReport",
  "meta" : {
    "profile" : [
      🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report"
    ]
  },
  "text" : {
    "status" : "generated",
    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: DiagnosticReport somaticReport</b></p><a name=\"somaticReport\"> </a><a name=\"hcsomaticReport\"> </a><a name=\"somaticReport-en-US\"> </a><h2><span title=\"Codes:{http://loinc.org 51969-4}\">Genetic analysis report</span> (<span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</span>) </h2><table class=\"grid\"><tr><td>When For</td><td>2023-02-02</td></tr><tr><td>Performers</td><td> <a href=\"Practitioner-pathologistPractitioner.html\">Practitioner Test Dolin </a> <a href=\"Organization-performingOrganization.html\">Organization My Test Pathology Laboratories</a></td></tr><tr><td>Identifier</td><td> Accession ID/23-0000345</td></tr></table><p><b>Report Details</b></p><table class=\"grid\"><tr><td><b>Code</b></td><td><b>Value</b></td><td><b>Flags</b></td><td><b>Note</b></td><td><b>When For</b></td><td><b>Reported</b></td></tr><tr><td><a href=\"Observation-NOTCH1-uncertain-var.html\"><span title=\"Codes:{http://loinc.org 69548-6}\">Genetic variant assessment</span></a></td><td><span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></td><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-ZFHX3-uncertain-var.html\"><span title=\"Codes:{http://loinc.org 69548-6}\">Genetic variant assessment</span></a></td><td><span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></td><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-MSH2-del-var.html\"><span title=\"Codes:{http://loinc.org 69548-6}\">Genetic variant assessment</span></a></td><td><span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></td><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-NTHL1-snv-var.html\"><span title=\"Codes:{http://loinc.org 69548-6}\">Genetic variant assessment</span></a></td><td><span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></td><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-STAG2-insertion-var.html\"><span title=\"Codes:{http://loinc.org 69548-6}\">Genetic variant assessment</span></a></td><td><span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></td><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-ATR-insertion-var.html\"><span title=\"Codes:{http://loinc.org 69548-6}\">Genetic variant assessment</span></a></td><td><span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></td><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-EGFR-L858R-var.html\"><span title=\"Codes:{http://loinc.org 69548-6}\">Genetic variant assessment</span></a></td><td><span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></td><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-ROS1-Fusion-var.html\"><span title=\"Codes:{http://loinc.org 69548-6}\">Genetic variant assessment</span></a></td><td><span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></td><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-NOTCH1-significance.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}\">Diagnostic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-ZFHX3-significance.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}\">Diagnostic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-MSH2-del-disease.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}\">Diagnostic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-NTHL1-snv-disease.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}\">Diagnostic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-STAG2-insertion-significance.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}\">Diagnostic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-ATR-insertion-significance.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}\">Diagnostic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-EGFR-L858R-significance.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}\">Diagnostic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-ROS1-Fusion-disease.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs diagnostic-implication}\">Diagnostic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-ROS1-Fusion-therapuTrial.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}\">Therapeutic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-ROS1-Fusion-therapuDrug.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}\">Therapeutic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-EGFR-L858R-therapuDrug1.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}\">Therapeutic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-EGFR-L858R-therapuDrug2.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}\">Therapeutic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-TMB-therapuDrug.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}\">Therapeutic Implication</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-NOTCH1-uncertain-molc.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs molecular-consequence}\">Molecular Consequence</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-ZFHX3-uncertain-molc.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs molecular-consequence}\">Molecular Consequence</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-MSH2-del-molc.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs molecular-consequence}\">Molecular Consequence</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-NTHL1-snv-molc.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs molecular-consequence}\">Molecular Consequence</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-STAG2-insertion-molc.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs molecular-consequence}\">Molecular Consequence</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-ATR-insertion-molc.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs molecular-consequence}\">Molecular Consequence</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-EGFR-L858R-molc.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs molecular-consequence}\">Molecular Consequence</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-ROS1-Fusion.html\"><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs molecular-consequence}\">Molecular Consequence</span></a></td><td/><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-TMBExample.html\"><span title=\"Codes:{http://loinc.org 94076-7}\">Mutations/Megabase [# Ratio] in Tumor</span></a></td><td>29.8</td><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-MSIExample.html\"><span title=\"Codes:{http://loinc.org 81695-9}\">Microsatellite instability [Interpretation] in Cancer specimen Qualitative</span></a></td><td><span title=\"Codes:{http://loinc.org LA26203-2}\">MSI-H</span></td><td>Final</td><td/><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-PDL1Example.html\"><span title=\"Codes:{http://loinc.org 85147-7}\">PD-L1 by clone 22C3 in Tissue by Immune stain Report</span></a></td><td><span title=\"Codes:{http://loinc.org LA6576-8}\">Positive</span></td><td>Final</td><td>5% tumor proportion score</td><td>2023-02-01</td><td/></tr><tr><td><a href=\"Observation-HLA-A-haplotype1.html\"><span title=\"Codes:{http://loinc.org 84414-2}\">Haplotype Name</span></a></td><td><span title=\"Codes:{http://www.ebi.ac.uk/ipd/imgt/hla A*24:02}\">HLA-A*24:02</span></td><td>Final</td><td/><td>2023-02-01</td><td>2023-02-01 00:00:00-0500</td></tr><tr><td><a href=\"Observation-HLA-A-haplotype2.html\"><span title=\"Codes:{http://loinc.org 84414-2}\">Haplotype Name</span></a></td><td><span title=\"Codes:{http://www.ebi.ac.uk/ipd/imgt/hla A*02:06}\">HLA-A*02:06</span></td><td>Final</td><td/><td>2023-02-01</td><td>2023-02-01 00:00:00-0500</td></tr><tr><td><a href=\"Observation-HLA-B-haplotype1.html\"><span title=\"Codes:{http://loinc.org 84414-2}\">Haplotype Name</span></a></td><td><span title=\"Codes:{http://www.ebi.ac.uk/ipd/imgt/hla B*35:01}\">HLA-B*35:01</span></td><td>Final</td><td/><td>2023-02-01</td><td>2023-02-01 00:00:00-0500</td></tr><tr><td><a href=\"Observation-HLA-B-haplotype2.html\"><span title=\"Codes:{http://loinc.org 84414-2}\">Haplotype Name</span></a></td><td><span title=\"Codes:{http://www.ebi.ac.uk/ipd/imgt/hla B*35:01}\">HLA-B*35:01</span></td><td>Final</td><td/><td>2023-02-01</td><td>2023-02-01 00:00:00-0500</td></tr><tr><td><a href=\"Observation-HLA-C-haplotype1.html\"><span title=\"Codes:{http://loinc.org 84414-2}\">Haplotype Name</span></a></td><td><span title=\"Codes:{http://www.ebi.ac.uk/ipd/imgt/hla C*03:03}\">HLA-C*03:03</span></td><td>Final</td><td/><td>2023-02-01</td><td>2023-02-01 00:00:00-0500</td></tr><tr><td><a href=\"Observation-HLA-C-haplotype2.html\"><span title=\"Codes:{http://loinc.org 84414-2}\">Haplotype Name</span></a></td><td><span title=\"Codes:{http://www.ebi.ac.uk/ipd/imgt/hla C*15:02}\">HLA-C*15:02</span></td><td>Final</td><td/><td>2023-02-01</td><td>2023-02-01 00:00:00-0500</td></tr></table><p>Patient is positive for Tier 1 / Level A variants, including variants with FDA-approved indications.</p><p><b>Coded Conclusions:</b></p><ul><li><span title=\"Codes:{http://loinc.org LA6576-8}\">Positive</span></li></ul></div>"
  },
  "extension" : [
    {
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-reference",
      "valueReference" : {
        🔗 "reference" : "Procedure/somaticStudy",
        "display" : "somaticStudy"
      }
    }
  ],
  "identifier" : [
    {
      "type" : {
        "coding" : [
          {
            "system" : "http://terminology.hl7.org/CodeSystem/v2-0203",
            "code" : "ACSN",
            "display" : "Accession ID"
          }
        ]
      },
      "value" : "23-0000345"
    }
  ],
  "basedOn" : [
    {
      🔗 "reference" : "ServiceRequest/somaticServiceRequest"
    }
  ],
  "status" : "final",
  "category" : [
    {
      "coding" : [
        {
          "system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
          "code" : "GE",
          "display" : "Genetics"
        }
      ]
    }
  ],
  "code" : {
    "coding" : [
      {
        "system" : "http://loinc.org",
        "code" : "51969-4",
        "display" : "Genetic analysis report"
      }
    ]
  },
  "effectiveDateTime" : "2023-02-02",
  "performer" : [
    {
      🔗 "reference" : "Practitioner/pathologistPractitioner"
    },
    {
      🔗 "reference" : "Organization/performingOrganization"
    }
  ],
  "resultsInterpreter" : [
    {
      🔗 "reference" : "Practitioner/supervisorPractitioner"
    },
    {
      🔗 "reference" : "Organization/performingOrganization"
    }
  ],
  "result" : [
    {
      🔗 "reference" : "Observation/NOTCH1-uncertain-var"
    },
    {
      🔗 "reference" : "Observation/ZFHX3-uncertain-var"
    },
    {
      🔗 "reference" : "Observation/MSH2-del-var"
    },
    {
      🔗 "reference" : "Observation/NTHL1-snv-var"
    },
    {
      🔗 "reference" : "Observation/STAG2-insertion-var"
    },
    {
      🔗 "reference" : "Observation/ATR-insertion-var"
    },
    {
      🔗 "reference" : "Observation/EGFR-L858R-var"
    },
    {
      🔗 "reference" : "Observation/ROS1-Fusion-var"
    },
    {
      🔗 "reference" : "Observation/NOTCH1-significance"
    },
    {
      🔗 "reference" : "Observation/ZFHX3-significance"
    },
    {
      🔗 "reference" : "Observation/MSH2-del-disease"
    },
    {
      🔗 "reference" : "Observation/NTHL1-snv-disease"
    },
    {
      🔗 "reference" : "Observation/STAG2-insertion-significance"
    },
    {
      🔗 "reference" : "Observation/ATR-insertion-significance"
    },
    {
      🔗 "reference" : "Observation/EGFR-L858R-significance"
    },
    {
      🔗 "reference" : "Observation/ROS1-Fusion-disease"
    },
    {
      🔗 "reference" : "Observation/ROS1-Fusion-therapuTrial"
    },
    {
      🔗 "reference" : "Observation/ROS1-Fusion-therapuDrug"
    },
    {
      🔗 "reference" : "Observation/EGFR-L858R-therapuDrug1"
    },
    {
      🔗 "reference" : "Observation/EGFR-L858R-therapuDrug2"
    },
    {
      🔗 "reference" : "Observation/TMB-therapuDrug"
    },
    {
      🔗 "reference" : "Observation/NOTCH1-uncertain-molc"
    },
    {
      🔗 "reference" : "Observation/ZFHX3-uncertain-molc"
    },
    {
      🔗 "reference" : "Observation/MSH2-del-molc"
    },
    {
      🔗 "reference" : "Observation/NTHL1-snv-molc"
    },
    {
      🔗 "reference" : "Observation/STAG2-insertion-molc"
    },
    {
      🔗 "reference" : "Observation/ATR-insertion-molc"
    },
    {
      🔗 "reference" : "Observation/EGFR-L858R-molc"
    },
    {
      🔗 "reference" : "Observation/ROS1-Fusion"
    },
    {
      🔗 "reference" : "Observation/TMBExample"
    },
    {
      🔗 "reference" : "Observation/MSIExample"
    },
    {
      🔗 "reference" : "Observation/PDL1Example"
    },
    {
      🔗 "reference" : "Observation/HLA-A-haplotype1"
    },
    {
      🔗 "reference" : "Observation/HLA-A-haplotype2"
    },
    {
      🔗 "reference" : "Observation/HLA-B-haplotype1"
    },
    {
      🔗 "reference" : "Observation/HLA-B-haplotype2"
    },
    {
      🔗 "reference" : "Observation/HLA-C-haplotype1"
    },
    {
      🔗 "reference" : "Observation/HLA-C-haplotype2"
    }
  ],
  "conclusion" : "Patient is positive for Tier 1 / Level A variants, including variants with FDA-approved indications.",
  "conclusionCode" : [
    {
      "coding" : [
        {
          "system" : "http://loinc.org",
          "code" : "LA6576-8",
          "display" : "Positive"
        }
      ]
    }
  ]
}