FHIR IG analytics

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Narrative

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Source1

{
  "resourceType": "GenomicStudy",
  "resourceDefinition": "http://hl7.org/fhir/StructureDefinition/GenomicStudy|0.1.0-ci-build",
  "id": "example-somaticStudy",
  "language": "en",
  "text": {
    "status": "generated",
    "div": "<!-- snip (see above) -->"
  },
  "identifier": [
    {
      "use": "temp",
      "system": "http://example.org/identifiers/genomicstudies",
      "value": "urn:uuid:somatic-study-0001"
    }
  ],
  "status": "available",
  "type": [
    {
      "text": "My Test Cancer 700 Gene Panel"
    }
  ],
  "subject": {
    "reference": "Patient/somaticPatient"
  },
  "startDate": "2023-02-02",
  "basedOn": [
    {
      "reference": "ServiceRequest/somaticServiceRequest"
    }
  ],
  "interpreter": [
    {
      "reference": "Practitioner/practitioner02"
    }
  ],
  "reason": [
    {
      "concept": {
        "coding": [
          {
            "system": "http://snomed.info/sct",
            "code": "424993006",
            "display": "Adenocarcinoma of lung, stage IV (disorder)"
          }
        ]
      }
    }
  ],
  "note": [
    {
      "text": "I. Assay Overview: The Genomic Cancer Testing Assay is a comprehensive molecular examination designed to detect and quantify specific DNA and RNA alterations associated with malignancies. The test incorporates Next Generation Sequencing (NGS) technology to profile tumor samples. II. Target Genes and Biomarkers: This assay evaluates an extensive panel of cancer-related genes. Sample Type: Formalin-fixed, paraffin-embedded (FFPE) tumor tissue. Sequencing Platform: Illumina-based NGS technology. Sensitivity: Detects variants with a mutant allele frequency (MAF) as low as 5%. Results are delivered within 10-14 working days from sample receipt."
    }
  ],
  "description": "Comprehensive somatic genomic profiling of lung adenocarcinoma (stage IV) using a 700-gene panel. Includes paired tumor/normal DNA sequencing for SNV, MNV, InDel and CNV detection, and RNA sequencing for gene fusion and transcript variant detection.",
  "analysis": [
    {
      "identifier": [
        {
          "use": "temp",
          "system": "http://example.org/identifiers/genomicAnalyses",
          "value": "urn:uuid:somatic-analysis-dna-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"
            }
          ]
        },
        {
          "coding": [
            {
              "system": "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-methodtype",
              "code": "deletion-duplication-analysis",
              "display": "Deletion/duplication analysis"
            }
          ]
        }
      ],
      "changeType": [
        {
          "coding": [
            {
              "system": "http://www.sequenceontology.org",
              "code": "SO:0001483",
              "display": "SNV"
            }
          ]
        },
        {
          "coding": [
            {
              "system": "http://www.sequenceontology.org",
              "code": "SO:0002007",
              "display": "MNV"
            }
          ]
        },
        {
          "coding": [
            {
              "system": "http://www.sequenceontology.org",
              "code": "SO:1000032",
              "display": "delins"
            }
          ]
        },
        {
          "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": "LA6684-0",
            "display": "Somatic"
          }
        ]
      },
      "title": "Tumor/Normal Paired DNA Sequencing - SNV, MNV, InDel, CNV",
      "focus": [
        {
          "reference": "Patient/somaticPatient"
        }
      ],
      "specimen": [
        {
          "reference": "Specimen/tumorSpecimen"
        },
        {
          "reference": "Specimen/normalSpecimen"
        }
      ],
      "date": "2023-02-02T01:01:10-06:00",
      "note": [
        {
          "text": "For technical reasons, BCR gene was deemed uncallable."
        }
      ],
      "metrics": {
        "readDepth": {
          "value": 500,
          "unit": "x",
          "system": "http://unitsofmeasure.org",
          "code": "1"
        },
        "sequencingCoverage": {
          "value": 97,
          "unit": "%",
          "system": "http://unitsofmeasure.org",
          "code": "%"
        },
        "description": "500x average tumor read depth, 97% target region coverage. Minimum allele frequency threshold 5%."
      },
      "genomicRegion": [
        {
          "type": {
            "coding": [
              {
                "system": "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype",
                "code": "studied",
                "display": "Studied"
              }
            ]
          },
          "locus": [
            {
              "reference": {
                "reference": "DocumentReference/WES-FullSequencedRegion-GRCh38"
              }
            }
          ]
        },
        {
          "type": {
            "coding": [
              {
                "system": "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype",
                "code": "called",
                "display": "Called"
              }
            ]
          },
          "locus": [
            {
              "reference": {
                "reference": "DocumentReference/somaticCalledRegions"
              }
            }
          ]
        },
        {
          "type": {
            "coding": [
              {
                "system": "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype",
                "code": "uncalled",
                "display": "Uncalled"
              }
            ]
          },
          "locus": [
            {
              "concept": {
                "coding": [
                  {
                    "system": "http://www.genenames.org",
                    "code": "HGNC:1014",
                    "display": "BCR"
                  }
                ]
              }
            }
          ],
          "description": "BCR was not callable due to low sequencing coverage in this tumor sample."
        }
      ],
      "output": [
        {
          "file": {
            "reference": "DocumentReference/somaticVCFfile"
          },
          "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"
              }
            ]
          }
        }
      ]
    },
    {
      "identifier": [
        {
          "use": "temp",
          "system": "http://example.org/identifiers/genomicAnalyses",
          "value": "urn:uuid:somatic-analysis-rna-0001"
        }
      ],
      "methodType": [
        {
          "coding": [
            {
              "system": "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-methodtype",
              "code": "rna-analysis",
              "display": "RNA analysis"
            }
          ]
        }
      ],
      "changeType": [
        {
          "coding": [
            {
              "system": "http://www.sequenceontology.org",
              "code": "SO:0001565",
              "display": "gene_fusion"
            }
          ]
        },
        {
          "coding": [
            {
              "system": "http://www.sequenceontology.org",
              "code": "SO:0001576",
              "display": "transcript_variant"
            }
          ]
        }
      ],
      "genomicSourceClass": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "LA6684-0",
            "display": "Somatic"
          }
        ]
      },
      "title": "Tumor RNA Sequencing - Gene Fusions and Transcript Variants",
      "focus": [
        {
          "reference": "Patient/somaticPatient"
        }
      ],
      "specimen": [
        {
          "reference": "Specimen/tumorSpecimen"
        }
      ],
      "date": "2023-02-02T01:01:10-06:00",
      "genomicRegion": [
        {
          "type": {
            "coding": [
              {
                "system": "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype",
                "code": "studied",
                "display": "Studied"
              }
            ]
          },
          "locus": [
            {
              "reference": {
                "reference": "DocumentReference/somaticRNAstudiedRegions"
              }
            }
          ]
        }
      ],
      "output": [
        {
          "file": {
            "reference": "DocumentReference/somaticFusionFile"
          },
          "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"
              }
            ]
          }
        }
      ]
    }
  ]
}