# lungMass-analysis1 - Genomics Reporting Implementation Guide v4.0.0-cibuild

* [**Table of Contents**](toc.md)
* [**Artifact List**](artifacts.md)
* **lungMass-analysis1**

## Example Procedure: lungMass-analysis1

| |
| :--- |
| *Page standards status:*[Informative](http://hl7.org/fhir/R4/versions.html#std-process) |

Profile: [Genomic Study Analysis](StructureDefinition-genomic-study-analysis.md)

**Genomic Study Analysis Method Type**: Sequence analysis of the entire coding region

**Genomic Study Analysis Source Class**: Somatic

**Genomic Study Analysis Change Type**: SNV

**Genomic Study Analysis Change Type**: MNV

**Genomic Study Analysis Change Type**: delins

**Genomic Study Analysis Genome Build**: GRCh38

**Genomic Study Analysis Specimen**: [Specimen: identifier = http://example.org/identifiers/specimens#4; status = available; type = Specimen from lung obtained by biopsy (specimen); receivedTime = 2019-03-01 01:01:01+0000](Specimen-genomicSpecimen.md)

**Genomic Study Analysis Focus**: [John Junior Doe (official) Unknown, DoB: 2001-01-01 ( Medical record number: 11117 (use: temp, period: 2021-01-01 --> (ongoing)))](Patient-genomicPatient.md)

> **Genomic Study Analysis Device**
* device: [Device: identifier = http://example.org/identifiers/devices#11112; status = active; manufacturer = Vanderbilt Genetics Institute; type = Software (physical object)](Device-triodenovo-software.md)

> **Genomic Study Analysis Regions**
* studied: [DocumentReference: identifier = http://example.org/identifiers/files#11117; status = current; docStatus = preliminary; description = WES_FullSequencedRegion_GRCh38: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline.; securityLabel = Restricted](DocumentReference-WES-FullSequencedRegion-GRCh38.md)
* uncalled: [DocumentReference: identifier = http://example.org/identifiers/files#11125; status = current; docStatus = preliminary; description = Representing a BED file that represents uncallable regions; securityLabel = Restricted](DocumentReference-UncallableRegions.md)
* called: [DocumentReference: identifier = http://example.org/identifiers/files#11118; status = current; docStatus = preliminary; description = SimpleVariantAnalysis_called: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline.; securityLabel = Restricted](DocumentReference-SimpleVariantAnalysis-called.md)

> **Genomic Study Analysis Output**
* type: VCF
* file: [DocumentReference: identifier = http://example.org/identifiers/files#11119; status = current; docStatus = preliminary; description = genomicVCFfile_simple: A sample Document Reference instance representing a VCF file that may be used as input or output of a genomic analysis pipeline.; securityLabel = Restricted](DocumentReference-genomicVCFfile-simple.md)

**instantiatesUri**: [https://pubmed.ncbi.nlm.nih.gov/33927380/](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)))](Patient-genomicPatient.md)

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

### Performers

| | | |
| :--- | :--- | :--- |
| - | **Function** | **Actor** |
| * | Performer | [Practitioner Jane Doel](Practitioner-practitioner02.md) |

**note**: 

> 

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




## Resource Content

```json
{
  "resourceType" : "Procedure",
  "id" : "lungMass-analysis1",
  "meta" : {
    "profile" : [
      "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis"
    ]
  },
  "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" : "sequence-analysis-of-the-entire-coding-region",
            "display" : "Sequence analysis of the entire coding region"
          }
        ]
      }
    },
    {
      "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:0001483",
            "display" : "SNV"
          }
        ]
      }
    },
    {
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-change-type",
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://www.sequenceontology.org",
            "code" : "SO:0002007",
            "display" : "MNV"
          }
        ]
      }
    },
    {
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-change-type",
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://www.sequenceontology.org",
            "code" : "SO:1000032",
            "display" : "delins"
          }
        ]
      }
    },
    {
      "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" : "device",
          "valueReference" : {
            "reference" : "Device/triodenovo-software"
          }
        }
      ],
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-device"
    },
    {
      "extension" : [
        {
          "url" : "studied",
          "valueReference" : {
            "reference" : "DocumentReference/WES-FullSequencedRegion-GRCh38"
          }
        },
        {
          "url" : "uncalled",
          "valueReference" : {
            "reference" : "DocumentReference/UncallableRegions"
          }
        },
        {
          "url" : "called",
          "valueReference" : {
            "reference" : "DocumentReference/SimpleVariantAnalysis-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-simple"
          }
        }
      ],
      "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."
    }
  ]
}

```
