# genomicstudyanalysis-trio2 - Genomics Reporting Implementation Guide v4.0.0-cibuild

* [**Table of Contents**](toc.md)
* [**Artifact List**](artifacts.md)
* **genomicstudyanalysis-trio2**

## Example Procedure: genomicstudyanalysis-trio2

| |
| :--- |
| *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 Genome Build**: GRCh38

**Genomic Study Analysis Focus**: [Father Denovo (official) (no stated gender), DoB Unknown ( Medical record number: 6789-11111 (use: temp, ))](Patient-denovoFather.md)

**Genomic Study Analysis Focus**: [Mother Denovo (official) (no stated gender), DoB Unknown ( Medical record number: 0987-11111 (use: temp, ))](Patient-denovoMother.md)

**Genomic Study Analysis Title**: Parental Sequence Variation Detection Using Next Generation Sequencing

**Genomic Study Analysis Protocol Performed**: [Procedure Sequencing of entire coding region of gene (procedure)](Procedure-SequencingProcedure.md)

> **Genomic Study Analysis Input**
* file: [DocumentReference: identifier = http://example.org/identifiers/files#11118; status = current; docStatus = preliminary; description = A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.; securityLabel = Restricted](DocumentReference-genomicFileProbandBAM.md)
* type: BAM

> **Genomic Study Analysis Input**
* file: [DocumentReference: identifier = http://example.org/identifiers/files#11125; status = current; docStatus = preliminary; description = A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.; securityLabel = Restricted](DocumentReference-genomicFileMotherBAM.md)
* type: BAM

> **Genomic Study Analysis Input**
* file: [DocumentReference: identifier = http://example.org/identifiers/files#11132; status = current; docStatus = preliminary; description = A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.; securityLabel = Restricted](DocumentReference-genomicFileFatherBAM.md)
* type: BAM

> **Genomic Study Analysis Output**
* file: [DocumentReference: identifier = http://example.org/identifiers/files#11150; status = current; docStatus = preliminary; description = A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.; securityLabel = Restricted](DocumentReference-genomicFileProbandVCF.md)
* type: VCF

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

**status**: Completed

**category**: Laboratory

**subject**: [Child Denovo (official) (no stated gender), DoB Unknown ( Medical record number: 1234-11111 (use: temp, ))](Patient-denovoChild.md)

**performed**: 2023-10-01



## Resource Content

```json
{
  "resourceType" : "Procedure",
  "id" : "genomicstudyanalysis-trio2",
  "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-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-focus",
      "valueReference" : {
        "reference" : "Patient/denovoFather"
      }
    },
    {
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-focus",
      "valueReference" : {
        "reference" : "Patient/denovoMother"
      }
    },
    {
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-title",
      "valueString" : "Parental Sequence Variation Detection Using Next Generation Sequencing"
    },
    {
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-protocol-performed",
      "valueReference" : {
        "reference" : "Procedure/SequencingProcedure"
      }
    },
    {
      "extension" : [
        {
          "url" : "file",
          "valueReference" : {
            "reference" : "DocumentReference/genomicFileProbandBAM"
          }
        },
        {
          "url" : "type",
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs",
                "code" : "bam",
                "display" : "BAM"
              }
            ]
          }
        }
      ],
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-input"
    },
    {
      "extension" : [
        {
          "url" : "file",
          "valueReference" : {
            "reference" : "DocumentReference/genomicFileMotherBAM"
          }
        },
        {
          "url" : "type",
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs",
                "code" : "bam",
                "display" : "BAM"
              }
            ]
          }
        }
      ],
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-input"
    },
    {
      "extension" : [
        {
          "url" : "file",
          "valueReference" : {
            "reference" : "DocumentReference/genomicFileFatherBAM"
          }
        },
        {
          "url" : "type",
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs",
                "code" : "bam",
                "display" : "BAM"
              }
            ]
          }
        }
      ],
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-input"
    },
    {
      "extension" : [
        {
          "url" : "file",
          "valueReference" : {
            "reference" : "DocumentReference/genomicFileProbandVCF"
          }
        },
        {
          "url" : "type",
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs",
                "code" : "vcf",
                "display" : "VCF"
              }
            ]
          }
        }
      ],
      "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/denovoChild"
  },
  "performedDateTime" : "2023-10-01"
}

```
