FHIRsmith: GenomicStudy/GenomicStudy-example.json

FHIR IG analytics

Package	hl7.fhir.uv.cg-incubator
Resource Type	GenomicStudy
Id	GenomicStudy-example.json
FHIR Version	R6

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Narrative

Note: links and images are rebased to the (stated) source

Generated Narrative: GenomicStudy example

Language: en

identifier: http://example.org/identifiers/genomicstudies/urn:uuid:1111-1111-1111-1111 (use: temp, )

status: Unknown

type: Familial variant segregation

subject: Child Junior Doe (official) Unknown, DoB: 2021-01-01 ( Medical record number: 11111 (use: temp, period: 2021-01-01 --> (ongoing)))

encounter: Encounter: status = in-progress; class = inpatient encounter

startDate: 2021-01-01

basedOn: ServiceRequest Carrier detection, molecular genetics (procedure)

referrer: Practitioner John Doel

interpreter: Practitioner Jane Doel

Reasons

Concept

Disorder of lipid metabolism (disorder)

note:

This de novo mutation is urgent and important for establishing the treatment plan.

description:

De novo mutation study of the patient.

analysis
identifier: http://example.org/identifiers/genomicAnalyses/urn:uuid:1111-1111-1111-1111 (use: temp, )
genomicSourceClass: Germline
title: Proband Sequence Variation Detection Using Next Generation Sequencing
specimen: Specimen: identifier = http://example.org/identifiers/specimens#1; status = available; type = Venous blood specimen; receivedTime = 2021-01-01 01:01:01+0000
date: 2021-01-01 01:01:10-0600
note:
This is a next generation sequencing analysis of a proband.

Inputs
- File Type
* DocumentReference: identifier = http://example.org/identifiers/files#11111; 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. VCF
Performers
- Actor Role
* Practitioner Jane Doel Performer
Devices
- Device Function
* Device: identifier = http://example.org/identifiers/devices#11111; status = active; manufacturer = Illumina; type = Device (physical object) Sequencing

analysis
identifier: http://example.org/identifiers/genomicAnalyses/urn:uuid:1111-1111-1111-1112 (use: temp, )
genomicSourceClass: Germline
title: Maternal Sequence Variation Detection Using Next Generation Sequencing
focus: Jane Mother Doe (official) Female, DoB: 2000-01-01 ( Medical record number: 11112 (use: temp, period: 2021-01-01 --> (ongoing)))
specimen: Specimen: identifier = http://example.org/identifiers/specimens#2; status = available; type = Venous blood specimen; receivedTime = 2021-01-01 01:01:01+0000
date: 2021-01-01 01:01:10-0600
note:
This is a next generation sequencing analysis of a mother of a proband.

Inputs
- File Type
* DocumentReference: identifier = http://example.org/identifiers/files#11112; 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. VCF
Performers
- Actor Role
* Practitioner Jane Doel Performer
Devices
- Device
* Device: identifier = http://example.org/identifiers/devices#11111; status = active; manufacturer = Illumina; type = Device (physical object)

analysis
identifier: http://example.org/identifiers/genomicAnalyses/urn:uuid:1111-1111-1111-1113 (use: temp, )
genomicSourceClass: Germline
title: Paternal Sequence Variation Detection Using Next Generation Sequencing
focus: John Father Doe (official) Male, DoB: 2000-01-01 ( Medical record number: 11113 (use: temp, period: 2021-01-01 --> (ongoing)))
specimen: Specimen: identifier = http://example.org/identifiers/specimens#3; status = available; type = Venous blood specimen; receivedTime = 2021-01-01 01:01:01+0000
date: 2021-01-01 01:01:10-0600
note:
This is a next generation sequencing analysis of a father of a proband.

Inputs
- File Type
* DocumentReference: identifier = http://example.org/identifiers/files#11113; 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. VCF
Performers
- Actor Role
* Practitioner Jane Doel Performer
Devices
- Device
* Device: identifier = http://example.org/identifiers/devices#11111; status = active; manufacturer = Illumina; type = Device (physical object)

analysis
identifier: http://example.org/identifiers/genomicAnalyses/urn:uuid:1111-1111-1111-1114 (use: temp, )
title: De Novo Mutation Detection and Interpretation
date: 2021-01-01 03:01:10-0600
note:
This is a next generation sequencing analysis of the comparison analysis of proband and parents sequences.

input
file: DocumentReference: identifier = http://example.org/identifiers/files#11111; 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.
type: VCF
input
file: DocumentReference: identifier = http://example.org/identifiers/files#11112; 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.
type: VCF
input
file: DocumentReference: identifier = http://example.org/identifiers/files#11113; 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.
type: VCF
Performers
- Actor Role
* Practitioner Jane Doel Performer
Devices
- Device
* Device: identifier = http://example.org/identifiers/devices#11112; status = active; manufacturer = Vanderbilt Genetics Institute; type = Software (physical object)

Source1

{
  "resourceType": "GenomicStudy",
  "resourceDefinition": "http://hl7.org/fhir/StructureDefinition/GenomicStudy|0.1.0-ci-build",
  "id": "example",
  "language": "en",
  "text": {
    "status": "generated",
    "div": "<!-- snip (see above) -->"
  },
  "identifier": [
    {
      "use": "temp",
      "system": "http://example.org/identifiers/genomicstudies",
      "value": "urn:uuid:1111-1111-1111-1111"
    }
  ],
  "status": "unknown",
  "type": [
    {
      "coding": [
        {
          "system": "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-type",
          "code": "fam-var-segr",
          "display": "Familial variant segregation"
        }
      ]
    }
  ],
  "subject": {
    "reference": "Patient/denovoChild"
  },
  "encounter": {
    "reference": "Encounter/denovoEncounter"
  },
  "startDate": "2021-01-01",
  "basedOn": [
    {
      "reference": "ServiceRequest/genomicServiceRequest"
    }
  ],
  "referrer": {
    "reference": "Practitioner/practitioner01"
  },
  "interpreter": [
    {
      "reference": "Practitioner/practitioner02"
    }
  ],
  "reason": [
    {
      "concept": {
        "coding": [
          {
            "system": "http://snomed.info/sct",
            "code": "267431006",
            "display": "Disorder of lipid metabolism (disorder)"
          }
        ]
      }
    }
  ],
  "note": [
    {
      "text": "This de novo mutation is urgent and important for establishing the treatment plan."
    }
  ],
  "description": "De novo mutation study of the patient.",
  "analysis": [
    {
      "identifier": [
        {
          "use": "temp",
          "system": "http://example.org/identifiers/genomicAnalyses",
          "value": "urn:uuid:1111-1111-1111-1111"
        }
      ],
      "genomicSourceClass": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "LA6683-2",
            "display": "Germline"
          }
        ]
      },
      "title": "Proband Sequence Variation Detection Using Next Generation Sequencing",
      "specimen": [
        {
          "reference": "Specimen/denovo-1"
        }
      ],
      "date": "2021-01-01T01:01:10-06:00",
      "note": [
        {
          "text": "This is a next generation sequencing analysis of a proband."
        }
      ],
      "input": [
        {
          "file": {
            "reference": "DocumentReference/genomicFile1"
          },
          "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:1111-1111-1111-1112"
        }
      ],
      "genomicSourceClass": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "LA6683-2",
            "display": "Germline"
          }
        ]
      },
      "title": "Maternal Sequence Variation Detection Using Next Generation Sequencing",
      "focus": [
        {
          "reference": "Patient/denovoMother"
        }
      ],
      "specimen": [
        {
          "reference": "Specimen/denovo-2"
        }
      ],
      "date": "2021-01-01T01:01:10-06:00",
      "note": [
        {
          "text": "This is a next generation sequencing analysis of a mother of a proband."
        }
      ],
      "input": [
        {
          "file": {
            "reference": "DocumentReference/genomicFile2"
          },
          "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"
          }
        }
      ]
    },
    {
      "identifier": [
        {
          "use": "temp",
          "system": "http://example.org/identifiers/genomicAnalyses",
          "value": "urn:uuid:1111-1111-1111-1113"
        }
      ],
      "genomicSourceClass": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "LA6683-2",
            "display": "Germline"
          }
        ]
      },
      "title": "Paternal Sequence Variation Detection Using Next Generation Sequencing",
      "focus": [
        {
          "reference": "Patient/denovoFather"
        }
      ],
      "specimen": [
        {
          "reference": "Specimen/denovo-3"
        }
      ],
      "date": "2021-01-01T01:01:10-06:00",
      "note": [
        {
          "text": "This is a next generation sequencing analysis of a father of a proband."
        }
      ],
      "input": [
        {
          "file": {
            "reference": "DocumentReference/genomicFile3"
          },
          "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"
          }
        }
      ]
    },
    {
      "identifier": [
        {
          "use": "temp",
          "system": "http://example.org/identifiers/genomicAnalyses",
          "value": "urn:uuid:1111-1111-1111-1114"
        }
      ],
      "title": "De Novo Mutation Detection and Interpretation",
      "date": "2021-01-01T03:01:10-06:00",
      "note": [
        {
          "text": "This is a next generation sequencing analysis of the comparison analysis of proband and parents sequences."
        }
      ],
      "input": [
        {
          "file": {
            "reference": "DocumentReference/genomicFile1"
          },
          "type": {
            "coding": [
              {
                "system": "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat",
                "code": "vcf",
                "display": "VCF"
              }
            ]
          }
        },
        {
          "file": {
            "reference": "DocumentReference/genomicFile2"
          },
          "type": {
            "coding": [
              {
                "system": "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat",
                "code": "vcf",
                "display": "VCF"
              }
            ]
          }
        },
        {
          "file": {
            "reference": "DocumentReference/genomicFile3"
          },
          "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/Triodenovo-SW"
          }
        }
      ]
    }
  ]
}