FHIR Genomics Implementation Guide

Notice

Important: This guidance is under active development by NHS England and content may be added or updated on a regular basis.
This Implementation Guide is currently in Draft and SHOULD NOT be used for development or active implementation without express direction from the NHS England Genomics Unit.

Bundle-NonWGSTestOrderFormUpdated-FetalScenario-Example

Example of an update to a Non-WGS test request sent to the central broker, as described in the Clinical Scenario:Fetus Management

Bundle

id : Bundle-NonWGSTestOrderFormUpdated-FetalScenario-Example

type : transaction

entry

fullUrl : http://example.org/fhir/ServiceRequest/ServiceRequest-NonWGSTestOrderFormUpdated-FetalScenario-Example

resource

id : ServiceRequest-NonWGSTestOrderFormUpdated-FetalScenario-Example

extension

url : https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-Coverage

value

coding

system : https://fhir.hl7.org.uk/CodeSystem/UKCore-FundingCategory

code : nhs-england

display : NHS England

status : active

intent : order

category

coding

system : https://fhir.hl7.org.uk/CodeSystem/UKCore-GenomeSequencingCategory

code : rare-disease-non-wgs

display : Rare Disease - Non-WGS

priority : urgent

code

coding

system : https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory

code : R21

display : Fetal anomalies with a likely genetic cause

version : 7

subject

reference : Patient/Patient-FoetusOfRyanneBoulder-Example

identifier

system : urn:oid:2.16.840.1.113883.2.1.3.2.4.18.24

value : FT-RWT13521

assigner

identifier

system : https://fhir.nhs.uk/Id/ods-organization-code

value : RAX

authoredOn : 2023-09-25

requester

reference : PractitionerRole/PractitionerRole-LoisLaneKingstonClinicalGenetics-Example

reasonCode

coding

system : https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics

code : staging-or-prognosis

display : Staging or Prognosis

supportingInfo

reference : Observation/Observation-HistoryOfFetalLoss-Example

supportingInfo

reference : Observation/Observation-NonConsanguinousUnion-Example

supportingInfo

reference : Observation/Observation-GenomicEthnicity-Example

supportingInfo

reference : Observation/Observation-PregnancyConfirmation-Example

supportingInfo

reference : Observation/Observation-NoTransplant-Example

supportingInfo

reference : Observation/Observation-NoFirstTrimesterFetalAnomalies-Example

supportingInfo

reference : Observation/Observation-NoSecondTrimesterFetalAnomalies-Example

supportingInfo

reference : Procedure/Procedure-InVitroFertilisation-Example

supportingInfo

reference : Specimen/Specimen-BloodEDTA-Example

supportingInfo

reference : Specimen/Specimen-RyanneBoulderSaliva-Example

supportingInfo

reference : Specimen/Specimen-RyanneBoulderPartnerSaliva-Example

supportingInfo

reference : RelatedPerson/RelatedPerson-RyanneBoulder-Example

supportingInfo

reference : Patient/Patient-RyanneBoulder-Example

supportingInfo

reference : RelatedPerson/RelatedPerson-RyanneBoulderPartner-Example

supportingInfo

reference : Patient/Patient-RyanneBoulderPartner-Example

note

text : No family history of relevant testing

note

text : Free text for diagnosis/reason for referral, relevant information including family history, phenotypic details/ HPO Terms/ E.g. large echogenic kidneys with normal bladder

request

method : PUT

url : ServiceRequest/ServiceRequest-NonWGSTestOrderForm-FetalScenario-Example

entry

fullUrl : http://example.org/fhir/Specimen/Specimen-RyanneBoulderParnerSaliva-Example

resource

id : Specimen-RyanneBoulderParnerSaliva-Example

identifier

system : https://fhir.kingstonhospital.nhs.uk//Id/specimenId

value : ROA-69050-FTH-RWT13521

status : available

type

coding

system : http://snomed.info/sct

code : 119342007

display : Saliva specimen

subject

reference : Patient/Patient-RyanneBoulderPartner-Example

container

description : Container:ROA-69050-FTH-RWT13521 contains Saliva for Father

request

reference : ServiceRequest/ServiceRequest-NonWGSTestOrderForm-FetalScenario-Example

request

method : POST

url : Specimen

{
    "resourceType": "Bundle",
    "id": "Bundle-NonWGSTestOrderFormUpdated-FetalScenario-Example",
    "type": "transaction",
    "entry":  [
        {
            "fullUrl": "http://example.org/fhir/ServiceRequest/ServiceRequest-NonWGSTestOrderFormUpdated-FetalScenario-Example",
            "resource": {
                "resourceType": "ServiceRequest",
                "id": "ServiceRequest-NonWGSTestOrderFormUpdated-FetalScenario-Example",
                "extension":  [
                    {
                        "url": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-Coverage",
                        "valueCodeableConcept": {
                            "coding":  [
                                {
                                    "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-FundingCategory",
                                    "code": "nhs-england",
                                    "display": "NHS England"
                                }
                            ]
                        }
                    }
                ],
                "status": "active",
                "intent": "order",
                "category":  [
                    {
                        "coding":  [
                            {
                                "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-GenomeSequencingCategory",
                                "code": "rare-disease-non-wgs",
                                "display": "Rare Disease - Non-WGS"
                            }
                        ]
                    }
                ],
                "priority": "urgent",
                "code": {
                    "coding":  [
                        {
                            "system": "https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory",
                            "code": "R21",
                            "display": "Fetal anomalies with a likely genetic cause",
                            "version": "7"
                        }
                    ]
                },
                "subject": {
                    "reference": "Patient/Patient-FoetusOfRyanneBoulder-Example",
                    "identifier": {
                        "system": "urn:oid:2.16.840.1.113883.2.1.3.2.4.18.24",
                        "value": "FT-RWT13521",
                        "assigner": {
                            "identifier": {
                                "system": "https://fhir.nhs.uk/Id/ods-organization-code",
                                "value": "RAX"
                            }
                        }
                    }
                },
                "authoredOn": "2023-09-25",
                "requester": {
                    "reference": "PractitionerRole/PractitionerRole-LoisLaneKingstonClinicalGenetics-Example"
                },
                "reasonCode":  [
                    {
                        "coding":  [
                            {
                                "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics",
                                "code": "staging-or-prognosis",
                                "display": "Staging or Prognosis"
                            }
                        ]
                    }
                ],
                "supportingInfo":  [
                    {
                        "reference": "Observation/Observation-HistoryOfFetalLoss-Example"
                    },
                    {
                        "reference": "Observation/Observation-NonConsanguinousUnion-Example"
                    },
                    {
                        "reference": "Observation/Observation-GenomicEthnicity-Example"
                    },
                    {
                        "reference": "Observation/Observation-PregnancyConfirmation-Example"
                    },
                    {
                        "reference": "Observation/Observation-NoTransplant-Example"
                    },
                    {
                        "reference": "Observation/Observation-NoFirstTrimesterFetalAnomalies-Example"
                    },
                    {
                        "reference": "Observation/Observation-NoSecondTrimesterFetalAnomalies-Example"
                    },
                    {
                        "reference": "Procedure/Procedure-InVitroFertilisation-Example"
                    },
                    {
                        "reference": "Specimen/Specimen-BloodEDTA-Example"
                    },
                    {
                        "reference": "Specimen/Specimen-RyanneBoulderSaliva-Example"
                    },
                    {
                        "reference": "Specimen/Specimen-RyanneBoulderPartnerSaliva-Example"
                    },
                    {
                        "reference": "RelatedPerson/RelatedPerson-RyanneBoulder-Example"
                    },
                    {
                        "reference": "Patient/Patient-RyanneBoulder-Example"
                    },
                    {
                        "reference": "RelatedPerson/RelatedPerson-RyanneBoulderPartner-Example"
                    },
                    {
                        "reference": "Patient/Patient-RyanneBoulderPartner-Example"
                    }
                ],
                "note":  [
                    {
                        "text": "No family history of relevant testing"
                    },
                    {
                        "text": "Free text for diagnosis/reason for referral, relevant information including family history, phenotypic details/ HPO Terms/ E.g. large echogenic kidneys with normal bladder"
                    }
                ]
            },
            "request": {
                "method": "PUT",
                "url": "ServiceRequest/ServiceRequest-NonWGSTestOrderForm-FetalScenario-Example"
            }
        },
        {
            "fullUrl": "http://example.org/fhir/Specimen/Specimen-RyanneBoulderParnerSaliva-Example",
            "resource": {
                "resourceType": "Specimen",
                "id": "Specimen-RyanneBoulderParnerSaliva-Example",
                "identifier":  [
                    {
                        "system": "https://fhir.kingstonhospital.nhs.uk//Id/specimenId",
                        "value": "ROA-69050-FTH-RWT13521"
                    }
                ],
                "status": "available",
                "type": {
                    "coding":  [
                        {
                            "system": "http://snomed.info/sct",
                            "code": "119342007",
                            "display": "Saliva specimen"
                        }
                    ]
                },
                "subject": {
                    "reference": "Patient/Patient-RyanneBoulderPartner-Example"
                },
                "container":  [
                    {
                        "description": "Container:ROA-69050-FTH-RWT13521 contains Saliva for Father"
                    }
                ],
                "request":  [
                    {
                        "reference": "ServiceRequest/ServiceRequest-NonWGSTestOrderForm-FetalScenario-Example"
                    }
                ]
            },
            "request": {
                "method": "POST",
                "url": "Specimen"
            }
        }
    ]
}

<Bundle xmlns="http://hl7.org/fhir">
    <id value="Bundle-NonWGSTestOrderFormUpdated-FetalScenario-Example" />
    <type value="transaction" />
    <entry>
        <fullUrl value="http://example.org/fhir/ServiceRequest/ServiceRequest-NonWGSTestOrderFormUpdated-FetalScenario-Example" />
        <resource>
            <ServiceRequest>
                <id value="ServiceRequest-NonWGSTestOrderFormUpdated-FetalScenario-Example" />
                <extension url="https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-Coverage">
                    <valueCodeableConcept>
                        <coding>
                            <system value="https://fhir.hl7.org.uk/CodeSystem/UKCore-FundingCategory" />
                            <code value="nhs-england" />
                            <display value="NHS England" />
                        </coding>
                    </valueCodeableConcept>
                </extension>
                <status value="active" />
                <intent value="order" />
                <category>
                    <coding>
                        <system value="https://fhir.hl7.org.uk/CodeSystem/UKCore-GenomeSequencingCategory" />
                        <code value="rare-disease-non-wgs" />
                        <display value="Rare Disease - Non-WGS" />
                    </coding>
                </category>
                <priority value="urgent" />
                <code>
                    <coding>
                        <system value="https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory" />
                        <version value="7" />
                        <code value="R21" />
                        <display value="Fetal anomalies with a likely genetic cause" />
                    </coding>
                </code>
                <subject>
                    <reference value="Patient/Patient-FoetusOfRyanneBoulder-Example" />
                    <identifier>
                        <system value="urn:oid:2.16.840.1.113883.2.1.3.2.4.18.24" />
                        <value value="FT-RWT13521" />
                        <assigner>
                            <identifier>
                                <system value="https://fhir.nhs.uk/Id/ods-organization-code" />
                                <value value="RAX" />
                            </identifier>
                        </assigner>
                    </identifier>
                </subject>
                <authoredOn value="2023-09-25" />
                <requester>
                    <reference value="PractitionerRole/PractitionerRole-LoisLaneKingstonClinicalGenetics-Example" />
                </requester>
                <reasonCode>
                    <coding>
                        <system value="https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics" />
                        <code value="staging-or-prognosis" />
                        <display value="Staging or Prognosis" />
                    </coding>
                </reasonCode>
                <supportingInfo>
                    <reference value="Observation/Observation-HistoryOfFetalLoss-Example" />
                </supportingInfo>
                <supportingInfo>
                    <reference value="Observation/Observation-NonConsanguinousUnion-Example" />
                </supportingInfo>
                <supportingInfo>
                    <reference value="Observation/Observation-GenomicEthnicity-Example" />
                </supportingInfo>
                <supportingInfo>
                    <reference value="Observation/Observation-PregnancyConfirmation-Example" />
                </supportingInfo>
                <supportingInfo>
                    <reference value="Observation/Observation-NoTransplant-Example" />
                </supportingInfo>
                <supportingInfo>
                    <reference value="Observation/Observation-NoFirstTrimesterFetalAnomalies-Example" />
                </supportingInfo>
                <supportingInfo>
                    <reference value="Observation/Observation-NoSecondTrimesterFetalAnomalies-Example" />
                </supportingInfo>
                <supportingInfo>
                    <reference value="Procedure/Procedure-InVitroFertilisation-Example" />
                </supportingInfo>
                <supportingInfo>
                    <reference value="Specimen/Specimen-BloodEDTA-Example" />
                </supportingInfo>
                <supportingInfo>
                    <reference value="Specimen/Specimen-RyanneBoulderSaliva-Example" />
                </supportingInfo>
                <supportingInfo>
                    <reference value="Specimen/Specimen-RyanneBoulderPartnerSaliva-Example" />
                </supportingInfo>
                <supportingInfo>
                    <reference value="RelatedPerson/RelatedPerson-RyanneBoulder-Example" />
                </supportingInfo>
                <supportingInfo>
                    <reference value="Patient/Patient-RyanneBoulder-Example" />
                </supportingInfo>
                <supportingInfo>
                    <reference value="RelatedPerson/RelatedPerson-RyanneBoulderPartner-Example" />
                </supportingInfo>
                <supportingInfo>
                    <reference value="Patient/Patient-RyanneBoulderPartner-Example" />
                </supportingInfo>
                <note>
                    <text value="No family history of relevant testing" />
                </note>
                <note>
                    <text value="Free text for diagnosis/reason for referral, relevant information including family history, phenotypic details/ HPO Terms/ E.g. large echogenic kidneys with normal bladder" />
                </note>
            </ServiceRequest>
        </resource>
        <request>
            <method value="PUT" />
            <url value="ServiceRequest/ServiceRequest-NonWGSTestOrderForm-FetalScenario-Example" />
        </request>
    </entry>
    <entry>
        <fullUrl value="http://example.org/fhir/Specimen/Specimen-RyanneBoulderParnerSaliva-Example" />
        <resource>
            <Specimen>
                <id value="Specimen-RyanneBoulderParnerSaliva-Example" />
                <identifier>
                    <system value="https://fhir.kingstonhospital.nhs.uk//Id/specimenId" />
                    <value value="ROA-69050-FTH-RWT13521" />
                </identifier>
                <status value="available" />
                <type>
                    <coding>
                        <system value="http://snomed.info/sct" />
                        <code value="119342007" />
                        <display value="Saliva specimen" />
                    </coding>
                </type>
                <subject>
                    <reference value="Patient/Patient-RyanneBoulderPartner-Example" />
                </subject>
                <request>
                    <reference value="ServiceRequest/ServiceRequest-NonWGSTestOrderForm-FetalScenario-Example" />
                </request>
                <container>
                    <description value="Container:ROA-69050-FTH-RWT13521 contains Saliva for Father" />
                </container>
            </Specimen>
        </resource>
        <request>
            <method value="POST" />
            <url value="Specimen" />
        </request>
    </entry>
</Bundle>

Notice

Bundle-NonWGSTestOrderFormUpdated-FetalScenario-Example

Propose a change to Bundle-NonWGSTestOrderFormUpdated-FetalScenario-Example