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.

CodeSystems

The CodeSystems created specifically for use in Genomics are listed below. Some of the CodeSystems listed may still be in draft and pending further changes once requirements for the GMS have been finalised.

Codes for requestable entities (Test Directory codes) are dependent upon the digitisation of the test directory. This is treated as a separate project.

CodeSystems

Genomic-Business-Status

Business status for test order Tasks in genomics

HTML View

This code system https://fhir.nhs.uk/CodeSystem/business-status-genomics defines the following codes:

Code	Display
AwaitingSpecimen	Awaiting Specimen
AwaitingRoDAndSpecimen	Awaiting Record of Discussion and Specimen
SpecimenReceived	Specimen Received
RemoteProcessingRequired	Remote Processing Required
AlignSequencing	Align Sequencing
RemoteGeneticDataProcessingRequired	Remote Genetic Data Processing Required
VariantsIdentified	Variants Identified
RemoteInterpretationRequired	Remote Interpretation Required
FurtherClinicalDetailsRequired	Further Clinical Details Required
FurtherClinicalDetailsProvided	Further Clinical Details Provided
ReflexTestRequired	Reflex Test Required
ReflexTestComplete	Reflex Test Complete

Table View

CodeSystem.id[0]	959a0a2f-73e3-4c6e-8e99-babb6b3a4296
CodeSystem.url[0]	https://fhir.nhs.uk/CodeSystem/business-status-genomics
CodeSystem.identifier[0].system[0]	https://fhir.nhs.uk/identifier/CodeSystem
CodeSystem.identifier[0].value[0]	business-status-genomics
CodeSystem.version[0]	0.2.0
CodeSystem.name[0]	BusinessStatusGenomics
CodeSystem.title[0]	Business Status Genomics
CodeSystem.status[0]	draft
CodeSystem.date[0]	2022-11-25
CodeSystem.publisher[0]	NHS Digital
CodeSystem.contact[0].name[0]	NHS Digital
CodeSystem.contact[0].telecom[0].system[0]	email
CodeSystem.contact[0].telecom[0].value[0]	interoperabilityteam@nhs.net
CodeSystem.contact[0].telecom[0].use[0]	work
CodeSystem.description[0]	Business status for test order Tasks in genomics
CodeSystem.copyright[0]	Copyright © 2022 NHS Digital
CodeSystem.caseSensitive[0]	True
CodeSystem.content[0]	complete
CodeSystem.concept[0].code[0]	AwaitingSpecimen
CodeSystem.concept[0].display[0]	Awaiting Specimen
CodeSystem.concept[1].code[0]	AwaitingRoDAndSpecimen
CodeSystem.concept[1].display[0]	Awaiting Record of Discussion and Specimen
CodeSystem.concept[2].code[0]	SpecimenReceived
CodeSystem.concept[2].display[0]	Specimen Received
CodeSystem.concept[3].code[0]	RemoteProcessingRequired
CodeSystem.concept[3].display[0]	Remote Processing Required
CodeSystem.concept[4].code[0]	AlignSequencing
CodeSystem.concept[4].display[0]	Align Sequencing
CodeSystem.concept[5].code[0]	RemoteGeneticDataProcessingRequired
CodeSystem.concept[5].display[0]	Remote Genetic Data Processing Required
CodeSystem.concept[6].code[0]	VariantsIdentified
CodeSystem.concept[6].display[0]	Variants Identified
CodeSystem.concept[7].code[0]	RemoteInterpretationRequired
CodeSystem.concept[7].display[0]	Remote Interpretation Required
CodeSystem.concept[8].code[0]	FurtherClinicalDetailsRequired
CodeSystem.concept[8].display[0]	Further Clinical Details Required
CodeSystem.concept[9].code[0]	FurtherClinicalDetailsProvided
CodeSystem.concept[9].display[0]	Further Clinical Details Provided
CodeSystem.concept[10].code[0]	ReflexTestRequired
CodeSystem.concept[10].display[0]	Reflex Test Required
CodeSystem.concept[11].code[0]	ReflexTestComplete
CodeSystem.concept[11].display[0]	Reflex Test Complete

XML View

<CodeSystem xmlns="http://hl7.org/fhir">
    <id value="959a0a2f-73e3-4c6e-8e99-babb6b3a4296" />
    <url value="https://fhir.nhs.uk/CodeSystem/business-status-genomics" />
    <identifier>
        <system value="https://fhir.nhs.uk/identifier/CodeSystem" />
        <value value="business-status-genomics" />
    </identifier>
    <version value="0.2.0" />
    <name value="BusinessStatusGenomics" />
    <title value="Business Status Genomics" />
    <status value="draft" />
    <date value="2022-11-25" />
    <publisher value="NHS Digital" />
    <contact>
        <name value="NHS Digital" />
        <telecom>
            <system value="email" />
            <value value="interoperabilityteam@nhs.net" />
            <use value="work" />
        </telecom>
    </contact>
    <description value="Business status for test order Tasks in genomics" />
    <copyright value="Copyright &#169; 2022 NHS Digital" />
    <caseSensitive value="true" />
    <content value="complete" />
    <concept>
        <code value="AwaitingSpecimen" />
        <display value="Awaiting Specimen" />
    </concept>
    <concept>
        <code value="AwaitingRoDAndSpecimen" />
        <display value="Awaiting Record of Discussion and Specimen" />
    </concept>
    <concept>
        <code value="SpecimenReceived" />
        <display value="Specimen Received" />
    </concept>
    <concept>
        <code value="RemoteProcessingRequired" />
        <display value="Remote Processing Required" />
    </concept>
    <concept>
        <code value="AlignSequencing" />
        <display value="Align Sequencing" />
    </concept>
    <concept>
        <code value="RemoteGeneticDataProcessingRequired" />
        <display value="Remote Genetic Data Processing Required" />
    </concept>
    <concept>
        <code value="VariantsIdentified" />
        <display value="Variants Identified" />
    </concept>
    <concept>
        <code value="RemoteInterpretationRequired" />
        <display value="Remote Interpretation Required" />
    </concept>
    <concept>
        <code value="FurtherClinicalDetailsRequired" />
        <display value="Further Clinical Details Required" />
    </concept>
    <concept>
        <code value="FurtherClinicalDetailsProvided" />
        <display value="Further Clinical Details Provided" />
    </concept>
    <concept>
        <code value="ReflexTestRequired" />
        <display value="Reflex Test Required" />
    </concept>
    <concept>
        <code value="ReflexTestComplete" />
        <display value="Reflex Test Complete" />
    </concept>
</CodeSystem>

JSON View

{
    "resourceType": "CodeSystem",
    "id": "959a0a2f-73e3-4c6e-8e99-babb6b3a4296",
    "url": "https://fhir.nhs.uk/CodeSystem/business-status-genomics",
    "identifier":  [
        {
            "system": "https://fhir.nhs.uk/identifier/CodeSystem",
            "value": "business-status-genomics"
        }
    ],
    "version": "0.2.0",
    "name": "BusinessStatusGenomics",
    "title": "Business Status Genomics",
    "status": "draft",
    "date": "2022-11-25",
    "publisher": "NHS Digital",
    "contact":  [
        {
            "name": "NHS Digital",
            "telecom":  [
                {
                    "system": "email",
                    "value": "interoperabilityteam@nhs.net",
                    "use": "work"
                }
            ]
        }
    ],
    "description": "Business status for test order Tasks in genomics",
    "copyright": "Copyright © 2022 NHS Digital",
    "caseSensitive": true,
    "content": "complete",
    "concept":  [
        {
            "code": "AwaitingSpecimen",
            "display": "Awaiting Specimen"
        },
        {
            "code": "AwaitingRoDAndSpecimen",
            "display": "Awaiting Record of Discussion and Specimen"
        },
        {
            "code": "SpecimenReceived",
            "display": "Specimen Received"
        },
        {
            "code": "RemoteProcessingRequired",
            "display": "Remote Processing Required"
        },
        {
            "code": "AlignSequencing",
            "display": "Align Sequencing"
        },
        {
            "code": "RemoteGeneticDataProcessingRequired",
            "display": "Remote Genetic Data Processing Required"
        },
        {
            "code": "VariantsIdentified",
            "display": "Variants Identified"
        },
        {
            "code": "RemoteInterpretationRequired",
            "display": "Remote Interpretation Required"
        },
        {
            "code": "FurtherClinicalDetailsRequired",
            "display": "Further Clinical Details Required"
        },
        {
            "code": "FurtherClinicalDetailsProvided",
            "display": "Further Clinical Details Provided"
        },
        {
            "code": "ReflexTestRequired",
            "display": "Reflex Test Required"
        },
        {
            "code": "ReflexTestComplete",
            "display": "Reflex Test Complete"
        }
    ]
}

Genomic-Message-Events

Common messaging events for Genomics Test Orders and Reports.

HTML View

This code system https://fhir.nhs.uk/CodeSystem/message-events-genomics defines the following codes:

Code	Display	Definition
genomictestrequest	Genomic Test Request	A Service Request bundle for ordering genomic tests
genomictestresponse	Genomic Test Response	A Diagnostic Report bundle for test results

Table View

CodeSystem.id[0]	message-events-genomics
CodeSystem.url[0]	https://fhir.nhs.uk/CodeSystem/message-events-genomics
CodeSystem.identifier[0].system[0]	https://fhir.nhs.uk/identifier/CodeSystem
CodeSystem.identifier[0].value[0]	message-events-genomics
CodeSystem.version[0]	0.1.0
CodeSystem.name[0]	MessageEventsGenomics
CodeSystem.title[0]	Message Events Genomics
CodeSystem.status[0]	draft
CodeSystem.date[0]	2022-11-25
CodeSystem.publisher[0]	NHS Digital
CodeSystem.contact[0].name[0]	NHS Digital
CodeSystem.contact[0].telecom[0].system[0]	email
CodeSystem.contact[0].telecom[0].value[0]	interoperabilityteam@nhs.net
CodeSystem.contact[0].telecom[0].use[0]	work
CodeSystem.description[0]	Common messaging events for Genomics Test Orders and Reports.
CodeSystem.copyright[0]	Copyright © 2022 NHS Digital
CodeSystem.caseSensitive[0]	True
CodeSystem.content[0]	complete
CodeSystem.concept[0].code[0]	genomictestrequest
CodeSystem.concept[0].display[0]	Genomic Test Request
CodeSystem.concept[0].definition[0]	A Service Request bundle for ordering genomic tests
CodeSystem.concept[1].code[0]	genomictestresponse
CodeSystem.concept[1].display[0]	Genomic Test Response
CodeSystem.concept[1].definition[0]	A Diagnostic Report bundle for test results

XML View

<CodeSystem xmlns="http://hl7.org/fhir">
    <id value="message-events-genomics" />
    <url value="https://fhir.nhs.uk/CodeSystem/message-events-genomics" />
    <identifier>
        <system value="https://fhir.nhs.uk/identifier/CodeSystem" />
        <value value="message-events-genomics" />
    </identifier>
    <version value="0.1.0" />
    <name value="MessageEventsGenomics" />
    <title value="Message Events Genomics" />
    <status value="draft" />
    <date value="2022-11-25" />
    <publisher value="NHS Digital" />
    <contact>
        <name value="NHS Digital" />
        <telecom>
            <system value="email" />
            <value value="interoperabilityteam@nhs.net" />
            <use value="work" />
        </telecom>
    </contact>
    <description value="Common messaging events for Genomics Test Orders and Reports." />
    <copyright value="Copyright &#169; 2022 NHS Digital" />
    <caseSensitive value="true" />
    <content value="complete" />
    <concept>
        <code value="genomictestrequest" />
        <display value="Genomic Test Request" />
        <definition value="A Service Request bundle for ordering genomic tests" />
    </concept>
    <concept>
        <code value="genomictestresponse" />
        <display value="Genomic Test Response" />
        <definition value="A Diagnostic Report bundle for test results" />
    </concept>
</CodeSystem>

JSON View

{
    "resourceType": "CodeSystem",
    "id": "message-events-genomics",
    "url": "https://fhir.nhs.uk/CodeSystem/message-events-genomics",
    "identifier":  [
        {
            "system": "https://fhir.nhs.uk/identifier/CodeSystem",
            "value": "message-events-genomics"
        }
    ],
    "version": "0.1.0",
    "name": "MessageEventsGenomics",
    "title": "Message Events Genomics",
    "status": "draft",
    "date": "2022-11-25",
    "publisher": "NHS Digital",
    "contact":  [
        {
            "name": "NHS Digital",
            "telecom":  [
                {
                    "system": "email",
                    "value": "interoperabilityteam@nhs.net",
                    "use": "work"
                }
            ]
        }
    ],
    "description": "Common messaging events for Genomics Test Orders and Reports.",
    "copyright": "Copyright © 2022 NHS Digital",
    "caseSensitive": true,
    "content": "complete",
    "concept":  [
        {
            "code": "genomictestrequest",
            "display": "Genomic Test Request",
            "definition": "A Service Request bundle for ordering genomic tests"
        },
        {
            "code": "genomictestresponse",
            "display": "Genomic Test Response",
            "definition": "A Diagnostic Report bundle for test results"
        }
    ]
}

Genomic-Patient-Choice-Category

A set of codes use to identify the categories of sources of obtaining the patient consent before undergoing Genomic test.

HTML View

This code system https://fhir.nhs.uk/CodeSystem/patient-choice-category-genomics defines the following codes:

Code	Display
AdultOwnChoice	Adult (made their own choice)
AdultLackCapacity	Adult lacking capacity (choices advised by consultee)
Child	Child (parent or guardian choices)
Clinician	Clinician has agreed to the test (in the patient`s best interest)
Deceased	Deceased (choices made on behalf of deceased individual)

Table View

CodeSystem.url[0]	https://fhir.nhs.uk/CodeSystem/patient-choice-category-genomics
CodeSystem.identifier[0].system[0]	https://fhir.nhs.uk/identifier/CodeSystem
CodeSystem.identifier[0].value[0]	patient-choice-category-genomics
CodeSystem.version[0]	0.1.0
CodeSystem.name[0]	PatientChoiceCategoryGenomics
CodeSystem.title[0]	Patient Choice Category Genomics
CodeSystem.status[0]	draft
CodeSystem.date[0]	2022-12-21T11:27:52.3231281+00:00
CodeSystem.publisher[0]	NHS Digital
CodeSystem.contact[0].name[0]	NHS Digital
CodeSystem.contact[0].telecom[0].system[0]	email
CodeSystem.contact[0].telecom[0].value[0]	interoperabilityteam@nhs.net
CodeSystem.contact[0].telecom[0].use[0]	work
CodeSystem.description[0]	A set of codes use to identify the categories of sources of obtaining the patient consent before undergoing Genomic test.
CodeSystem.copyright[0]	Copyright © 2022 NHS Digital
CodeSystem.caseSensitive[0]	True
CodeSystem.content[0]	complete
CodeSystem.concept[0].code[0]	AdultOwnChoice
CodeSystem.concept[0].display[0]	Adult (made their own choice)
CodeSystem.concept[1].code[0]	AdultLackCapacity
CodeSystem.concept[1].display[0]	Adult lacking capacity (choices advised by consultee)
CodeSystem.concept[2].code[0]	Child
CodeSystem.concept[2].display[0]	Child (parent or guardian choices)
CodeSystem.concept[3].code[0]	Clinician
CodeSystem.concept[3].display[0]	Clinician has agreed to the test (in the patient`s best interest)
CodeSystem.concept[4].code[0]	Deceased
CodeSystem.concept[4].display[0]	Deceased (choices made on behalf of deceased individual)

XML View

<CodeSystem xmlns="http://hl7.org/fhir">
    <url value="https://fhir.nhs.uk/CodeSystem/patient-choice-category-genomics" />
    <identifier>
        <system value="https://fhir.nhs.uk/identifier/CodeSystem" />
        <value value="patient-choice-category-genomics" />
    </identifier>
    <version value="0.1.0" />
    <name value="PatientChoiceCategoryGenomics" />
    <title value="Patient Choice Category Genomics" />
    <status value="draft" />
    <date value="2022-12-21T11:27:52.3231281+00:00" />
    <publisher value="NHS Digital" />
    <contact>
        <name value="NHS Digital" />
        <telecom>
            <system value="email" />
            <value value="interoperabilityteam@nhs.net" />
            <use value="work" />
        </telecom>
    </contact>
    <description value="A set of codes use to identify the categories of sources of obtaining the patient consent before undergoing Genomic test." />
    <copyright value="Copyright &#169; 2022 NHS Digital" />
    <caseSensitive value="true" />
    <content value="complete" />
    <concept>
        <code value="AdultOwnChoice" />
        <display value="Adult (made their own choice)" />
    </concept>
    <concept>
        <code value="AdultLackCapacity" />
        <display value="Adult lacking capacity (choices advised by consultee)" />
    </concept>
    <concept>
        <code value="Child" />
        <display value="Child (parent or guardian choices)" />
    </concept>
    <concept>
        <code value="Clinician" />
        <display value="Clinician has agreed to the test (in the patient`s best interest)" />
    </concept>
    <concept>
        <code value="Deceased" />
        <display value="Deceased (choices made on behalf of deceased individual)" />
    </concept>
</CodeSystem>

JSON View

{
    "resourceType": "CodeSystem",
    "url": "https://fhir.nhs.uk/CodeSystem/patient-choice-category-genomics",
    "identifier":  [
        {
            "system": "https://fhir.nhs.uk/identifier/CodeSystem",
            "value": "patient-choice-category-genomics"
        }
    ],
    "version": "0.1.0",
    "name": "PatientChoiceCategoryGenomics",
    "title": "Patient Choice Category Genomics",
    "status": "draft",
    "date": "2022-12-21T11:27:52.3231281+00:00",
    "publisher": "NHS Digital",
    "contact":  [
        {
            "name": "NHS Digital",
            "telecom":  [
                {
                    "system": "email",
                    "value": "interoperabilityteam@nhs.net",
                    "use": "work"
                }
            ]
        }
    ],
    "description": "A set of codes use to identify the categories of sources of obtaining the patient consent before undergoing Genomic test.",
    "copyright": "Copyright © 2022 NHS Digital",
    "caseSensitive": true,
    "content": "complete",
    "concept":  [
        {
            "code": "AdultOwnChoice",
            "display": "Adult (made their own choice)"
        },
        {
            "code": "AdultLackCapacity",
            "display": "Adult lacking capacity (choices advised by consultee)"
        },
        {
            "code": "Child",
            "display": "Child (parent or guardian choices)"
        },
        {
            "code": "Clinician",
            "display": "Clinician has agreed to the test (in the patient`s best interest)"
        },
        {
            "code": "Deceased",
            "display": "Deceased (choices made on behalf of deceased individual)"
        }
    ]
}

Genomic-Patient-Consultee

A code to identify if patient guardian is a Consultee

HTML View

This code system https://fhir.nhs.uk/CodeSystem/patient-consultee-genomics defines the following codes:

Code	Display
Consultee	Consultee

Table View

CodeSystem.url[0]	https://fhir.nhs.uk/CodeSystem/patient-consultee-genomics
CodeSystem.identifier[0].system[0]	https://fhir.nhs.uk/identifier/CodeSystem
CodeSystem.identifier[0].value[0]	patient-consultee-genomics
CodeSystem.version[0]	0.1.0
CodeSystem.name[0]	PatientConsulteeGenomics
CodeSystem.title[0]	Patient Consultee Genomics
CodeSystem.status[0]	draft
CodeSystem.date[0]	2022-12-28T16:41:15.0168724+00:00
CodeSystem.publisher[0]	NHS Digital
CodeSystem.contact[0].name[0]	NHS Digital
CodeSystem.contact[0].telecom[0].system[0]	email
CodeSystem.contact[0].telecom[0].value[0]	interoperabilityteam@nhs.net
CodeSystem.contact[0].telecom[0].use[0]	work
CodeSystem.description[0]	A code to identify if patient guardian is a Consultee
CodeSystem.copyright[0]	Copyright © 2022 NHS Digital
CodeSystem.caseSensitive[0]	True
CodeSystem.content[0]	complete
CodeSystem.concept[0].code[0]	Consultee
CodeSystem.concept[0].display[0]	Consultee

XML View

<CodeSystem xmlns="http://hl7.org/fhir">
    <url value="https://fhir.nhs.uk/CodeSystem/patient-consultee-genomics" />
    <identifier>
        <system value="https://fhir.nhs.uk/identifier/CodeSystem" />
        <value value="patient-consultee-genomics" />
    </identifier>
    <version value="0.1.0" />
    <name value="PatientConsulteeGenomics" />
    <title value="Patient Consultee Genomics" />
    <status value="draft" />
    <date value="2022-12-28T16:41:15.0168724+00:00" />
    <publisher value="NHS Digital" />
    <contact>
        <name value="NHS Digital" />
        <telecom>
            <system value="email" />
            <value value="interoperabilityteam@nhs.net" />
            <use value="work" />
        </telecom>
    </contact>
    <description value="A code to identify if patient guardian is a Consultee" />
    <copyright value="Copyright &#169; 2022 NHS Digital" />
    <caseSensitive value="true" />
    <content value="complete" />
    <concept>
        <code value="Consultee" />
        <display value="Consultee" />
    </concept>
</CodeSystem>

JSON View

{
    "resourceType": "CodeSystem",
    "url": "https://fhir.nhs.uk/CodeSystem/patient-consultee-genomics",
    "identifier":  [
        {
            "system": "https://fhir.nhs.uk/identifier/CodeSystem",
            "value": "patient-consultee-genomics"
        }
    ],
    "version": "0.1.0",
    "name": "PatientConsulteeGenomics",
    "title": "Patient Consultee Genomics",
    "status": "draft",
    "date": "2022-12-28T16:41:15.0168724+00:00",
    "publisher": "NHS Digital",
    "contact":  [
        {
            "name": "NHS Digital",
            "telecom":  [
                {
                    "system": "email",
                    "value": "interoperabilityteam@nhs.net",
                    "use": "work"
                }
            ]
        }
    ],
    "description": "A code to identify if patient guardian is a Consultee",
    "copyright": "Copyright © 2022 NHS Digital",
    "caseSensitive": true,
    "content": "complete",
    "concept":  [
        {
            "code": "Consultee",
            "display": "Consultee"
        }
    ]
}

Genomic-Patient-Research-Choice

A set of codes use to identify the sources of obtaining the patient consent in participating in the National Genomic Research.

HTML View

This code system https://fhir.nhs.uk/CodeSystem/patient-choice-researchparticipation defines the following codes:

Code	Display
LiketoDiscussLater	Patient would like to discuss at a later date
PatientLackCapacity	Patient lacks capacity and no consultee available
InappropriatetoDiscuss	Inappropriate to have discussion
Other	Other

Table View

CodeSystem.url[0]	https://fhir.nhs.uk/CodeSystem/patient-choice-researchparticipation
CodeSystem.identifier[0].system[0]	https://fhir.nhs.uk/identifier/CodeSystem
CodeSystem.identifier[0].value[0]	patient-choice-researchparticipation
CodeSystem.version[0]	0.1.0
CodeSystem.name[0]	PatientChoiceResearchParticipation
CodeSystem.title[0]	Patient Choice Research Participation
CodeSystem.status[0]	draft
CodeSystem.date[0]	2022-12-21T11:27:52.3231281+00:00
CodeSystem.publisher[0]	NHS Digital
CodeSystem.contact[0].name[0]	NHS Digital
CodeSystem.contact[0].telecom[0].system[0]	email
CodeSystem.contact[0].telecom[0].value[0]	interoperabilityteam@nhs.net
CodeSystem.contact[0].telecom[0].use[0]	work
CodeSystem.description[0]	A set of codes use to identify the sources of obtaining the patient consent in participating in the National Genomic Research.
CodeSystem.copyright[0]	Copyright © 2022 NHS Digital
CodeSystem.caseSensitive[0]	True
CodeSystem.content[0]	complete
CodeSystem.concept[0].code[0]	LiketoDiscussLater
CodeSystem.concept[0].display[0]	Patient would like to discuss at a later date
CodeSystem.concept[1].code[0]	PatientLackCapacity
CodeSystem.concept[1].display[0]	Patient lacks capacity and no consultee available
CodeSystem.concept[2].code[0]	InappropriatetoDiscuss
CodeSystem.concept[2].display[0]	Inappropriate to have discussion
CodeSystem.concept[3].code[0]	Other
CodeSystem.concept[3].display[0]	Other

XML View

<CodeSystem xmlns="http://hl7.org/fhir">
    <url value="https://fhir.nhs.uk/CodeSystem/patient-choice-researchparticipation" />
    <identifier>
        <system value="https://fhir.nhs.uk/identifier/CodeSystem" />
        <value value="patient-choice-researchparticipation" />
    </identifier>
    <version value="0.1.0" />
    <name value="PatientChoiceResearchParticipation" />
    <title value="Patient Choice Research Participation" />
    <status value="draft" />
    <date value="2022-12-21T11:27:52.3231281+00:00" />
    <publisher value="NHS Digital" />
    <contact>
        <name value="NHS Digital" />
        <telecom>
            <system value="email" />
            <value value="interoperabilityteam@nhs.net" />
            <use value="work" />
        </telecom>
    </contact>
    <description value="A set of codes use to identify the sources of obtaining the patient consent in participating in the National Genomic Research." />
    <copyright value="Copyright &#169; 2022 NHS Digital" />
    <caseSensitive value="true" />
    <content value="complete" />
    <concept>
        <code value="LiketoDiscussLater" />
        <display value="Patient would like to discuss at a later date" />
    </concept>
    <concept>
        <code value="PatientLackCapacity" />
        <display value="Patient lacks capacity and no consultee available" />
    </concept>
    <concept>
        <code value="InappropriatetoDiscuss" />
        <display value="Inappropriate to have discussion" />
    </concept>
    <concept>
        <code value="Other" />
        <display value="Other" />
    </concept>
</CodeSystem>

JSON View

{
    "resourceType": "CodeSystem",
    "url": "https://fhir.nhs.uk/CodeSystem/patient-choice-researchparticipation",
    "identifier":  [
        {
            "system": "https://fhir.nhs.uk/identifier/CodeSystem",
            "value": "patient-choice-researchparticipation"
        }
    ],
    "version": "0.1.0",
    "name": "PatientChoiceResearchParticipation",
    "title": "Patient Choice Research Participation",
    "status": "draft",
    "date": "2022-12-21T11:27:52.3231281+00:00",
    "publisher": "NHS Digital",
    "contact":  [
        {
            "name": "NHS Digital",
            "telecom":  [
                {
                    "system": "email",
                    "value": "interoperabilityteam@nhs.net",
                    "use": "work"
                }
            ]
        }
    ],
    "description": "A set of codes use to identify the sources of obtaining the patient consent in participating in the National Genomic Research.",
    "copyright": "Copyright © 2022 NHS Digital",
    "caseSensitive": true,
    "content": "complete",
    "concept":  [
        {
            "code": "LiketoDiscussLater",
            "display": "Patient would like to discuss at a later date"
        },
        {
            "code": "PatientLackCapacity",
            "display": "Patient lacks capacity and no consultee available"
        },
        {
            "code": "InappropriatetoDiscuss",
            "display": "Inappropriate to have discussion"
        },
        {
            "code": "Other",
            "display": "Other"
        }
    ]
}

Genomic-Task-Code

Codes for Tasks in genomics, mapped to NGTP stages (codes for equivalent NGTP stages are visible from the Table, XML and JSON views)

HTML View

This code system https://fhir.nhs.uk/CodeSystem/task-code-genomics defines the following codes:

Code	Display
ProcessGenomicTestRequest	Process Genomic Test Request
RequestSampleAlignment	Request & Sample Alignment
SamplePreparation	Sample Preparation
SampleProcessing	Sample Processing
GeneticGenomicDataProcessing	Genetic/Genomic Data Processing
Interpretation	Interpretation
ProduceInterimReport	Produce Interim Report
GenomicMDT	Genomic MDT
ProduceFinalReport	Produce Final Report
DistributeReport	Distribute Report

Table View

CodeSystem.url[0]	https://fhir.nhs.uk/CodeSystem/task-code-genomics
CodeSystem.identifier[0].system[0]	https://fhir.nhs.uk/identifier/CodeSystem
CodeSystem.identifier[0].value[0]	task-code-genomics
CodeSystem.version[0]	0.2.0
CodeSystem.name[0]	TaskCodeGenomics
CodeSystem.title[0]	Task Code Genomics
CodeSystem.status[0]	draft
CodeSystem.date[0]	2024-02-28T15:33:00+00:00
CodeSystem.publisher[0]	NHS England
CodeSystem.contact[0].name[0]	NHS England
CodeSystem.contact[0].telecom[0].system[0]	email
CodeSystem.contact[0].telecom[0].value[0]	interoperabilityteam@nhs.net
CodeSystem.contact[0].telecom[0].use[0]	work
CodeSystem.description[0]	A set of codes use to identify the type of task for Genomic Order Management
CodeSystem.copyright[0]	Copyright © 2023 NHS England
CodeSystem.caseSensitive[0]	True
CodeSystem.content[0]	complete
CodeSystem.concept[0].code[0]	ProcessGenomicTestRequest
CodeSystem.concept[0].display[0]	Process Genomic Test Request
CodeSystem.concept[0].designation[0].use[0].system[0]	http://snomed.info/sct
CodeSystem.concept[0].designation[0].use[0].code[0]	900000000000013009
CodeSystem.concept[0].designation[0].use[0].display[0]	Synonym
CodeSystem.concept[0].designation[0].value[0]	50.00
CodeSystem.concept[1].code[0]	RequestSampleAlignment
CodeSystem.concept[1].display[0]	Request & Sample Alignment
CodeSystem.concept[1].designation[0].use[0].system[0]	http://snomed.info/sct
CodeSystem.concept[1].designation[0].use[0].code[0]	900000000000013009
CodeSystem.concept[1].designation[0].use[0].display[0]	Synonym
CodeSystem.concept[1].designation[0].value[0]	100.00
CodeSystem.concept[2].code[0]	SamplePreparation
CodeSystem.concept[2].display[0]	Sample Preparation
CodeSystem.concept[2].designation[0].use[0].system[0]	http://snomed.info/sct
CodeSystem.concept[2].designation[0].use[0].code[0]	900000000000013009
CodeSystem.concept[2].designation[0].use[0].display[0]	Synonym
CodeSystem.concept[2].designation[0].value[0]	150.00
CodeSystem.concept[3].code[0]	SampleProcessing
CodeSystem.concept[3].display[0]	Sample Processing
CodeSystem.concept[3].designation[0].use[0].system[0]	http://snomed.info/sct
CodeSystem.concept[3].designation[0].use[0].code[0]	900000000000013009
CodeSystem.concept[3].designation[0].use[0].display[0]	Synonym
CodeSystem.concept[3].designation[0].value[0]	200.00
CodeSystem.concept[4].code[0]	GeneticGenomicDataProcessing
CodeSystem.concept[4].display[0]	Genetic/Genomic Data Processing
CodeSystem.concept[4].designation[0].use[0].system[0]	http://snomed.info/sct
CodeSystem.concept[4].designation[0].use[0].code[0]	900000000000013009
CodeSystem.concept[4].designation[0].use[0].display[0]	Synonym
CodeSystem.concept[4].designation[0].value[0]	250.00
CodeSystem.concept[5].code[0]	Interpretation
CodeSystem.concept[5].display[0]	Interpretation
CodeSystem.concept[5].designation[0].use[0].system[0]	http://snomed.info/sct
CodeSystem.concept[5].designation[0].use[0].code[0]	900000000000013009
CodeSystem.concept[5].designation[0].use[0].display[0]	Synonym
CodeSystem.concept[5].designation[0].value[0]	300.00
CodeSystem.concept[6].code[0]	ProduceInterimReport
CodeSystem.concept[6].display[0]	Produce Interim Report
CodeSystem.concept[6].designation[0].use[0].system[0]	http://snomed.info/sct
CodeSystem.concept[6].designation[0].use[0].code[0]	900000000000013009
CodeSystem.concept[6].designation[0].use[0].display[0]	Synonym
CodeSystem.concept[6].designation[0].value[0]	350.00
CodeSystem.concept[7].code[0]	GenomicMDT
CodeSystem.concept[7].display[0]	Genomic MDT
CodeSystem.concept[7].designation[0].use[0].system[0]	http://snomed.info/sct
CodeSystem.concept[7].designation[0].use[0].code[0]	900000000000013009
CodeSystem.concept[7].designation[0].use[0].display[0]	Synonym
CodeSystem.concept[7].designation[0].value[0]	400.00
CodeSystem.concept[8].code[0]	ProduceFinalReport
CodeSystem.concept[8].display[0]	Produce Final Report
CodeSystem.concept[8].designation[0].use[0].system[0]	http://snomed.info/sct
CodeSystem.concept[8].designation[0].use[0].code[0]	900000000000013009
CodeSystem.concept[8].designation[0].use[0].display[0]	Synonym
CodeSystem.concept[8].designation[0].value[0]	450.00
CodeSystem.concept[9].code[0]	DistributeReport
CodeSystem.concept[9].display[0]	Distribute Report
CodeSystem.concept[9].designation[0].use[0].system[0]	http://snomed.info/sct
CodeSystem.concept[9].designation[0].use[0].code[0]	900000000000013009
CodeSystem.concept[9].designation[0].use[0].display[0]	Synonym
CodeSystem.concept[9].designation[0].value[0]	500.00

XML View

<CodeSystem xmlns="http://hl7.org/fhir">
    <url value="https://fhir.nhs.uk/CodeSystem/task-code-genomics" />
    <identifier>
        <system value="https://fhir.nhs.uk/identifier/CodeSystem" />
        <value value="task-code-genomics" />
    </identifier>
    <version value="0.2.0" />
    <name value="TaskCodeGenomics" />
    <title value="Task Code Genomics" />
    <status value="draft" />
    <date value="2024-02-28T15:33:00+00:00" />
    <publisher value="NHS England" />
    <contact>
        <name value="NHS England" />
        <telecom>
            <system value="email" />
            <value value="interoperabilityteam@nhs.net" />
            <use value="work" />
        </telecom>
    </contact>
    <description value="A set of codes use to identify the type of task for Genomic Order Management" />
    <copyright value="Copyright &#169; 2023 NHS England" />
    <caseSensitive value="true" />
    <content value="complete" />
    <concept>
        <code value="ProcessGenomicTestRequest" />
        <display value="Process Genomic Test Request" />
        <designation>
            <use>
                <system value="http://snomed.info/sct" />
                <code value="900000000000013009" />
                <display value="Synonym" />
            </use>
            <value value="50.00" />
        </designation>
    </concept>
    <concept>
        <code value="RequestSampleAlignment" />
        <display value="Request &amp; Sample Alignment" />
        <designation>
            <use>
                <system value="http://snomed.info/sct" />
                <code value="900000000000013009" />
                <display value="Synonym" />
            </use>
            <value value="100.00" />
        </designation>
    </concept>
    <concept>
        <code value="SamplePreparation" />
        <display value="Sample Preparation" />
        <designation>
            <use>
                <system value="http://snomed.info/sct" />
                <code value="900000000000013009" />
                <display value="Synonym" />
            </use>
            <value value="150.00" />
        </designation>
    </concept>
    <concept>
        <code value="SampleProcessing" />
        <display value="Sample Processing" />
        <designation>
            <use>
                <system value="http://snomed.info/sct" />
                <code value="900000000000013009" />
                <display value="Synonym" />
            </use>
            <value value="200.00" />
        </designation>
    </concept>
    <concept>
        <code value="GeneticGenomicDataProcessing" />
        <display value="Genetic/Genomic Data Processing" />
        <designation>
            <use>
                <system value="http://snomed.info/sct" />
                <code value="900000000000013009" />
                <display value="Synonym" />
            </use>
            <value value="250.00" />
        </designation>
    </concept>
    <concept>
        <code value="Interpretation" />
        <display value="Interpretation" />
        <designation>
            <use>
                <system value="http://snomed.info/sct" />
                <code value="900000000000013009" />
                <display value="Synonym" />
            </use>
            <value value="300.00" />
        </designation>
    </concept>
    <concept>
        <code value="ProduceInterimReport" />
        <display value="Produce Interim Report" />
        <designation>
            <use>
                <system value="http://snomed.info/sct" />
                <code value="900000000000013009" />
                <display value="Synonym" />
            </use>
            <value value="350.00" />
        </designation>
    </concept>
    <concept>
        <code value="GenomicMDT" />
        <display value="Genomic MDT" />
        <designation>
            <use>
                <system value="http://snomed.info/sct" />
                <code value="900000000000013009" />
                <display value="Synonym" />
            </use>
            <value value="400.00" />
        </designation>
    </concept>
    <concept>
        <code value="ProduceFinalReport" />
        <display value="Produce Final Report" />
        <designation>
            <use>
                <system value="http://snomed.info/sct" />
                <code value="900000000000013009" />
                <display value="Synonym" />
            </use>
            <value value="450.00" />
        </designation>
    </concept>
    <concept>
        <code value="DistributeReport" />
        <display value="Distribute Report" />
        <designation>
            <use>
                <system value="http://snomed.info/sct" />
                <code value="900000000000013009" />
                <display value="Synonym" />
            </use>
            <value value="500.00" />
        </designation>
    </concept>
</CodeSystem>

JSON View

{
    "resourceType": "CodeSystem",
    "url": "https://fhir.nhs.uk/CodeSystem/task-code-genomics",
    "identifier":  [
        {
            "system": "https://fhir.nhs.uk/identifier/CodeSystem",
            "value": "task-code-genomics"
        }
    ],
    "version": "0.2.0",
    "name": "TaskCodeGenomics",
    "title": "Task Code Genomics",
    "status": "draft",
    "date": "2024-02-28T15:33:00+00:00",
    "publisher": "NHS England",
    "contact":  [
        {
            "name": "NHS England",
            "telecom":  [
                {
                    "system": "email",
                    "value": "interoperabilityteam@nhs.net",
                    "use": "work"
                }
            ]
        }
    ],
    "description": "A set of codes use to identify the type of task for Genomic Order Management",
    "copyright": "Copyright © 2023 NHS England",
    "caseSensitive": true,
    "content": "complete",
    "concept":  [
        {
            "code": "ProcessGenomicTestRequest",
            "display": "Process Genomic Test Request",
            "designation":  [
                {
                    "use": {
                        "system": "http://snomed.info/sct",
                        "code": "900000000000013009",
                        "display": "Synonym"
                    },
                    "value": "50.00"
                }
            ]
        },
        {
            "code": "RequestSampleAlignment",
            "display": "Request & Sample Alignment",
            "designation":  [
                {
                    "use": {
                        "system": "http://snomed.info/sct",
                        "code": "900000000000013009",
                        "display": "Synonym"
                    },
                    "value": "100.00"
                }
            ]
        },
        {
            "code": "SamplePreparation",
            "display": "Sample Preparation",
            "designation":  [
                {
                    "use": {
                        "system": "http://snomed.info/sct",
                        "code": "900000000000013009",
                        "display": "Synonym"
                    },
                    "value": "150.00"
                }
            ]
        },
        {
            "code": "SampleProcessing",
            "display": "Sample Processing",
            "designation":  [
                {
                    "use": {
                        "system": "http://snomed.info/sct",
                        "code": "900000000000013009",
                        "display": "Synonym"
                    },
                    "value": "200.00"
                }
            ]
        },
        {
            "code": "GeneticGenomicDataProcessing",
            "display": "Genetic/Genomic Data Processing",
            "designation":  [
                {
                    "use": {
                        "system": "http://snomed.info/sct",
                        "code": "900000000000013009",
                        "display": "Synonym"
                    },
                    "value": "250.00"
                }
            ]
        },
        {
            "code": "Interpretation",
            "display": "Interpretation",
            "designation":  [
                {
                    "use": {
                        "system": "http://snomed.info/sct",
                        "code": "900000000000013009",
                        "display": "Synonym"
                    },
                    "value": "300.00"
                }
            ]
        },
        {
            "code": "ProduceInterimReport",
            "display": "Produce Interim Report",
            "designation":  [
                {
                    "use": {
                        "system": "http://snomed.info/sct",
                        "code": "900000000000013009",
                        "display": "Synonym"
                    },
                    "value": "350.00"
                }
            ]
        },
        {
            "code": "GenomicMDT",
            "display": "Genomic MDT",
            "designation":  [
                {
                    "use": {
                        "system": "http://snomed.info/sct",
                        "code": "900000000000013009",
                        "display": "Synonym"
                    },
                    "value": "400.00"
                }
            ]
        },
        {
            "code": "ProduceFinalReport",
            "display": "Produce Final Report",
            "designation":  [
                {
                    "use": {
                        "system": "http://snomed.info/sct",
                        "code": "900000000000013009",
                        "display": "Synonym"
                    },
                    "value": "450.00"
                }
            ]
        },
        {
            "code": "DistributeReport",
            "display": "Distribute Report",
            "designation":  [
                {
                    "use": {
                        "system": "http://snomed.info/sct",
                        "code": "900000000000013009",
                        "display": "Synonym"
                    },
                    "value": "500.00"
                }
            ]
        }
    ]
}

Genomic-Task-StatusReason

Codes for status reasons within Tasks in genomics

HTML View

This code system https://fhir.nhs.uk/CodeSystem/task-statusReason-genomics defines the following codes:

Code	Display
FurtherClinicalDetailsRequired	Further Clinical Details Required
AwaitingSpecimen	Awaiting Specimen
AwaitingRoDAndSpecimen	Awaiting Record of Discussion and Specimen
InvalidRequest	Invalid Request
PipelineActivityFailure	Pipeline Activity Failure
TaskTimeExceeded	Task Time Exceeded
UnableToInterpret	Unable To Interpret
SpecimenReceived	SpecimenReceived
SpecimenQualityNotOK	Specimen Quality Not OK
TestNoLongerRequired	Test No Longer Required
MultipleTestRequestedOnTheSamePatient	Multiple Test Requested On The Same Patient(only one test required)
DecisionNotToProgressWithTestRequest	Decision Not To Progress With Test Request
TestCouldNotBeDeliveredDueToProcessFailures	Test Could Not Be Delivered Due To Process Failures
WrongPatient(Mark-in-Error)	Wrong Patient (Mark-in-Error)
SampleAlignedToWrongPatient(Mark-in-Error)	Sample Aligned To Wrong Patient (Mark-in-Error)
PatienceChoiceIncorrectlyRecorded(WGS Only)-Mark-in-Error	Patience Choice Incorrectly Recorded (WGS Only)-Mark-in-Error
CorrectionOfClinicalData(Mark-in-Error)	Correction Of Clinical Data (Mark-in-Error)

Table View

CodeSystem.url[0]	https://fhir.nhs.uk/CodeSystem/task-statusReason-genomics
CodeSystem.identifier[0].system[0]	https://fhir.nhs.uk/identifier/CodeSystem
CodeSystem.identifier[0].value[0]	task-statusReason-genomics
CodeSystem.version[0]	0.1.0
CodeSystem.name[0]	TaskStatusReasonGenomics
CodeSystem.title[0]	Task StatusReason Genomics
CodeSystem.status[0]	draft
CodeSystem.date[0]	2023-12-06
CodeSystem.publisher[0]	NHS England
CodeSystem.contact[0].name[0]	NHS England
CodeSystem.contact[0].telecom[0].system[0]	email
CodeSystem.contact[0].telecom[0].value[0]	interoperabilityteam@nhs.net
CodeSystem.contact[0].telecom[0].use[0]	work
CodeSystem.description[0]	Status reasons for Tasks in genomics
CodeSystem.copyright[0]	Copyright © 2023 NHS England
CodeSystem.caseSensitive[0]	True
CodeSystem.content[0]	complete
CodeSystem.concept[0].code[0]	FurtherClinicalDetailsRequired
CodeSystem.concept[0].display[0]	Further Clinical Details Required
CodeSystem.concept[1].code[0]	AwaitingSpecimen
CodeSystem.concept[1].display[0]	Awaiting Specimen
CodeSystem.concept[2].code[0]	AwaitingRoDAndSpecimen
CodeSystem.concept[2].display[0]	Awaiting Record of Discussion and Specimen
CodeSystem.concept[3].code[0]	InvalidRequest
CodeSystem.concept[3].display[0]	Invalid Request
CodeSystem.concept[4].code[0]	PipelineActivityFailure
CodeSystem.concept[4].display[0]	Pipeline Activity Failure
CodeSystem.concept[5].code[0]	TaskTimeExceeded
CodeSystem.concept[5].display[0]	Task Time Exceeded
CodeSystem.concept[6].code[0]	UnableToInterpret
CodeSystem.concept[6].display[0]	Unable To Interpret
CodeSystem.concept[7].code[0]	SpecimenReceived
CodeSystem.concept[7].display[0]	SpecimenReceived
CodeSystem.concept[8].code[0]	SpecimenQualityNotOK
CodeSystem.concept[8].display[0]	Specimen Quality Not OK
CodeSystem.concept[9].code[0]	TestNoLongerRequired
CodeSystem.concept[9].display[0]	Test No Longer Required
CodeSystem.concept[10].code[0]	MultipleTestRequestedOnTheSamePatient
CodeSystem.concept[10].display[0]	Multiple Test Requested On The Same Patient(only one test required)
CodeSystem.concept[11].code[0]	DecisionNotToProgressWithTestRequest
CodeSystem.concept[11].display[0]	Decision Not To Progress With Test Request
CodeSystem.concept[12].code[0]	TestCouldNotBeDeliveredDueToProcessFailures
CodeSystem.concept[12].display[0]	Test Could Not Be Delivered Due To Process Failures
CodeSystem.concept[13].code[0]	WrongPatient(Mark-in-Error)
CodeSystem.concept[13].display[0]	Wrong Patient (Mark-in-Error)
CodeSystem.concept[14].code[0]	SampleAlignedToWrongPatient(Mark-in-Error)
CodeSystem.concept[14].display[0]	Sample Aligned To Wrong Patient (Mark-in-Error)
CodeSystem.concept[15].code[0]	PatienceChoiceIncorrectlyRecorded(WGS Only)-Mark-in-Error
CodeSystem.concept[15].display[0]	Patience Choice Incorrectly Recorded (WGS Only)-Mark-in-Error
CodeSystem.concept[16].code[0]	CorrectionOfClinicalData(Mark-in-Error)
CodeSystem.concept[16].display[0]	Correction Of Clinical Data (Mark-in-Error)

XML View

<CodeSystem xmlns="http://hl7.org/fhir">
    <url value="https://fhir.nhs.uk/CodeSystem/task-statusReason-genomics" />
    <identifier>
        <system value="https://fhir.nhs.uk/identifier/CodeSystem" />
        <value value="task-statusReason-genomics" />
    </identifier>
    <version value="0.1.0" />
    <name value="TaskStatusReasonGenomics" />
    <title value="Task StatusReason Genomics" />
    <status value="draft" />
    <date value="2023-12-06" />
    <publisher value="NHS England" />
    <contact>
        <name value="NHS England" />
        <telecom>
            <system value="email" />
            <value value="interoperabilityteam@nhs.net" />
            <use value="work" />
        </telecom>
    </contact>
    <description value="Status reasons for Tasks in genomics" />
    <copyright value="Copyright &#169; 2023 NHS England" />
    <caseSensitive value="true" />
    <content value="complete" />
    <concept>
        <code value="FurtherClinicalDetailsRequired" />
        <display value="Further Clinical Details Required" />
    </concept>
    <concept>
        <code value="AwaitingSpecimen" />
        <display value="Awaiting Specimen" />
    </concept>
    <concept>
        <code value="AwaitingRoDAndSpecimen" />
        <display value="Awaiting Record of Discussion and Specimen" />
    </concept>
    <concept>
        <code value="InvalidRequest" />
        <display value="Invalid Request" />
    </concept>
    <concept>
        <code value="PipelineActivityFailure" />
        <display value="Pipeline Activity Failure" />
    </concept>
    <concept>
        <code value="TaskTimeExceeded" />
        <display value="Task Time Exceeded" />
    </concept>
    <concept>
        <code value="UnableToInterpret" />
        <display value="Unable To Interpret" />
    </concept>
    <concept>
        <code value="SpecimenReceived" />
        <display value="SpecimenReceived" />
    </concept>
    <concept>
        <code value="SpecimenQualityNotOK" />
        <display value="Specimen Quality Not OK" />
    </concept>
    <concept>
        <code value="TestNoLongerRequired" />
        <display value="Test No Longer Required" />
    </concept>
    <concept>
        <code value="MultipleTestRequestedOnTheSamePatient" />
        <display value="Multiple Test Requested On The Same Patient(only one test required)" />
    </concept>
    <concept>
        <code value="DecisionNotToProgressWithTestRequest" />
        <display value="Decision Not To Progress With Test Request" />
    </concept>
    <concept>
        <code value="TestCouldNotBeDeliveredDueToProcessFailures" />
        <display value="Test Could Not Be Delivered Due To Process Failures" />
    </concept>
    <concept>
        <code value="WrongPatient(Mark-in-Error)" />
        <display value="Wrong Patient (Mark-in-Error)" />
    </concept>
    <concept>
        <code value="SampleAlignedToWrongPatient(Mark-in-Error)" />
        <display value="Sample Aligned To Wrong Patient (Mark-in-Error)" />
    </concept>
    <concept>
        <code value="PatienceChoiceIncorrectlyRecorded(WGS Only)-Mark-in-Error" />
        <display value="Patience Choice Incorrectly Recorded (WGS Only)-Mark-in-Error" />
    </concept>
    <concept>
        <code value="CorrectionOfClinicalData(Mark-in-Error)" />
        <display value="Correction Of Clinical Data (Mark-in-Error)" />
    </concept>
</CodeSystem>

JSON View

{
    "resourceType": "CodeSystem",
    "url": "https://fhir.nhs.uk/CodeSystem/task-statusReason-genomics",
    "identifier":  [
        {
            "system": "https://fhir.nhs.uk/identifier/CodeSystem",
            "value": "task-statusReason-genomics"
        }
    ],
    "version": "0.1.0",
    "name": "TaskStatusReasonGenomics",
    "title": "Task StatusReason Genomics",
    "status": "draft",
    "date": "2023-12-06",
    "publisher": "NHS England",
    "contact":  [
        {
            "name": "NHS England",
            "telecom":  [
                {
                    "system": "email",
                    "value": "interoperabilityteam@nhs.net",
                    "use": "work"
                }
            ]
        }
    ],
    "description": "Status reasons for Tasks in genomics",
    "copyright": "Copyright © 2023 NHS England",
    "caseSensitive": true,
    "content": "complete",
    "concept":  [
        {
            "code": "FurtherClinicalDetailsRequired",
            "display": "Further Clinical Details Required"
        },
        {
            "code": "AwaitingSpecimen",
            "display": "Awaiting Specimen"
        },
        {
            "code": "AwaitingRoDAndSpecimen",
            "display": "Awaiting Record of Discussion and Specimen"
        },
        {
            "code": "InvalidRequest",
            "display": "Invalid Request"
        },
        {
            "code": "PipelineActivityFailure",
            "display": "Pipeline Activity Failure"
        },
        {
            "code": "TaskTimeExceeded",
            "display": "Task Time Exceeded"
        },
        {
            "code": "UnableToInterpret",
            "display": "Unable To Interpret"
        },
        {
            "code": "SpecimenReceived",
            "display": "SpecimenReceived"
        },
        {
            "code": "SpecimenQualityNotOK",
            "display": "Specimen Quality Not OK"
        },
        {
            "code": "TestNoLongerRequired",
            "display": "Test No Longer Required"
        },
        {
            "code": "MultipleTestRequestedOnTheSamePatient",
            "display": "Multiple Test Requested On The Same Patient(only one test required)"
        },
        {
            "code": "DecisionNotToProgressWithTestRequest",
            "display": "Decision Not To Progress With Test Request"
        },
        {
            "code": "TestCouldNotBeDeliveredDueToProcessFailures",
            "display": "Test Could Not Be Delivered Due To Process Failures"
        },
        {
            "code": "WrongPatient(Mark-in-Error)",
            "display": "Wrong Patient (Mark-in-Error)"
        },
        {
            "code": "SampleAlignedToWrongPatient(Mark-in-Error)",
            "display": "Sample Aligned To Wrong Patient (Mark-in-Error)"
        },
        {
            "code": "PatienceChoiceIncorrectlyRecorded(WGS Only)-Mark-in-Error",
            "display": "Patience Choice Incorrectly Recorded (WGS Only)-Mark-in-Error"
        },
        {
            "code": "CorrectionOfClinicalData(Mark-in-Error)",
            "display": "Correction Of Clinical Data (Mark-in-Error)"
        }
    ]
}

Genomic-Coverage

A set of codes that define the funding category for a patient.

HTML View

This code system https://fhir.hl7.org.uk/CodeSystem/UKCore-FundingCategory defines the following codes:

Code	Display
nhs	NHS
private	Private
devolved-nations	Devolved nations

Table View

CodeSystem.id[0]	UKCore-FundingCategory
CodeSystem.url[0]	https://fhir.hl7.org.uk/CodeSystem/UKCore-FundingCategory
CodeSystem.version[0]	1.0.0
CodeSystem.name[0]	UKCoreFundingCategory
CodeSystem.title[0]	UK Core Funding Category
CodeSystem.status[0]	active
CodeSystem.date[0]	2023-04-28
CodeSystem.publisher[0]	HL7 UK
CodeSystem.contact[0].name[0]	HL7 UK
CodeSystem.contact[0].telecom[0].system[0]	email
CodeSystem.contact[0].telecom[0].value[0]	ukcore@hl7.org.uk
CodeSystem.contact[0].telecom[0].use[0]	work
CodeSystem.contact[0].telecom[0].rank[0]	1
CodeSystem.description[0]	A set of codes that define the funding category for a patient.
CodeSystem.copyright[0]	Copyright © 2021+ HL7 UK Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at https://www.hl7.org/fhir/license.html.
CodeSystem.caseSensitive[0]	True
CodeSystem.content[0]	complete
CodeSystem.concept[0].code[0]	nhs
CodeSystem.concept[0].display[0]	NHS
CodeSystem.concept[1].code[0]	private
CodeSystem.concept[1].display[0]	Private
CodeSystem.concept[2].code[0]	devolved-nations
CodeSystem.concept[2].display[0]	Devolved nations

XML View

<CodeSystem xmlns="http://hl7.org/fhir">
    <id value="UKCore-FundingCategory" />
    <url value="https://fhir.hl7.org.uk/CodeSystem/UKCore-FundingCategory" />
    <version value="1.0.0" />
    <name value="UKCoreFundingCategory" />
    <title value="UK Core Funding Category" />
    <status value="active" />
    <date value="2023-04-28" />
    <publisher value="HL7 UK" />
    <contact>
        <name value="HL7 UK" />
        <telecom>
            <system value="email" />
            <value value="ukcore@hl7.org.uk" />
            <use value="work" />
            <rank value="1" />
        </telecom>
    </contact>
    <description value="A set of codes that define the funding category for a patient." />
    <copyright value="Copyright &#169; 2021+ HL7 UK Licensed under the Apache License, Version 2.0 (the &quot;License&quot;); you may not use this file except in compliance with the License. You may obtain a copy of the License at  http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an &quot;AS IS&quot; BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7&#174; FHIR&#174; standard Copyright &#169; 2011+ HL7 The HL7&#174; FHIR&#174; standard is used under the FHIR license. You may obtain a copy of the FHIR license at  https://www.hl7.org/fhir/license.html." />
    <caseSensitive value="true" />
    <content value="complete" />
    <concept>
        <code value="nhs" />
        <display value="NHS" />
    </concept>
    <concept>
        <code value="private" />
        <display value="Private" />
    </concept>
    <concept>
        <code value="devolved-nations" />
        <display value="Devolved nations" />
    </concept>
</CodeSystem>

JSON View

{
    "resourceType": "CodeSystem",
    "id": "UKCore-FundingCategory",
    "url": "https://fhir.hl7.org.uk/CodeSystem/UKCore-FundingCategory",
    "version": "1.0.0",
    "name": "UKCoreFundingCategory",
    "title": "UK Core Funding Category",
    "status": "active",
    "date": "2023-04-28",
    "publisher": "HL7 UK",
    "contact":  [
        {
            "name": "HL7 UK",
            "telecom":  [
                {
                    "system": "email",
                    "value": "ukcore@hl7.org.uk",
                    "use": "work",
                    "rank": 1
                }
            ]
        }
    ],
    "description": "A set of codes that define the funding category for a patient.",
    "copyright": "Copyright © 2021+ HL7 UK Licensed under the Apache License, Version 2.0 (the \"License\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at  http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at  https://www.hl7.org/fhir/license.html.",
    "caseSensitive": true,
    "content": "complete",
    "concept":  [
        {
            "code": "nhs",
            "display": "NHS"
        },
        {
            "code": "private",
            "display": "Private"
        },
        {
            "code": "devolved-nations",
            "display": "Devolved nations"
        }
    ]
}

Genomic-NHSNumber-Unvailable-Reason

A set of concepts that define the reason that an NHS number is not available for use as an identifier.

HTML View

This code system https://fhir.hl7.org.uk/CodeSystem/UKCore-NHSNumberUnavailableReason defines the following codes:

Code	Display
nhs-number-not-known	NHS number not known
overseas-patient	Overseas patient
devolved-nation	Devolved nation

Table View

CodeSystem.id[0]	UKCore-NHSNumberUnavailableReason
CodeSystem.url[0]	https://fhir.hl7.org.uk/CodeSystem/UKCore-NHSNumberUnavailableReason
CodeSystem.version[0]	1.0.0
CodeSystem.name[0]	UKCoreNHSNumberUnavailableReason
CodeSystem.title[0]	UK Core NHS Number Unavailable Reason
CodeSystem.status[0]	active
CodeSystem.date[0]	2023-04-28
CodeSystem.publisher[0]	HL7 UK
CodeSystem.contact[0].name[0]	HL7 UK
CodeSystem.contact[0].telecom[0].system[0]	email
CodeSystem.contact[0].telecom[0].value[0]	ukcore@hl7.org.uk
CodeSystem.contact[0].telecom[0].use[0]	work
CodeSystem.contact[0].telecom[0].rank[0]	1
CodeSystem.description[0]	A set of concepts that define the reason that an NHS number is not available for use as an identifier.
CodeSystem.copyright[0]	Copyright © 2021+ HL7 UK Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at https://www.hl7.org/fhir/license.html.
CodeSystem.caseSensitive[0]	True
CodeSystem.content[0]	complete
CodeSystem.concept[0].code[0]	nhs-number-not-known
CodeSystem.concept[0].display[0]	NHS number not known
CodeSystem.concept[1].code[0]	overseas-patient
CodeSystem.concept[1].display[0]	Overseas patient
CodeSystem.concept[2].code[0]	devolved-nation
CodeSystem.concept[2].display[0]	Devolved nation

XML View

<CodeSystem xmlns="http://hl7.org/fhir">
    <id value="UKCore-NHSNumberUnavailableReason" />
    <url value="https://fhir.hl7.org.uk/CodeSystem/UKCore-NHSNumberUnavailableReason" />
    <version value="1.0.0" />
    <name value="UKCoreNHSNumberUnavailableReason" />
    <title value="UK Core NHS Number Unavailable Reason" />
    <status value="active" />
    <date value="2023-04-28" />
    <publisher value="HL7 UK" />
    <contact>
        <name value="HL7 UK" />
        <telecom>
            <system value="email" />
            <value value="ukcore@hl7.org.uk" />
            <use value="work" />
            <rank value="1" />
        </telecom>
    </contact>
    <description value="A set of concepts that define the reason that an NHS number is not available for use as an identifier." />
    <copyright value="Copyright &#169; 2021+ HL7 UK Licensed under the Apache License, Version 2.0 (the &quot;License&quot;); you may not use this file except in compliance with the License. You may obtain a copy of the License at  http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an &quot;AS IS&quot; BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7&#174; FHIR&#174; standard Copyright &#169; 2011+ HL7 The HL7&#174; FHIR&#174; standard is used under the FHIR license. You may obtain a copy of the FHIR license at  https://www.hl7.org/fhir/license.html." />
    <caseSensitive value="true" />
    <content value="complete" />
    <concept>
        <code value="nhs-number-not-known" />
        <display value="NHS number not known" />
    </concept>
    <concept>
        <code value="overseas-patient" />
        <display value="Overseas patient" />
    </concept>
    <concept>
        <code value="devolved-nation" />
        <display value="Devolved nation" />
    </concept>
</CodeSystem>

JSON View

{
    "resourceType": "CodeSystem",
    "id": "UKCore-NHSNumberUnavailableReason",
    "url": "https://fhir.hl7.org.uk/CodeSystem/UKCore-NHSNumberUnavailableReason",
    "version": "1.0.0",
    "name": "UKCoreNHSNumberUnavailableReason",
    "title": "UK Core NHS Number Unavailable Reason",
    "status": "active",
    "date": "2023-04-28",
    "publisher": "HL7 UK",
    "contact":  [
        {
            "name": "HL7 UK",
            "telecom":  [
                {
                    "system": "email",
                    "value": "ukcore@hl7.org.uk",
                    "use": "work",
                    "rank": 1
                }
            ]
        }
    ],
    "description": "A set of concepts that define the reason that an NHS number is not available for use as an identifier.",
    "copyright": "Copyright © 2021+ HL7 UK Licensed under the Apache License, Version 2.0 (the \"License\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at  http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at  https://www.hl7.org/fhir/license.html.",
    "caseSensitive": true,
    "content": "complete",
    "concept":  [
        {
            "code": "nhs-number-not-known",
            "display": "NHS number not known"
        },
        {
            "code": "overseas-patient",
            "display": "Overseas patient"
        },
        {
            "code": "devolved-nation",
            "display": "Devolved nation"
        }
    ]
}

Genomic-Organization-Type

A set of codes to define additional genomic lab concepts for an organisation type.

HTML View

This code system https://fhir.hl7.org.uk/CodeSystem/UKCore-OrganizationTypeGenomics defines the following codes:

Code	Display
GLH	Genomic Lab Hub
GEL	Genomics England
LAB	Other Genomics Laboratory

Table View

CodeSystem.id[0]	UKCore-OrganizationTypeGenomics
CodeSystem.url[0]	https://fhir.hl7.org.uk/CodeSystem/UKCore-OrganizationTypeGenomics
CodeSystem.version[0]	1.0.0
CodeSystem.name[0]	UKCoreOrganizationTypeGenomics
CodeSystem.title[0]	UK Core Organization Type Genomics
CodeSystem.status[0]	active
CodeSystem.date[0]	2023-04-28
CodeSystem.publisher[0]	HL7 UK
CodeSystem.contact[0].name[0]	HL7 UK
CodeSystem.contact[0].telecom[0].system[0]	email
CodeSystem.contact[0].telecom[0].value[0]	ukcore@hl7.org.uk
CodeSystem.contact[0].telecom[0].use[0]	work
CodeSystem.contact[0].telecom[0].rank[0]	1
CodeSystem.description[0]	A set of codes to define additional genomic lab concepts for an organisation type.
CodeSystem.copyright[0]	Copyright © 2021+ HL7 UK Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at https://www.hl7.org/fhir/license.html.
CodeSystem.caseSensitive[0]	True
CodeSystem.content[0]	complete
CodeSystem.concept[0].code[0]	GLH
CodeSystem.concept[0].display[0]	Genomic Lab Hub
CodeSystem.concept[1].code[0]	GEL
CodeSystem.concept[1].display[0]	Genomics England
CodeSystem.concept[2].code[0]	LAB
CodeSystem.concept[2].display[0]	Other Genomics Laboratory

XML View

<CodeSystem xmlns="http://hl7.org/fhir">
    <id value="UKCore-OrganizationTypeGenomics" />
    <url value="https://fhir.hl7.org.uk/CodeSystem/UKCore-OrganizationTypeGenomics" />
    <version value="1.0.0" />
    <name value="UKCoreOrganizationTypeGenomics" />
    <title value="UK Core Organization Type Genomics" />
    <status value="active" />
    <date value="2023-04-28" />
    <publisher value="HL7 UK" />
    <contact>
        <name value="HL7 UK" />
        <telecom>
            <system value="email" />
            <value value="ukcore@hl7.org.uk" />
            <use value="work" />
            <rank value="1" />
        </telecom>
    </contact>
    <description value="A set of codes to define additional genomic lab concepts for an organisation type." />
    <copyright value="Copyright &#169; 2021+ HL7 UK Licensed under the Apache License, Version 2.0 (the &quot;License&quot;); you may not use this file except in compliance with the License. You may obtain a copy of the License at  http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an &quot;AS IS&quot; BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7&#174; FHIR&#174; standard Copyright &#169; 2011+ HL7 The HL7&#174; FHIR&#174; standard is used under the FHIR license. You may obtain a copy of the FHIR license at  https://www.hl7.org/fhir/license.html." />
    <caseSensitive value="true" />
    <content value="complete" />
    <concept>
        <code value="GLH" />
        <display value="Genomic Lab Hub" />
    </concept>
    <concept>
        <code value="GEL" />
        <display value="Genomics England" />
    </concept>
    <concept>
        <code value="LAB" />
        <display value="Other Genomics Laboratory" />
    </concept>
</CodeSystem>

JSON View

{
    "resourceType": "CodeSystem",
    "id": "UKCore-OrganizationTypeGenomics",
    "url": "https://fhir.hl7.org.uk/CodeSystem/UKCore-OrganizationTypeGenomics",
    "version": "1.0.0",
    "name": "UKCoreOrganizationTypeGenomics",
    "title": "UK Core Organization Type Genomics",
    "status": "active",
    "date": "2023-04-28",
    "publisher": "HL7 UK",
    "contact":  [
        {
            "name": "HL7 UK",
            "telecom":  [
                {
                    "system": "email",
                    "value": "ukcore@hl7.org.uk",
                    "use": "work",
                    "rank": 1
                }
            ]
        }
    ],
    "description": "A set of codes to define additional genomic lab concepts for an organisation type.",
    "copyright": "Copyright © 2021+ HL7 UK Licensed under the Apache License, Version 2.0 (the \"License\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at  http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at  https://www.hl7.org/fhir/license.html.",
    "caseSensitive": true,
    "content": "complete",
    "concept":  [
        {
            "code": "GLH",
            "display": "Genomic Lab Hub"
        },
        {
            "code": "GEL",
            "display": "Genomics England"
        },
        {
            "code": "LAB",
            "display": "Other Genomics Laboratory"
        }
    ]
}

Genomic-Sample-State

A CodeSystem to record the categorisation of a specimen, either sourced from a Tumour or Germline.

HTML View

This code system https://fhir.hl7.org.uk/CodeSystem/UKCore-SampleCategory defines the following codes:

Code	Display
tumour	Tumour
germline	Germline

Table View

CodeSystem.id[0]	UKCore-SampleCategory
CodeSystem.url[0]	https://fhir.hl7.org.uk/CodeSystem/UKCore-SampleCategory
CodeSystem.version[0]	1.0.0
CodeSystem.name[0]	UKCoreSampleCategory
CodeSystem.title[0]	UK Core Sample Category
CodeSystem.status[0]	active
CodeSystem.date[0]	2023-04-28
CodeSystem.publisher[0]	HL7 UK
CodeSystem.contact[0].name[0]	HL7 UK
CodeSystem.contact[0].telecom[0].system[0]	email
CodeSystem.contact[0].telecom[0].value[0]	ukcore@hl7.org.uk
CodeSystem.contact[0].telecom[0].use[0]	work
CodeSystem.contact[0].telecom[0].rank[0]	1
CodeSystem.description[0]	A CodeSystem to record the categorisation of a specimen, either sourced from a Tumour or Germline.
CodeSystem.copyright[0]	Copyright © 2021+ HL7 UK Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at https://www.hl7.org/fhir/license.html.
CodeSystem.caseSensitive[0]	True
CodeSystem.content[0]	complete
CodeSystem.concept[0].code[0]	tumour
CodeSystem.concept[0].display[0]	Tumour
CodeSystem.concept[1].code[0]	germline
CodeSystem.concept[1].display[0]	Germline

XML View

<CodeSystem xmlns="http://hl7.org/fhir">
    <id value="UKCore-SampleCategory" />
    <url value="https://fhir.hl7.org.uk/CodeSystem/UKCore-SampleCategory" />
    <version value="1.0.0" />
    <name value="UKCoreSampleCategory" />
    <title value="UK Core Sample Category" />
    <status value="active" />
    <date value="2023-04-28" />
    <publisher value="HL7 UK" />
    <contact>
        <name value="HL7 UK" />
        <telecom>
            <system value="email" />
            <value value="ukcore@hl7.org.uk" />
            <use value="work" />
            <rank value="1" />
        </telecom>
    </contact>
    <description value="A CodeSystem to record the categorisation of a specimen, either sourced from a Tumour or Germline." />
    <copyright value="Copyright &#169; 2021+ HL7 UK Licensed under the Apache License, Version 2.0 (the &quot;License&quot;); you may not use this file except in compliance with the License. You may obtain a copy of the License at  http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an &quot;AS IS&quot; BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7&#174; FHIR&#174; standard Copyright &#169; 2011+ HL7 The HL7&#174; FHIR&#174; standard is used under the FHIR license. You may obtain a copy of the FHIR license at  https://www.hl7.org/fhir/license.html." />
    <caseSensitive value="true" />
    <content value="complete" />
    <concept>
        <code value="tumour" />
        <display value="Tumour" />
    </concept>
    <concept>
        <code value="germline" />
        <display value="Germline" />
    </concept>
</CodeSystem>

JSON View

{
    "resourceType": "CodeSystem",
    "id": "UKCore-SampleCategory",
    "url": "https://fhir.hl7.org.uk/CodeSystem/UKCore-SampleCategory",
    "version": "1.0.0",
    "name": "UKCoreSampleCategory",
    "title": "UK Core Sample Category",
    "status": "active",
    "date": "2023-04-28",
    "publisher": "HL7 UK",
    "contact":  [
        {
            "name": "HL7 UK",
            "telecom":  [
                {
                    "system": "email",
                    "value": "ukcore@hl7.org.uk",
                    "use": "work",
                    "rank": 1
                }
            ]
        }
    ],
    "description": "A CodeSystem to record the categorisation of a specimen, either sourced from a Tumour or Germline.",
    "copyright": "Copyright © 2021+ HL7 UK Licensed under the Apache License, Version 2.0 (the \"License\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at  http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at  https://www.hl7.org/fhir/license.html.",
    "caseSensitive": true,
    "content": "complete",
    "concept":  [
        {
            "code": "tumour",
            "display": "Tumour"
        },
        {
            "code": "germline",
            "display": "Germline"
        }
    ]
}

Genomic-Test-Types

A CodeSystem to categorise if the service request is for Whole Genome Sequencing (WGS)/non-WGS Rare Disease/Cancer.

HTML View

This code system https://fhir.hl7.org.uk/CodeSystem/UKCore-GenomeSequencingCategory defines the following codes:

Code	Display
rare-disease-wgs	Rare Disease - WGS
rare-disease-non-wgs	Rare Disease - Non-WGS
cancer-wgs	Cancer - WGS
cancer-non-wgs	Cancer - Non-WGS

Table View

CodeSystem.id[0]	UKCore-GenomeSequencingCategory
CodeSystem.url[0]	https://fhir.hl7.org.uk/CodeSystem/UKCore-GenomeSequencingCategory
CodeSystem.version[0]	1.0.0
CodeSystem.name[0]	UKCoreGenomeSequencingCategory
CodeSystem.title[0]	UK Core Genome Sequencing Category
CodeSystem.status[0]	active
CodeSystem.date[0]	2023-04-28
CodeSystem.publisher[0]	HL7 UK
CodeSystem.contact[0].name[0]	HL7 UK
CodeSystem.contact[0].telecom[0].system[0]	email
CodeSystem.contact[0].telecom[0].value[0]	ukcore@hl7.org.uk
CodeSystem.contact[0].telecom[0].use[0]	work
CodeSystem.contact[0].telecom[0].rank[0]	1
CodeSystem.description[0]	A CodeSystem to categorise if the service request is for Whole Genome Sequencing (WGS)/non-WGS Rare Disease/Cancer.
CodeSystem.copyright[0]	Copyright © 2021+ HL7 UK Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at https://www.hl7.org/fhir/license.html.
CodeSystem.caseSensitive[0]	True
CodeSystem.content[0]	complete
CodeSystem.concept[0].code[0]	rare-disease-wgs
CodeSystem.concept[0].display[0]	Rare Disease - WGS
CodeSystem.concept[1].code[0]	rare-disease-non-wgs
CodeSystem.concept[1].display[0]	Rare Disease - Non-WGS
CodeSystem.concept[2].code[0]	cancer-wgs
CodeSystem.concept[2].display[0]	Cancer - WGS
CodeSystem.concept[3].code[0]	cancer-non-wgs
CodeSystem.concept[3].display[0]	Cancer - Non-WGS

XML View

<CodeSystem xmlns="http://hl7.org/fhir">
    <id value="UKCore-GenomeSequencingCategory" />
    <url value="https://fhir.hl7.org.uk/CodeSystem/UKCore-GenomeSequencingCategory" />
    <version value="1.0.0" />
    <name value="UKCoreGenomeSequencingCategory" />
    <title value="UK Core Genome Sequencing Category" />
    <status value="active" />
    <date value="2023-04-28" />
    <publisher value="HL7 UK" />
    <contact>
        <name value="HL7 UK" />
        <telecom>
            <system value="email" />
            <value value="ukcore@hl7.org.uk" />
            <use value="work" />
            <rank value="1" />
        </telecom>
    </contact>
    <description value="A CodeSystem to categorise if the service request is for Whole Genome Sequencing (WGS)/non-WGS Rare Disease/Cancer." />
    <copyright value="Copyright &#169; 2021+ HL7 UK Licensed under the Apache License, Version 2.0 (the &quot;License&quot;); you may not use this file except in compliance with the License. You may obtain a copy of the License at  http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an &quot;AS IS&quot; BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7&#174; FHIR&#174; standard Copyright &#169; 2011+ HL7 The HL7&#174; FHIR&#174; standard is used under the FHIR license. You may obtain a copy of the FHIR license at  https://www.hl7.org/fhir/license.html." />
    <caseSensitive value="true" />
    <content value="complete" />
    <concept>
        <code value="rare-disease-wgs" />
        <display value="Rare Disease - WGS" />
    </concept>
    <concept>
        <code value="rare-disease-non-wgs" />
        <display value="Rare Disease - Non-WGS" />
    </concept>
    <concept>
        <code value="cancer-wgs" />
        <display value="Cancer - WGS" />
    </concept>
    <concept>
        <code value="cancer-non-wgs" />
        <display value="Cancer - Non-WGS" />
    </concept>
</CodeSystem>

JSON View

{
    "resourceType": "CodeSystem",
    "id": "UKCore-GenomeSequencingCategory",
    "url": "https://fhir.hl7.org.uk/CodeSystem/UKCore-GenomeSequencingCategory",
    "version": "1.0.0",
    "name": "UKCoreGenomeSequencingCategory",
    "title": "UK Core Genome Sequencing Category",
    "status": "active",
    "date": "2023-04-28",
    "publisher": "HL7 UK",
    "contact":  [
        {
            "name": "HL7 UK",
            "telecom":  [
                {
                    "system": "email",
                    "value": "ukcore@hl7.org.uk",
                    "use": "work",
                    "rank": 1
                }
            ]
        }
    ],
    "description": "A CodeSystem to categorise if the service request is for Whole Genome Sequencing (WGS)/non-WGS Rare Disease/Cancer.",
    "copyright": "Copyright © 2021+ HL7 UK Licensed under the Apache License, Version 2.0 (the \"License\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at  http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at  https://www.hl7.org/fhir/license.html.",
    "caseSensitive": true,
    "content": "complete",
    "concept":  [
        {
            "code": "rare-disease-wgs",
            "display": "Rare Disease - WGS"
        },
        {
            "code": "rare-disease-non-wgs",
            "display": "Rare Disease - Non-WGS"
        },
        {
            "code": "cancer-wgs",
            "display": "Cancer - WGS"
        },
        {
            "code": "cancer-non-wgs",
            "display": "Cancer - Non-WGS"
        }
    ]
}