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.

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"
                }
            ]
        }
    ]
}