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.
Structured Reporting
Data Mapping
Structured Reporting is currently being investigated by the NHS England Genomics Unit. The following page outlines the initial data mapping to FHIR, using the ACGS guidelines as the business requirements, which imply an underlying reporting data model. This will be further refined as the NHS England Genomics Unit starts a focused reporting business analysis activity.
| ACGS Section | ACGS Guidance | Conformance Requirement | FHIR Element | Notes |
|---|---|---|---|---|
| Report Format - General format | Interpretation and implications | SHALL | DiagnosticReport.conclusionCode and DiagnosticReport.result | Using diagnostic and therapeutic implication slices |
| Report Format - General format | Overall result and conclusion | SHALL | DiagnosticReport.conclusion | TBC Coding scheme used for conclusion codes |
| Report Format - General format | Report only goes to authorised recipients | SHALL | Composition.extension:informationRecipient | MAY also use subscriptions via DiagnosticReport.basedOn(ServiceRequest.requester) |
| Report Format - General format | Supporting information in appendices with patient identifier | SHOULD | DiagnosticReport.extension:supporting-info | Each resource would additionally reference the patient |
| Report Format - General format | Background/context as may be seen by patient or other HCP | MAY | DiagnosticReport.basedOn or DiagnosticReport.extension:supporting-info | Used basedOn where context is captured in a ServiceRequest |
| Report Format - Recipients of reports | - Name, contact details (or unique identifier), referral unit for requesting clinician and additional copy recipients | SHALL | ServiceRequest.requester(PractitionerRole) | Multiple elements in PractitionerRole including identifier, practitioner, organization, telecom |
| Report Format - Recipients of reports | Comply with laws around archiving | SHALL | N/A | Part of surrounding governance, not payload |
| Report Format - Recipients of reports | Copy to requesting lab for out of region tests | SHOULD | Composition.extension:informationRecipient | |
| Report Format - Recipients of reports | Direct patient reporting not recommended | SHOULD NOT | DiagnosticReport.meta(security=NOPAT) | |
| Report Format - Laboratory identification | Issuing lab and contact details | SHALL | DiagnosticReport.performer(PractitionerRole/Organization TBC)/Composition.author | |
| Report Format - Laboratory identification | Title and issue date | SHOULD | Composition.title and DiagnosticReport.issued | |
| Report Format - Laboratory identification | Accreditation status of lab test (in compliance with lab accreditation status) | SHOULD | RegulatedAuthorization | There is also a proposed extension for LabAccreditationStatus for procedure being develoepd by HL7 EU |
| Report Format - Patient and Sample Identification | Patient identified by name and DoB | SHALL | DiagnosticReport.subject(Patient) | This information would likely be included in the Patient name/birthDate. In FHIR, for NHS patients, this would be in the PDS record only |
| Report Format - Patient and Sample Identification | - Unique lab number/nhs number | SHALL | DiagnosticReport.subject.identifier | |
| Report Format - Patient and Sample Identification | Prenatal result from fetus, not mother, clearly indicated if multiple samples from one pregnancy, multiple fetuses etc. | SHALL | Observation.subject | Could also be obtained from the Observation.specimen.subject. TBC Pregnancy identifier is still under investigation |
| Report Format - Patient and Sample Identification | For infant samples, include DoB and hospital/nhs number (future siblings will have the same, Baby FamilyName name) |
SHALL | Specimen.subject(Patient) | NHS registered patients expected to have NHS Number, birthDate on PDS record |
| Report Format - Patient and Sample Identification | For infant samples, may also include phenotypic gender or genetic sex | MAY | Specimen.subject(Patient) | NHS registered patients expected to have gender on PDS record (sexAtBirth extension usage TBC). Genetic sex MAY be represented as an Observation |
| Report Format - Patient and Sample Identification | Where clinically relevant, sex or gender | SHOULD | Patient.extension:birthSex and Patient.gender | For sex at birth, currently QuestionnaireResponse.item(linkId=1345193002).answer is being used as an interim measure for PDS registered patients. |
| Report Format - Patient and Sample Identification | Stand-alone report for each patient | SHOULD | DiagnosticReport.subject | Separate DiagnosticReport for each subject |
| Report Format - Patient and Sample Identification | Limit family information e.g. family members, unless pertinent | SHOULD NOT | RelatedPerson | RelatedPersons, FamilyMemberHistory etc. to reduce patient identifiable information included wherever possible |
| Report Format - Results and Interpretation | ACMG guidelines used for Sequence variant classification and interpretation | SHALL | TBC | Data requirements not yet investigated |
| Report Format - Results and Interpretation - Correct and appropriate nomenclature | Nomenclature for variants to use ISCN or HGVS | SHALL | DiagnosticReport.result:variant(Observation) | Observation.component:genomic-hgvs/cytogenetic-nomenclature coding system to use the CodeSystem for HGVS or ISCN |
| Report Format - Results and Interpretation - Correct and appropriate nomenclature | - If the test is FISH, ISCN not mandatory, results described in both headline summary and text instead | SHALL | Observation.component.code.text | |
| Report Format - Results and Interpretation - Correct and appropriate nomenclature | - If results include repeat expansions, HGVS not mandatory, results presented in words | SHALL | Observation.component.code.text | |
| Report Format - Results and Interpretation - Correct and appropriate nomenclature | - Key including size ranges for normal, intermediate/premutation, affected, with reference | SHALL | Observation.referenceRange and Observation.extension:workflow-relatedArtifact | |
| Report Format - Results and Interpretation - Correct and appropriate nomenclature | If reporting nucleotide coordinates, codon numbering, protein amino acid numbering used, the gene reference sequence/genome build is required | SHALL | Observation.component:coordinate-system | |
| Report Format - Results and Interpretation - Correct and appropriate nomenclature | - If genomic coordinates used, genome build required | SHALL | Observation.component:reference-sequence-assembly | |
| Report Format - Results and Interpretation - Correct and appropriate nomenclature | - If gene specific coordinates used, reference sequence for gene required | SHALL | Observation.component:genomic-ref-seq | Only public approved/finalised Locus Reference Genomic (LRG) Sequences can be used, otherwise NCBI Reference Sequence is required |
| Report Format - Results and Interpretation - Correct and appropriate nomenclature | - If coding nucleotide numbering used, transcript number required | SHALL | Observation.component:representative-transcript-ref-seq | |
| Report Format - Results and Interpretation - Correct and appropriate nomenclature | - Additional notes to clarify numbering as necessary | MAY | Observation.component.code.text/Observation.note | |
| Report Format - Results and Interpretation - Correct and appropriate nomenclature | If exon numbering included, reference/explanation of numbering required | SHALL | Observation.component:coordinate-system and Observation.extension:workflow-relatedArtifact | LRG exon preferred including a statement that exon numbering in accordance with LRG quoted (Observation.note), otherwise numbering referenced |
| Report Format - Results and Interpretation - Correct and appropriate nomenclature | - For intragenic copy number variants (deletions/duplications of exons), recommended to describe in words | SHOULD | TBC Observation.component:coding-change-type/copy-number | |
| Report Format - Results and Interpretation - Correct and appropriate nomenclature | - CNV description acceptable as ISCN/HGVS | MAY | TBC Observation.component:genomic-hgvs/cytogenetic-nomenclature | |
| Report Format - Results and Interpretation - Correct and appropriate nomenclature | If other nomenclature is used, state system and ISCN/HGVS equivalents | SHOULD | Observation.component.coding.system and Observation.component:genomic-hgvs/cytogenetic-nomenclature.coding.system = HGVS/ISCN | |
| Report Format - Results and Interpretation - Restate the clinical question being asked | Restate clinical question (either referral or in report) | SHALL | DiagnosticReport.basedOn | |
| Report Format - Results and Interpretation - Restate the clinical question being asked | - Additional information from referral which has bearing on clinical question | SHALL | DiagnosticReport.extension:supporting-info | |
| Report Format - Results and Interpretation - Clinical interpretation | Restate information used for interpretation | SHALL | DiagnosticReport.extension:supporting-info/Observation.basedOn/derivedFrom | |
| Report Format - Results and Interpretation - Clinical interpretation | - Relationship between patient and index where family history exists | MAY | RelatedPerson/FamilyMemberHistory | |
| Report Format - Results and Interpretation - Clinical interpretation | - Ethnic background | MAY | Patient.extension:ethnicCategory/QuestionnaireResponse.item(linkId=364699009).answer | QuestionnaireResponse used as an interim measure for collecting ethnicity for PDS registered patients |
| Report Format - Results and Interpretation - Clinical interpretation | - Lab investigations | MAY | Procedure/Observation | For referencing genomic analyses use the GenomicStudyAnalysis profile |
| Report Format - Results and Interpretation - Clinical interpretation | - Suspicious clinical picture | MAY | ServiceRequest.supportingInfo(Media) | |
| Report Format - Results and Interpretation - Clinical interpretation | Guidance from latest guidelines for interpretation | SHALL | DiagnosticReport.extension:workflow-relatedArtifact | |
| Report Format - Results and Interpretation - Clinical interpretation | Where 2 (likely)pathogenic variants detected in a proband, and are unclear whether cis or trans, text should include ‘assuming these variants are inherited in trans, the result is consistent with a genetic diagnosis of disorder X’ | SHOULD | Observation.note | Text likely in Observation.note unless in unstructured report text only |
| Report Format - Results and Interpretation - Clinical interpretation | Positive/negative for variant not recommended, must be defined if used | SHOULD NOT | Observation.valueCodeableConcept | Concepts used should match those used by the HL7 Genomics Reporting Implementation Guide, which includes definitions of terms |
| Report Format - Results and Interpretation - Clinical interpretation | Term 'carrier' only used for autosomal/x-linked recessive disorder/incomplete penetrance | SHOULD | TBC | Recording of carrier status to be investigated |
| Report Format - Results and Interpretation - Clinical interpretation - Autosomal recessive disorders | For recessive disorders with pathogenic variants, text to state ‘this patient is at least a carrier' | SHOULD | Observation.note | |
| Report Format - Results and Interpretation - Clinical interpretation - Autosomal recessive disorders | For 2 pathogenic variants in a child, confirmatory carrier testing of parents recommended before prenatal diagnosis | SHOULD | DiagnosticReport.extension:recommended-action | Referencing a Task recommending a confirmatory request (unless directly raised as part of the order management service interactions) |
| Report Format - Results and Interpretation - Clinical interpretation - Autosomal recessive disorders | State ‘these results support the clinical diagnosis’ | MAY | Observation.derivedFrom | DiagnosticImplication observation referencing lower level findings such as variant |
| Report Format - Results and Interpretation - Clinical interpretation - X-linked disorders | Offer/exclude prenatal testing if report on pregnancy | MAY | DiagnosticReport.extension:recommended-action | |
| Report Format - Results and Interpretation - Clinical interpretation - Reporting variants of uncertain significance (VUS) | ACGS guidelines on variant classification to be used for VUS | SHALL | TBC | Data requirements not yet investigated |
| Report Format - Results and Interpretation - Clinical interpretation - Reporting variants of uncertain significance (VUS) | - State if no clear diagnosis can be made | SHALL | DiagnosticReport.conclusion | |
| Report Format - Results and Interpretation - Clinical interpretation - Acquired genetic abnormalities in leukaemias and solid tumours | Link report to assessment by haematologist of proportion of neoplastic cells in sample (if no link, report qualified to point out malignant clone not represented, i.e. possible false negative) | SHOULD | DiagnosticReport.supporting-info or Observation.interpretation | Reference to Observation following neoplastic cell example |
| Report Format - Results and Interpretation - Clinical interpretation - Acquired genetic abnormalities in leukaemias and solid tumours | Abnormal results classified according to WHO | SHOULD | DiagnosticReport.conclusionCode.coding.system=WHO | |
| Report Format - Results and Interpretation - Clinical interpretation - Acquired genetic abnormalities in leukaemias and solid tumours | Cite studies linking variant to prognosis | MAY | Observation.extension:workflow-relatedArtifact | |
| Report Format - Results and Interpretation - Family studies | If family results are complex, include pedigree (drawn using Oxford Desk Reference, only include those relevant to interpretation) | SHOULD | DiagnosticReport.media or DiagnosticReport.extension:supporting-info | Dependent on whether the pedigree is an image or structured (FamilyMemberHistory) |
| Report Format - Results and Interpretation - Family studies | - Include date of issue and key | SHOULD | Media.issued/FamilyMemberHistory.date | |
| Report Format - Results and Interpretation - Family studies | - Consider confidentiality | SHOULD | Media.subject = Group/FamilyMemberHistory.identifier | No patient identifiable data required in the reference to the related person |
| Report Format - Results and Interpretation - Family studies | Include pedigree number | SHOULD | Group.identifier | |
| Report Format - Results and Interpretation - Family studies | Complex family data in tables | MAY | TBC DiagnosticReport.media | |
| Report Format - Results and Interpretation - Reporting carrier status in prenatal samples | For prenatal x-linked/autosomal recessive, genotype and carrier status of fetus | SHOULD | DiagnosticReport.result:genotype | |
| Report Format - Results and Interpretation - Assessment/calculation of risk/recurrence | State Genetic carrier risk, bayesian calculation | SHOULD | DiagnosticReport.extension:genomic-risk-assessment | |
| Report Format - Results and Interpretation - Assessment/calculation of risk/recurrence | Comment on risk of expansion for diseases which show anticipation | SHOULD | DiagnosticReport.result:diagnostic-implication | Likely via Observation.note |
| Report Format - Results and Interpretation - Assessment/calculation of risk/recurrence | State implications on family members | SHOULD | DiagnosticReport.result:diagnostic-implication | May also be captured in report text only or in DiagnosticReport.conclusion |
| Report Format - Results and Interpretation - A clear written description of the genetic abnormality | Description of genetic abnormality and interpretation | SHALL | DiagnosticReport.result:molecular-consequence/genotype and DiagnosticReport.conclusion | |
| Report Format - Results and Interpretation - A clear written description of the genetic abnormality | - Avoid the term abnormal where carrier has constitutional balanced rearrangement | SHALL | N/A | Guidance applicable to text/code used |
| Report Format - Results and Interpretation - The name of any associated syndrome/disease/prognosis | Appropriate to include names of associated syndrome, disease, prognosis where relevant | MAY | DiagnosticReport.result:diagnosticImplication | |
| Report Format - Results and Interpretation - The basis of the test | Test methodology and technical details relevant to interpretation | SHALL | Procedure(GenomicStudyAnalysis).extension:method-type | Technical details can be found elsewhere within the GenomicStudyAnalysis Procedure resource |
| Report Format - Results and Interpretation - The basis of the test | Technical sensitivity and practical resolution | SHALL | Procedure(GenomicStudyAnalysis).extension:metrics | |
| Report Format - Results and Interpretation - The basis of the test | - Which information on referral influenced decision on sensitivity, including references | SHALL | DiagnosticReport.extension:supporting-info/workflow-relatedArtifact | Ideally the extensions would be placed on the Procedure resource as they impact the methodology used, but Procedure is not an allowed context for workflow-relatedArtifact |
| Report Format - Results and Interpretation - The basis of the test | State if testing incomplete or minimum quality not achieved | SHALL | DiagnosticReport.conclusionCode | TBC Codes to be determined |
| Report Format - Results and Interpretation - The basis of the test | Manufacturer, kit number, version of commercial kit, probes, software recorded (not necessarily on report) | MAY | Procedure(GenomicStudyAnalysis).extension:device | |
| Report Format - Results and Interpretation - Reporting of results from sequencing | Follow ACGS guidelines for targeted next gen seq, for WES/WGS | SHALL | TBC | Data requirements not yet investigated |
| Report Format - Results and Interpretation - Referral for genetic counselling | Recommend referral for patient and family to genetic counselling for cases from non-genetic specialty | SHOULD | DiagnosticReport.extension:recommended-action | |
| Report Format - Results and Interpretation - Referral for genetic counselling | - State support available from clinical genetics, for benefit of other HCPs | SHOULD | N/A | Likely part of report text only |
| Report Format - Results and Interpretation - Referral for genetic counselling | - Offer referral to clinical genetics for testing offered to family | SHOULD | DiagnosticReport.extension:recommended-action | Task.for referencing related person |
| Report Format - Results and Interpretation - Further tests and/or information | Indicate further tests to improve accuracy/scope | MAY | DiagnosticReport.extension:recommended-action | |
| Report Format - Results and Interpretation - Further tests and/or information | - Suggest alternative labs where these are not offered by the reporting lab | MAY | N/A | Would likely be informed by DGTS routing |
| Report Format - Results and Interpretation - Further tests and/or information | - Can state no further testing planned | MAY | N/A | Unstructured text only |
| Report Format - Results and Interpretation - Further tests and/or information | - Contact for lab to discuss results | MAY | DiagnosticReport.resultsInterpreter | |
| Report Format - Results and Interpretation - No testing performed | Requests for sample storage (where testing is not performed) must have report | SHALL | DiagnosticReport/Composition | |
| Report Format - Results and Interpretation - Reporting of results performed by another laboratory | Validation of transcription/accuracy when re-reporting | MAY | N/A | Not part of FHIR payload |
| Report Format - Results and Interpretation - Reporting of results requested by another laboratory | The lab receiving samples for testing shall report directly to referring clinician (cc'ing referring lab) | SHALL | Composition.extension:informationRecipient | |
| Report Format - Results and Interpretation - Reporting of results requested by another laboratory | - Referring lab may also need to forward report | MAY | N/A | The Genomic Order Management Service is intended to remove the need for forwarding reports |
| Report Format - Results and Interpretation - Integrated reporting | Integrated reporting, i.e. multiple tests for one event in single report, encouranged | SHOULD | DiagnosticReport.extension:genomic-study | Multiple tests recorded via GenomicStudy profile |
| Report Format - Results and Interpretation - Integrated reporting | - Must have overarching interpretation for all results | SHALL | DiagnosticReport.conclusion | |
| Authorisers of Reports | Authoriser must have professional registration | SHALL | Composition.attester:validator | Note that recording of professional registration in the FHIR payload is out of scope |
| Authorisers of Reports | - Indicate report has been authorised but name/signature not required if stored on LIMS | SHALL | DiagnosticReport.status=final | Reference to Practitioner not required |
| Authorisers of Reports - Competence | - Competency may be on a category/template/test basis | SHALL | N/A | Competencies outside scope of FHIR reporting |
| Interim/Preliminary Reports | Final report issued to requester | SHOULD | Composition.extension:informationRecipient | |
| Interim/Preliminary Reports | May issue prelim report, must be marked as preliminary | MAY | DiagnosticReport.status=preliminary | |
| Addendum/Revised Reports | Addendum report stand-alone, identified as revision, reference to date and patient identity in original report | SHOULD | DiagnosticReport.status=amended | Following Acknowledgement Framework approach for ammendments and corrections |
| Addendum/Revised Reports | - Requester should be made aware | SHOULD | N/A | MNS notification |
| Addendum/Revised Reports | - Must state whether report is a replacement or supersedes original (where it replaces, the original should be destroyed) | SHOULD | DiagnosticReport.status=amended/DiagnosticReport.extension:diagnosticReport-replaces | |
| Addendum/Revised Reports | - Retained by lab in cumulative reports | SHOULD | N/A | Business process outside payload |
| Disclaimers | No disclaimers about samples, relationships or long-term DNA storage required | MAY NOT | N/A | Only appropriate where errors are due to factors outside of lab control |
| Disclaimers | - Caution when reports are based on DNA or reports from other labs | MAY NOT | DiagnosticReport.extension:supporting-info(DiagnosticReport) | Could be recorded via DiagnosticReport.performer. The caution is likely free text only |
| References Within Reports | References included when key to interpretation | SHOULD | DiagnosticReport.extension:workflow-relatedArtifact | |
| References Within Reports | - Necessary when data is new/not widely accepted, e.g. patient leaflets | SHALL | DiagnosticReport.extension:workflow-relatedArtifact | |
| References Within Reports | - State which used when conflicting publications exist | SHOULD | N/A | Only references which are used are expected to be referenced within the DiagnosticReport |
| References Within Reports | - Readable referencing format | SHOULD | RelatedArtifact.citation | Using recognised referencing format |
| References Within Reports | - Reflect best practice guidelines | SHOULD | N/A | Part of lab standard operating procedures |
| Reporting Time Targets | Maintain adequate reporting times | SHOULD | DiagnosticReport.issued | Turn around times are expected to be the difference between the date a sample is received with all the data or when the investigation is activated, if on stored sample, and when results are available in authorised state (not necessarily sent out by lab) |
| Validation of Results from Research Laboratories or Projects | Validate results from non-accredited labs in accredited lab before use and review research interpretation | SHOULD | N/A | Part of lab workflow |
| Archiving and Storage | Follow information govenance, data protection and storage guidance, ISO 15189, for records and specimens | SHOULD | N/A | Part of data retention and privacy protection implementation |