Known Issues

This page lists the current known issues planned to be addressed in future iterations of the Implementation Guide as well as deviations from standards best practice to due current external limitations.

The full list of issues to still be addressed, either within guidance or through clarifications, can be found on the Simplifier issue log

Patient extensions represented as QuestionnaireResponses

The patient extensions for birthSex and ethnicity, as modelled in the FHIR R4 UK Core, are currently required to be sent with a ServiceRequest as a QuestionnaireResponse resource (see QuestionnaireResponse-Patient-Extensions-Example), referenced from ServiceRequest.supportingInfo. This is due to limitations of the Personal Demographics Service in being able to save this information.

An example of an order Bundle using this approach is available at Bundle-NonWGSTestOrderFormQRPatientExtensions-Example.

This modelling change applies to both NHS and non-NHS patients, to ensure consistency. Patient extension MAY still be provided for non-NHS patients but the entries for birthSex and ethnicity SHALL be replicated in a QuestionnaireResponse.

GenomicDataFile examples use non-conformant context.related targets

The GenomicDataFile DocumentReference examples, used for the Genomic Data and Access Management API do not currently conform to the Genomics Reporting IG profile for GenomicDataFile. The NHS England examples use references to Specimen and ServiceRequest within DocumentReference.context.related to support retrival of data for analysis. However, the Genomics Reporting IG only suports references to DiagnosticReport. A widening of the target profiles has been requested, and is pending review by the HL7 Clinical Genomics WG.

Detailed guidance and mappings for Structured Reporting are missing

Whilst structured reports are intended to align to the Genomics Reporting IG GenomicReport profile, guidance regarding minimal data items required to support order management and use of data in the UK is missing. This will be informed by analysis of UK guidelines for reporting and development of an NHS England Master Dataset for Genomic Reporting (differentiated from the existing reporting dataset for MI/PLCM). From this mappings to FHIR and additional constraints on the GenomicReport profile will be developed, including codes to be used in reports.

Sharing of reports does not align with international standards

Within current Genomic Order Management Guidance, Transaction Bundles is used for the sharing of reports. Further investigation will be done alongside structured reporting business analysis to align to document sharing standards such as HL7 EU Lab and IHE MHDS guidance, i.e. sharing of Composition/Document bundles rather than individual resources.

DGTS ValueSets for Genomic-DGTS-GenomicTest-Method-Type and Genomic-DGTS-Clinical-Specialty-Genomics do not align with currently approved lists for these items nationally/internationally, e.g. NHS Data Dictionary Main Specialty Codes or Genomics Reporting Method Types. Work is underway internally to map between internal and standardised lists.

MDS Updates needed to support business

Further clarifications and updates are required to the MDS. These will be released as MDS v1.06 (not for use within the Genomic Order Management Private Beta). This will help to address the following open issues:

  • #2688 Dropping disease status boolean from MDS in preference of HPO terms per condition
  • #2693 Adding specimen collection details to MDS
  • #2705 Adding Tumour Stage and Grade to MDS
  • #2722 Need for discerning date submitted vs. date authored for test orders

Other Further Work

  • Modelling of AccreditationStatus to support dWGS
  • Additional guidance on authentication mechanisms
  • Examples and guidance for mark-in-error and request failure scenarios as well as guidance on how CPGCs should be modelled
  • Guidance on how to share and structure information to support meaningful use in other care settings, e.g. primary care
  • ValueSets for ConceptMaps, to allow binding to profile elements and support filtering
  • Updates to code lists and concept mappings based on terminology review, including concepts for observable related to specimens
  • Modelling and guidance for recording and sharing of interim operational data in order management, e.g. child samples, sequence data, preliminary reports etc.
  • Creation of a Questionnaire representation of the Test Order dataset, to support consistent form creation within supplier systems
  • Guidance on how outcomes from genomic testing (where care of a patient has been affected) may be recorded, to inform benefits realisation
  • Restructuring of the IG to build out interactions/sequence diagrams for the core Genomics informatics projects
  • Guidance on use of request vs. sample IDs in LIMS systems
  • Guidance on additional operations to be supported, e.g. $diff
  • Addition of MDS derived, and GEL supplied, business logic to support validation prior to submission, and develop TestScript resources for automated testing
  • Modelling of when tests are available for reanalysis
  • Develop mappings to other data standards, e.g. OpenEHR/GA4GH or engage with relevant accelerators to provide this