Genomic Reports for GP and future AI use

mayfield.g.kev · 2 April 2026 17:45

`sct` - Modern, fast SNOMED-CT tooling for the agentic age

Important waffle. As ex GP I would be interested to explore what GPs need / want from Rare Disease Genomics Reports and how that can best be conveyed in a structured manner. Would also be interesting to hear more about difficulties with the ‘NHS system’. Am involved with some work on replacing the aged PMIP / EDIFACT pathology links message with FHIR / SNOMED CT. A number of us keep asking why there is not more collaboration with the genomics folk about getting reports into GP systems. The ‘system’ seems to be siloed. For the future we need a very much wider spectrum of reports to reach GP systems than the very limited selection that we currently get via PMIP. We also need to close the loop so that meaningful requests go the other way - and all designed to accommodate decision support / AI in its various forms. We too have our problems with the ‘NHS system’. Sounds as if this may at some point need a thread separate from SCT

My current view is in this diagram (originally on linkedin Reflecting on System Design in Healthcare and Genomics | Kevin Mayfield posted on the topic | LinkedIn )

I think:

The final report (which is currently PDF + metadata) probably needs SNOMED coded items for DiagnosticImplication + other genomic information such as variants. I’m hoping to get a definite list from NHS England around this which I hope contains what GPs want.
The Genomic Data Repository is probably going to be more detailed genomic data, probably from converting the VCF files to FHIR following this standard Home Page - Genomics Reporting Implementation Guide v4.0.0-cibuild Is some open source projects for performing this conversion vcf2fhir/vcf2fhir at master · elimuinformatics/vcf2fhir · GitHub Suspect the users of this database is analytics (inc Federated Data Platform) and AI.

mayfield.g.kev · 2 April 2026 17:53

This is the domain archetype we have at the moment for orders North West Genomics Test Order - NHS North West Genomics v0.2.1
This is for secondary care trusts, the questions are not 100% SNOMED as it doesn’t cover several questions.

The initial thoughts on the final/structured report is North West Genomics Test Report - NHS North West Genomics v0.2.1 only the top part is present in the report at present, the information from Results Mapping onwards is suggestions.
We will probably NOT send the detailed part to secondary or primary care but make it available (to all with direct care need) via National Record Locator (NRL) instead.

So far cancer reports are available in Greater Manchester via the shared care record system, hoping rare disease and cancer reports will be made available soon for Merseyside + Cheshire…… and maybe other regions.

mayfield.g.kev · 2 April 2026 18:04

And on the PMIP / EDIFACT replacement.

For secondary care and LIMS, this standard is downstream and occurs once we’ve sent ORU_R01 to order comms.
In order to get some standardisation, I’ve followed Wales ORU_R01 HL7 standard and made some minor modifications. HL7 v2 Standards - NHS North West Genomics v0.2.1 , this also includes some example conversions to FHIR e.g. Testing/Output/FHIR/R01/ORU_R01_R125.1_R0A.txt.json at main · nw-gmsa/Testing · GitHub with original message Testing/Input/V2/R01/ORU_R01_R125.1_R0A.txt at main · nw-gmsa/Testing · GitHub

These are examples of ‘Send’, and probably won’t be extended to include structured. For detailed/structured reports I’m intending to follow EU data sharing API’s EU Health Data API - European Interoperability Specifications for Digital Solutions in Healthcare

Once we have done this, we can move to what NHS England is intending to replace EDIFACT/PMIP ….. again this is a EU standard for documents EU Laboratory Report Specification - European Interoperability Specifications for Digital Solutions in Healthcare it may take us 1-2 years before we can do this, we need to build the prior APIs and data models first.

p.s. For the last part, if needed I could probably get something ready for this Connectathon Key Benefits | Connectathon in 2027 in the Hague….. but would likely need some central support.