openEHR: UK 100,000 Genomes project

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An overview of the use of openEHR for clinical phenotyping in the UK 100,000 Genomes project. Given at Medinfo2017, Hangzhou, China

Santé

openEHR: the UK 100,000
Genomes project
Dr Ian McNicoll
Co-Chair openEHR Foundation
Interopen member - openEHR
Director freshEHR
CCIO inidus limited

Genomics England: 100,000 Genomes
DNA analysis of 100,000 Rare
Disease and Cancer participants ‘opt-
in’
Clinical phenotypics provided by
‘Genomic Centres’
symptoms, signs, diagnoses, clinical
scores, laboratory results, imaging,
histopathology ……
GEL-defined reporting dataset
Custom curation/ reporting tool (GENIE)
XML data export to GEL
https://www.genomicsengland.co.uk/

GEL and openEHR
2 Genomic centres using
openEHR CDRs to manage
local repositories for clinical
phenotypic
pool and normalise source data
from local clinical systems
emulate GEL reporting dataset in
openEHR archetypes/templates
North Thames Genomic Centres
7 London hospitals, each with a
CDR.

Input - curation - Output
Lab input
template Source
Diagnosis
templates
GEL Lab report
GEL Diagnosis
Report
AQL
Lab input
template Source
Diagnosis
templates
“Find candidate lab results”
“Find related problem-diagnoses”
GEN
IE
app
GOSH CDR
UCLH CDR
NTGMC CDR
GEL XML

GEL dataset to openEHR
26 templates
13 RD ‘output’
11 Cancer
‘output’
2 ‘input’
99 archetypes
44
international
27 localised
28 purely local
http://ckm.apperta.org/ckm/#showProject_1051.61.28

Localisation challenges
Very large dataset > 1500
datapoint
Mismatch between reporting data
and operational data patterns
Long tail of unusual Rare Disease
investigations
Family history / pedigree in the
“age of genomics”
Adding AQL paths back into GEL
metadata repository

NTGMC - why openEHR?
based on a common, open information
model
open specifications
open source clinical content definitions
other parts of the ecosystem need not
be open source
critical infrastructure for new app
developers / other research projects
substantially faster development
much lower barriers to market
no vendor / technology lock-in

openEHR CDR
openEHR Rest API + AQL
Best of Breed 3.0:
’open platform’ architecture
open Information Model
App App App

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