Archive training session
Past training sessions may include information that is no longer true, in either the presentation or the Q&A. Please double check against the relevant documentation pages.
Getting medical records for participants, September 2025¶
The Genomics England dataset includes a rich array of clinical data for all participants, rare disease probands and relatives, and cancer participants. Beyond the phenotypes recorded when participants were recruited into Genomics England, medical history was retroactively retrieved from NHS England for all participants and continues to be updated, allowing you to analyse secondary phenotypes, common disease and risk factors.
This training session will introduce you to the type of data we have available, including hospital episode statistics and mental health data, and the time periods when different data types were collected. We will show you how to access these data in table and graphical format using Participant Explorer, and how to compare medical history between participants. The raw data are stored in LabKey, so we will cover the tables that include these data and their structure, plus how to access these programmatically.
Timetable¶
13.30 Introduction and admin
13.35 NHS Digital data in the RE
13.45 Mental health data in the RE
13.50 Accessing NHS Digital data with Participant Explorer
14.00 Comparing participants’ medical history with Participant Explorer
14.10 LabKey tables: Hospital Episode Statistics
14.20 LabKey tables: Mental Health
14.30 Accessing medical history programmatically
14.45 Getting help and questions
Learning objectives¶
After this training you will be able to:
- Understand what medical history data is available for participants in the GEL RE
- Visualise and compare medical histories using Participant Explorer
- Access the LabKey tables of medical history data
Target audience¶
This training is aimed at researchers:
- working with the Genomics England Research Environment
- (preferably) who can programme in python and/or R (most of the training is suitable for non-programmers)
Date¶
9th September 2025
Materials¶
You can access the redacted slides and video below. All sensitive data has been censored. You can access and copy code from the Jupyter and R notebooks used in the training at:
/gel_data_resources/example_scripts/workshop_scripts/medical_history_2025
Slides¶
Video¶
Give us feedback on this tutorial
Q&A¶
Q&A
For diagnoses of cancer types, in other trainings you use some of these tables you just showed to cross-check a specific diagnosis/ICD code. Should we also be doing this for building pan-cancer cohorts?
live answered
Is it still necessary if I am using study codes? Fron the GEL docs, it says they have already been assigned using hes tables ICD codes right?
live answered