Research Environment Training Sessions: Getting medical history for participants

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.

You are only allowed to attend this session if you are eligible for data access. This means that you are a GECIP or Discovery Forum member that has met the necessary verification checks and passed our Information Governance training course. If you do not meet this criterion by 21 August 2023, you will be unregistered for this session.

You can find materials from past training sessions and information on upcoming training sessions on the Genomics England Research Environment User Guide.

Agenda

13.30 Welcome and introduction

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 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)