Research Environment Training Session: Building cancer cohorts

Building a cohort is a vital first step in many kinds of genomics studies, such as GWAS, survival analysis and identifying cancer characteristics. The vast array of phenotypic data available in the Genomics England Research Environment, both recruited disease and electronic health records, is a great resource for cohort building and verification.  

This training session will go over some of the ways you can build cohorts in the Genomics England Research Environment: Participant Explorer for no-code creation and programmatic construction and verification. Using both methods, we will show how you can pull out the genomic file locations, or the participant identifiers to use with variant aggregation files.  

You are only allowed to attend this session if you are eligible for data access. This means that you are a Research Network member that has met the necessary verification checks and passed our Information Governance training course. If you do not meet this criterion by 13th April 2026, you will be unregistered for this session. 

Timetable 

• 13.30 Introduction and admin
• 13.35 Parameters and considerations for building a cohort
• 13.45 No code cohort building with Participant Explorer
• 13.55 Tables for cohort building in cancer
• 14.05 Building cohorts programmatically in Python and R
• 14.25 Getting genomic filepaths for your cohort
• 14.35 Using your cohort with aggregate VCFs and bcftools
• 14.45 Getting help and questions 

Learning objectives 

After this training you will know: 

• Where to find phenotypic and covariate data for building cohorts in the Genomics England Research Environment
• How to create cohorts using the Participant Explorer no code interface
• How to create and verify cohorts with Python or R 

Target audience 

This training is aimed at researchers: 

• working with the Genomics England Research Environment
• working in cancer genomics
• who can programme in python and/or R (a small segment of the training is suitable for non-programmers)