Research Environment Training Sessions: Building cancer cohorts and survival analysis

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 the Labkey API for 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. We will also look at how to pull out the relevant data for survival analysis, and run this on cohorts.

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 11 March 2024, 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 Introduction and admin
13.35 Parameters and considerations for building a cohort
13.45 Point-and-click cohort building with participant explorer
13.55 Labkey tables for cohort building in cancer
14.05 Using the Labkey API in Python and R
14.15 Survival analysis for cancer cohorts
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 point-and-click interface
• how to use the Labkey API to create and verify cohorts with Python or R

Target audience

This training is aimed at researchers who:

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