This introductory course explores the complex interplay between genes and the environment in shaping human phenotypes. Participants will gain knowledge of cohort datasets, environmental readouts, and computational resources to investigate gene-environment interactions. Ethical and legal frameworks related to data privacy, consent, and genetic discrimination will be discussed. The course also covers computational modelling techniques for integrating genotype and environmental effects. By the end, attendees will be equipped to analyse cohort datasets, make use of computational resources, and interpret the results. 

Please note that you will not analyse your own data as part of the course. There will, however, be ample opportunity to discuss your research and ideas with other course participants and trainers

Who is this course for?

This introductory course is  aimed at MRes/PhD students, researchers, clinicians, and other professionals working in the fields of genomics, exposomics, epidemiology, or toxicology with an interest in understanding how interactions between genes and the environment underlie human phenotypes. The course will cover the underlying concepts, computational resources, and computational modelling methods available to investigate interactions between genes and the environment (including social, biological, and physical exposures). No prior bioinformatics skills are required although a basic understanding of statistics and Unix experience would be helpful.

Prerequisites

We recommend all successful applicants acquire/brush up on their basic command line skills before attending the course. R Studio experience is also required. There are many tutorials available online and here are some that may be of help.

To complete the following suggested tutorials you may want to install Ubuntu for Windows Users if you are using a computer with a Windows Operating System.

1. Basic introduction to the Unix environment
2. Hands-on programming with R

What will I learn?

Learning outcomes

After the course you should be able to: 

• Discuss the types, limitations, and advantages of human cohort datasets.
• Discuss the types, limitations, and advantages of different environmental readouts, including proxies for exposures in human cohorts.
• Explain the ethical and legal frameworks governing human data reuse and request access to datasets of interest in compliance with legal and ethical standards. 
• Use and explain the need for Federated/Trusted Research Environments.
• Employ relevant computational methods and resources to investigate gene and environment interactions and interpret the results.
• Understand how to apply techniques (GWAS and predictive modelling) to analyse cohort datasets and how to interpret these results.

Course content

During this course you will learn about: 

• How to predict gene and environment interactions in human cohort datasets: study design, analysis techniques and interpretation.
• Tools and services available for investigating gene and environment interaction: GWAS catalogue, EGA, OpenTargets.
• Computational modelling strategies to integrate Genotype * Environmental effects. 
• Ethical and legal frameworks relating to human cohorts considering: privacy and data security, informed consent, issues related to genetic discrimination, and ethical issues related to new technologies.

Trainers

Please read our page on application support before starting your application. In order to be considered for a place on this course, you must do the following:

• Complete the online application form.
• Ensure you add relevant information to the ‘submission details’ section where you are asked to provide information on your:
  • pre-requisite skills and knowledge
  • current work and course expectations
  • data availability
• Upload one letter of support from your supervisor or a senior colleague detailing reasons why you should be selected for the course.

Please submit all documents during the application process by 11:59 GMT Sunday 12 November 2023. Items marked * in the application are mandatory. Incomplete registrations will not be processed. 

All applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by Monday 20 November 2023. If you have any questions regarding the application process please contact Sophie Spencer. 

The registration fee of £450.00 includes:

• Catering as detailed on the course programme
• Accommodation for four nights (19, 20, 21, and 22 February 2024)
• Bespoke course handbook with links to all course materials
• Use of a computer in the EMBL-EBI training suite throughout the course
• Shuttle bus on the final course day to Cambridge train station 

Accommodation 

Hotel rooms will be provided onsite at Hinxton Hall Conference Centre. Please contact them directly if you wish to arrange to stay additional nights around the course dates.

Catering

The course includes catering as detailed on the programme tab. Successful applicants will be asked for any dietary requirements and allergies upon registration. 

Posters

All participants are expected to present a poster that will be displayed during the course outside the training room. Successful applicants will be asked to submit their poster upon registration. We will print these for you and have them available when you arrive on site.

All posters should:

•         be A2 in size – 420mm x 594 mm
•         be in a portrait orientation
•         include your photograph and contact information

We expect the posters to act as a talking point between you, other participants, and the trainers on the course. The posters will be displayed throughout the week so people can view them during breaks and lunch. They should give the reader an idea of the work you are engaged in, what you are planning to do next, and anything of interest that might be useful for sharing with the gathered participants.