This course will focus on the analysis of data from genomic studies of cancer. It will also highlight the application of transcriptomic analysis and single-cell technologies in cancer. Talks and interactive sessions will give an insight into the bioinformatic concepts required to analyse such data, whilst practical sessions will enable the participants to apply statistical methods to the analysis of cancer genomics data under the guidance of the trainers.

In-person course

We plan to deliver this course in an in-person manner onsite at our training suite at EMBL-EBI, Hinxton.  Please be aware that we are continually evaluating the ongoing pandemic situation and, as such, may need to change the format of courses at short notice. Your safety is paramount to us; you can read our COVID guidance policy for more information. All information is correct at time of publishing.

Who is this course for?

We welcome applications from PhD students, post-doc researchers, and those working in industry. This course is well-suited for those who are applying, or planning to apply, high throughput sequencing and single-cell technologies in cancer research and wish to familiarise themselves with bioinformatics tools and data analysis methodologies specific to cancer data.

Familiarity with the technology and biological use cases of high throughput sequencing (HTS) is required, as is some experience with R/Bioconductor (basic understanding of the R syntax and ability to manipulate R objects) and the Unix/Linux operating system.

If you are not already familiar with these then please ensure that you complete these free tutorials before you attend the course:

• Basic introduction to the Unix environment: www.ee.surrey.ac.uk/Teaching/Unix
• Basic R concept tutorials: www.r-tutor.com/r-introduction

What will I learn?

Learning outcomes

After this course you should be able to:

• Evaluate the applications and challenges of HTS in the study of cancer genomics
• Detect, visualise, and annotate copy number variation
• Interpret complex genomic rearrangements such as structural variants
• Explain the principles of tumour purity, heterogeneity and evolution, and how we detect or quantify them using bioinformatic approaches
• Explore the application of CRISPR-Cas9 genome editing in cancer studies
• Perform alignment and quantification of expression of RNA-seq datasets
• Explore the application of single-cell sequencing in cancer studies

Course content

During this course you will learn about:

• Application of high throughput sequencing (HTS) in cancer
• Introduction to cancer genomics and epigenetics
• Structural variation, SNV and CNV analysis, and data visualisation
• Application of CRISPR-Cas9 genome editing in studying cancer
• RNA-seq analysis (both short and long reads)
• Single-cell research in cancer

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 23:59 on 10 April 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 24 April 2023. If you have any questions regarding the application process please contact Sophie Spencer.

The registration fee of £825.00 includes:

• Catering as detailed on the course programme
• Accommodation for four nights (10, 11, 12, and 13 July)
• 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. 

Course materials

The course materials from the 2022 edition of the course are now live and available for you to use. They provide a mixture of pre-recorded lectures, presentations, and practicals from the course, and will give you a snapshot of what to expect in the 2023 edition.

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.