This course will focus on the analysis of data from genomic studies of 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?

This course is aimed at PhD students and post-doctoral researchers who are applying or planning to apply high throughput sequencing 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.

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 advice 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 "application submission" section where you are asked to provide information on your:
  • pre-requisite skills and knowledge
  • current work and course expectations
  • current research interests
• Upload a 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 midnight on 25 March 2022. 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, rejected) by 8 April 2022. If you have any questions regarding the application process please contact Jane Reynolds.

Note that the registration fee includes:

• All meals (breakfast, lunch, dinner and refreshment breaks)
• Accommodation for four nights
• Course materials
• Use of a computer in the EMBL-EBI training room throughout the course

Accommodation

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

The course includes evening meals, as well as breaks and lunches outside the EMBL-EBI training rooms.

Participant elevator pitch for poster

All participants will be asked to give a two minute 'elevator pitch’ about their research work. These provide an opportunity to share your research as well as to invite other attendees to their posters for discussion. Further details will be provided if you are accepted for this course.

Poster

All participants are expected to present a poster that will be displayed during the course outside the training room. If you are accepted for the course, you will be asked to send a poster in PDF format to Jane Reynolds so that it can be printed for display. 

All posters should:

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

We cannot display posters of a different size or orientation. Further details will be provided if you are accepted for this course.