Course at EMBL-EBI

Cancer genomics

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

Mathieu Bourgey
McGill University
Isidro Cortes-Ciriano
EMBL-EBI
Francesco Iorio
Human Technopole
Alexey Larionov
Cranfield University
Ajay Mishra
EMBL-EBI
Tobias Rausch
EMBL
Matthew Young
Wellcome Sanger Institute

Programme

All times are given in BST

The session times may change between now and when the course takes place

Day one – 20 June 2022

Time 

Subject

Trainer

09:00 - 09:30

Arrival and registration

 

09:30 - 09:45

Welcome

Ajay Mishra

09:45 - 10:45

Course introduction

Isidro Cortes-Ciriano

10:45 - 11:00

Break

 

11:00 - 12:30

Introduction to cancer genomics and its caveats

Tobias Rausch

12:30 - 13:15

Lunch

 
13:15 - 13:30 Elevator pitch Course participants

13:30 - 15:00

Introduction to high-throughput sequencing and its application in cancer

Mathieu Bourgey

15:00 - 15:15

Break

 

15:15 - 15:30 Elevator pitch Course participants

15:30 - 16:30

Lecture: SNV analysis

Mathieu Bourgey

16:30 - 18:00

Practical: variant annotation, filtration, and visualisation

Mathieu Bourgey

18:00

End of day

 

18:30

Dinner

 

 

Day two – 21 June 2022

Time 

Subject

Trainer

09:30 - 11:30

Practical: variant annotation, filtration, and visualisation

Mathieu Bourgey

11:30 - 11:45

Break

 

11:45 - 12:00

Elevator pitch

Course participants

12:00 - 12:30 Cancer epigenetics Tobias Rausch

12:30 - 13:15

Lunch

 
13:15 - 13:30 Elevator pitch Course participants

13:30 - 14:00

Talk: SV analysis

Tobias Rausch

14:00 - 14:30

Long read sequencing for cancer genomics

Tobias Rausch

14:30 - 14:45

Break

 

14:45 - 16:00

Practical: SV analysis

Tobias Rausch

16:00 - 16:15 Break  
16:15 - 17:45 Practical: SV analysis Tobias Rausch

17:45

End of day

 

18:30

Dinner

 

 

Day three – 22 June 2022

Time 

Subject

Trainer

09:30 - 09:45 Elevator pitch Course participants

09:45 - 11:30

Lecture: CNV analysis using NGS data

Mathieu Bourgey

11:30 - 11:45

Break

 

11:45 - 12:00

Elevator pitch

Course participants

12:00 - 12:30 CNV analysis - deletion/amplification, calling CNVs, visualisation, interpretation Mathieu Bourgey

12:30 - 13:15

Lunch

 

13:15 - 14:45

CNV analysis - deletion/amplification, calling CNVs, visualisation, interpretation

Mathieu Bourgey

14:45 - 15:00

Break

 

15:00 - 16:30

Practical: data visualisation

Mathieu Bourgey

16:30 - 16:45

Break

 

16:45 - 18:00

Practical: data visualisation

Mathieu Bourgey

18:00

End of day

 

18:30

Dinner

 

 

Day four – 23 June 2022

Time 

Subject

Trainer

09:30 - 10:30

CRISPR-Cas9 genome editing for identifying cancer dependencies and new therapeutic targets

Francesco Iorio

10:30 - 10:45

Break

 

10:45 - 12:30

Pre-processing, QC assessment and visualisation of gene essentiality profiles from CRISPR-Cas9 screens (practicals and troubleshooting)

Francesco Iorio

12:30 - 13:15

Lunch

 

13:15 - 14:15

Poster session

 

14:15 - 15:45

Short-read RNA-seq analysis 

Alexey Larionov

15:45 - 16:00

Break

 

16:00 - 18:00

Short-read RNA-seq analysis (practicals and troubleshooting)

Alexey Larionov

18:00

End of day

 

18:30

Dinner

 

 

Day five – 24 June 2022

Time 

Subject

Trainer

09:30 - 10:30

Long-read RNA-seq analysis 

Alexey Larionov

10:30 - 10:45

Break

 

10:45 - 12:15

Long-read RNA-seq analysis (practicals and troubleshooting)

Alexey Larionov

12:15 - 13:00

Lunch

 

13:00 - 14:30

Single-cell sequencing in cancer

Matthew Young

14:30 - 14:40

Break

 

14:40 - 15:00

Course wrap-up and feedback

Ajay Mishra

15:00

End of course

 

15:30

Coach to Cambridge train station

 

 

 

 

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.

This course has ended

20 - 24 June 2022
European Bioinformatics Institute United Kingdom
£825
Contact
Jane Reynolds

Organisers
  • Isidro Cortes-Ciriano
    EMBL-EBI
  • Ajay Mishra
    EMBL-EBI
  • Tobias Rausch
    EMBL

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