This course will focus on the analysis of data from genomic studies of Cancer. Interactive sessions with lectures 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 lecturers and teaching assistants.
The course will involve participants learning via pre-recorded lectures, live presentations, and trainer Q&A sessions. The content will be delivered over Zoom, with additional text communication over Slack.
Computational practicals will be run on EMBL-EBI's virtual training infrastructure; this means there is no need to have a powerful computer to run exercises or a requirement to install complex software before the course. Trainers will be available to provide support, answer questions, and further explain the analysis during these practicals.
Participants will need to be available between the hours of 09:30-18:00 BST each day of the course.
Who is this course for?
This course is aimed at advanced 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 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?
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
- Indicate the principles of tumour purity, heterogeneity and evolution and how these influence/impact upon bioinformatics analysis
- Perform alignment and quantification of expression of RNA-seq datasets
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
McGill University, Canada
EMBL, Heidelberg, Germany
Medical Genetics Department, University of Cambridge, UK
Wellcome Sanger Institute, UK
McGill University and Genome Quebec Innovation Centre, Canada
DKFZ, Heidelberg, Germany
Department of Haematology, University of Cambridge, UK
|Day 1 – Monday 17 May 2021|
|10:00-10:30||EMBL-EBI introduction||Ajay Mishra|
|10:30-11:00||Course introduction||Moritz Gerstung|
|11:15-12:15||Introduction to cancer genomics and its caveats (Lecture recap and live Q&A session)||Tobias Rausch|
|14:00-15:00||Introduction to high throughput sequencing and its application in cancer (lecture recap and live Q&A session)||Mathieu Bourgey|
|15:15-16:15||Cancer epigenetics and whole-genome haplotyping||Tobias Rausch|
|17:30||End of the day|
|Day 2 – Tuesday 18 May 2021|
|10:00-11:00||Structural variation||Tobias Rausch|
|13:00-14:15||SNV analysis||Mathieu Bourgey|
|14:30-15:30||Variant annotation, filtration and visualisation (practical demonstration)||Robert Eveleigh|
|15:45-16:45||Variant annotation, filtration and visualisation (troubleshooting)||Robert Eveleigh|
|17:00-18:00||Variant annotation, filtration and visualisation (troubleshooting)||Robert Eveleigh|
|18:00||End of the day|
|Day 3 – Wednesday 19 May 2021|
|10:00-11:00||Keynote lecture||Aurélie Ernst|
|13:15-14:30||Copy Number Variation (CNV) analysis using NGS data||Mathieu Bourgey|
|14:45-15:45||CNV analysis: Deletion/amplification, calling CNVs, visualisation, interpretation||Robert Eveleigh|
|16:00-17:00||CNV analysis: Deletion/amplification, calling CNVs, visualisation, interpretation||Robert Eveleigh|
|17:10-18:00||Data visualisation (Practical demonstration and troubleshooting)||Robert Eveleigh|
|18:00||End of the day|
|Day 4 – Thursday 20 May 2021|
|10:00-11:15||CRISPR-Cas9 genome editing for identifying cancer dependencies and new therapeutic targets||Francesco Iorio|
|11:30-12:30||Pre-processing, QC assessment and visualization of gene essentiality profiles from CRISPR-Cas9 screens (practicals and troubleshooting)||Francesco Iorio|
|14:45-16:00||Short-read RNA-seq analysis||Alexey Larionov|
|16:15-17:30||Short-read RNA-seq analysis (practicals and troubleshooting)||Alexey Larionov|
|17:30||End of the day|
|Day 5 – Friday 21 May 2021|
|10:00-11:00||Long-read RNA-seq analysis||Alexey Larionov|
|11:15-12:15||Long-read RNA-seq analysis||Alexey Larionov|
|13:00-14:00||Single cell approaches (keynote lecture)||Ana Cvejic|
|14:00-14:30||Course wrap-up and feedback||Ajay Mishra|
|14:30||End of the course|
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 providing answers as directed
- Ensure you add relevant information to the "Application submission" section where you are asked to provide three 300-word paragraphs that cover your:
- scientific biography
- work history
- 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 Friday 26 Feb 2021.
Incomplete applications will not be considered.
All applicants will be informed of the status of their application (successful, waiting list, rejected) by Friday 12 March 2021. If you have any questions regarding the application process please contact Jane Reynolds at email@example.com.
Participant flash talks
All participants will be asked to give a short presentation about their research work as part of the course. These provide an opportunity to share their research with the other participants and provide a forum for discussion. Further details will be provided if you are accepted for this course.