Course at EMBL-EBI
This course will focus on the analysis of data from genomic studies of Cancer. Lectures will give an insight into the bioinformatic concepts required to analyze 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.
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
EMBL Heidelberg, Germany
Cancer Research UK Cambridge Institute, UK
Wellcome Sanger Institute, UK
McGill University and Genome Quebec Innovation Centre, Canada
Day 1 – Monday 17 June 2019
|08:30-09:00||Arrival, registration and coffee|
|09:00-09:30||Course introduction||Anna Swan & Moritz Gerstung|
|09:30-11:00||Lecture: Introduction to high-throughput sequencing and its application in cancer||Mathieu Bourgey|
|11:15-12:45||Lecture: Introduction to cancer genomics and its caveats||Tobias Rausch|
|13:30-14:30||Lecture: SNV analysis||Mathieu Bourgey|
|14:30-15:30||Practical: Variant annotation, filtration and visualisation||Mathieu Bourgey|
|15:45-18:00||Practical: Variant annotation, filtration and visualisation||Mathieu Bourgey|
|18:00||End of day|
Day 2 – Tuesday 18 June 2019
|09:00-10:00||Lecture: Cancer Epigenetics and Whole-Genome Haplotyping||Tobias Rausch|
|10:00-11:00||Lecture: SV analysis||Tobias Rausch|
|11:15-13:00||Practical: SV analysis||Tobias Rausch|
|14:00-15:30||Lecture: CNV analysis using NGS data||Mathieu Bourgey|
|15:45-18:00||CNV analysis - deletion/amplification, calling CNVs, visualisation, interpretation||Mathieu Bourgey|
|18:00||End of day|
Day 3 – Wednesday 19 June 2019
|09:00-10:30||Practical: Data visualisation||Mathieu Bourgey|
|10:45-12:30||Data visualisation||Mathieu Bourgey|
|13:30-14:30||CRISPR-Cas9 genome editing for identifying cancer dependencies and new therapeutic targets||Francesco Iorio|
|15:00-17:00||Pre-processing, QC assessment and visualization of gene essentiality profiles from CRISPR-Cas9 screens||Francesco Iorio|
|18:00||End of day|
Day 4 – Thursday 20 June 2019
|09:00-10:00||Lecture: RNA-Seq analysis||Alexey Larionov|
|10:30-12:00||Practical: RNA-Seq analysis||Alexey Larionov|
|13:00-14:30||Single-cell transcriptomics: Overview & challenges||Wendi Bacon|
|15:00-16:00||Single-cell approaches||Yuanhua Huang|
|16:00-16:15||Course wrap-up and feedback||Anna Swan|
|16:15||End of course|
|16:30||Shuttle 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
- Provide a Microsoft Word (.docx) document containing three short paragraphs with a biography, work history and description of your current research interests; each paragraph should be no more than 100 words
- Provide a letter of support from a supervisor or a senior co-worker explaining why you should be selected for this course
Please submit all documents to Marina Pujol (firstname.lastname@example.org) by 12:00 GMT on Friday 22 March, 2019.
Incomplete applications will not be considered.
Accommodation will be provided in the Wellcome Genome Campus Conference Centre Monday-Thursday inclusive. Please contact the Conference Centre directly if you wish to arrange to stay additional nights. The course fee includes breakfast and evening meals at Hinxton Hall, as well as breaks and lunches outside the EMBL-EBI training rooms.