Cancer Genomics
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Date:
Monday 18 - Thursday 21 June 2018Venue:
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United KingdomApplication opens:
Thursday 05 January 2017Application deadline:
Friday 16 March 2018Participation:
Open application with selectionContact:
EMBL-EBI Training TeamRegistration fee:
£530 (Including Accommodation)Registration closed
Overview
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.
Audience
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.
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
- 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
- Explore network deregulation in cancer
Programme
| Time | Topic | Trainer |
|---|---|---|
| Day 1 - Monday 18 June 2018 | ||
| 08:30 - 09:00 | Registration | |
| 09:00 - 09:30 | Course introduction | Sarah Morgan / Moritz Gerstung |
| 09:30 - 10:30 | Lecture: Introduction to high-throughput sequencing and its application in cancer | Mathieu Bourgey |
| 10:30 - 10:45 | Tea/coffee Break | |
| 10:45 - 12:30 | Lecture: Introduction to cancer genomics and its caveats | Tobias Rasuch |
| 12:30 - 13:30 | Lunch | |
| 13:30 - 14:30 | Lecture: SNV analysis | Mathieu Bourgey |
| 14:30 - 15:30 | Practical: Variant annotation, filtration and visualization | Mathieu Bourgey |
| 15:30 - 15:45 | Tea/coffee break | |
| 15:45 - 18:00 | Practical: Variant annotation, filtration and visualization | Mathieu Bourgey |
| 19:00 | Evening meal at Hinxton Hall | |
| Day 2 - Tuesday 19 June 2018 | ||
| 08:30 - 09:30 | Lecture: SV analysis | Tobias Rausch |
| 09:30 - 10:30 | Lecture: Single-Molecule Sequencing and Whole-Genome Haplotyping | Tobias Rausch |
| 10:30 - 10:45 | Tea/coffee break | |
| 10:45 - 12:30 | Practical: SV analysis | Tobias Rausch |
| 12:30 - 13:30 | Lunch | |
| 13:30 - 14:30 | Lecture: CNV analysis using NGS Data | Mathieu Bourgey |
| 14:30 - 15:30 | Practical: CNV analysis - deletion/amplification, calling CNVs, visualisation, interpretation | Mathieu Bourgey |
| 15:30 - 15:45 | Tea/coffee break | |
| 15:45 - 18:00 | Practical: CNV analysis - deletion/amplification, calling CNVs, visualisation, interpretation | Mathieu Bourgey |
| 19:00 | Evening meal at Hinxton Hall | |
| Day 3 - Wednesday 20 June 2018 | ||
| 09:00 - 10:30 | Practical: Data visualization | Mathieu Bourgey |
| 10:30 - 10:45 | Tea/coffee break | |
| 10:45 - 12:30 | Practical: Data visualization | Mathieu Bourgey |
| 12:30 - 13:30 | Lunch | |
| 13:30 - 14:30 | Lecture: RNA-Seq analysis | Alexey Larionov |
|
14:30 - 15:30 |
Practical: RNA-Seq analysis | Alexey Larionov |
| 15:30 - 15:45 | Tea/coffee break | |
| 15:45 - 18:00 | Practical: RNA-Seq analysis | Alexey Larionov |
| 19:15 | Evening meal at The Red Lion Pub, Hinxton | |
| Day 4 - Thursday 21 June 2018 | ||
| 09:00 - 10:00 | Lecture: CRISPR-Cas9 genome editing for identifying cancer dependencies and new therapeutic targets | Francesco Iorio |
| 10:00 - 10:30 | Tea/coffee break | |
| 10:30 - 12:00 | Practical: Pre-processing, QC assessment and visualization of gene essentiality profiles from CRISPR-Cas9 screens | Francesco Iorio |
| 12:00 - 13:00 | Lunch | |
| 13:00 - 14:30 | Cancer genomics in the cloud | Anmol Hemrom |
| 14:30 - 15:00 | Tea/coffee break | |
| 15:00 - 16:00 | Cancer genomics in the cloud | Anmol Hemrom |
| 16:00 - 16:30 | Course wrap up and feedback | Sarah Morgan |
| 16:30 | End of course and departures | |