Virtual course
Cancer genomics (Virtual)
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 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.
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?
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
- 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
Trainers
Ajay Mishra
EMBL-EBI, UK Moritz Gerstung
EMBL-EBI, UK Robert Eveleigh
McGill University, Canada Tobias Rausch
EMBL, Heidelberg, Germany Wendi Bacon
EMBL-EBI, UK Alexey Larionov
Cancer Research UK Cambridge Institute Francesco Iorio
Wellcome Sanger Institute, UK Mathieu Bourgey
McGill University and Genome Quebec Innovation Centre, Canada
Programme
Day 1 – Monday 06 July 2020
10:00-10:30
EMBL-EBI introduction
Ajay Mishra
10:30-11:00
Course introduction
Moritz Gerstung
11:00-11:15
Break
11:15-12:15
Introduction to High Throughput Sequencing and its Application in Cancer (Lecture Recap and Live Q&A Session)
Mathieu Bourgey
12:15-14:00
Break
14:00-15:00
Introduction to cancer genomics and its caveats (Lecture Recap and Live Q&A Session)
Tobias Rausch
15:00-15:15
Break
15:15-15:45
Cancer epigenetics and whole-genome haplotyping (Lecture Recap and Live Q&A Session)
Tobias Rausch
15:45-16:45
Networking/Poster session
All
16:45
End of the day
Day 2 – Tuesday 30 June 2020
09:45-10:00
Morning challenge
All
10:00-10:45
Structural Variation (Lecture Recap and Live Q&A)
Tobias Rausch
10:45-11:00
break
11:00-11:30
SNV Analysis (Lecture recap and Live Q&A)
Mathieu Bourgey
11:30-12:30
Variant Annotation, Filtration and Visualisation (Practical Demonstration)
Robert Eveleigh
12:30-13:30
Break
13:30-14:15
Variant Annotation, Filtration and Visualisation (Troubleshooting)
Robert Eveleigh
14:15
Quick comfort break
14:15-15:15
Variant Annotation, Filtration and Visualisation (Troubleshooting)
Robert Eveleigh
15:15-16:15
Networking/Poster session
All
16:15
End of the day
Day 3 – Wednesday 01 July 2020
09:45-10:00
Morning challenge
All
10:00-11:25
Copy Number Variation (CNV) Analysis Using NGS data (Lecture Recap and Live Q&A Session)
Mathieu Bourgey
11:25-11:30
Break
11:30-12:15
CNV Analysis: Deletion/Amplification, Calling CNVs, Visualisation, Interpretation
Robert Eveleigh
12:15-13:05
Lunch
13:05-14:05
CNV Analysis: Deletion/Amplification, Calling CNVs, Visualisation, Interpretation
Robert Eveleigh
14:05-14:15
Tea/coffee break
14:15-15:15
Data Visualisation (Practical Demonstration and Troubleshooting)
Robert Eveleigh
15:15-16:16
Networking/Poster session
All
16:15
End of the day
Day 4 – Thursday 02 July 2020
09:45-10:00
Morning challenge
All
10:00-10:45
CRISPR-Cas9 Genome Editing for Identifying Cancer Dependencies and New Therapeutic Targets (Lecture Recap and Live Q&A Session)
Francesco Iorio
10:45-11:00
Break
11:00-12:00
Pre-processing, QC Assessment and Visualization of Gene Essentiality Profiles from CRISPR-Cas9 Screens (Practicals and Troubleshooting)
Francesco Iorio
12:00-13:00
Break
13:00-13:45
RNA-seq Analysis (Lecture Recap and Live Q&A Session)
Alexey Lorionov
13:45-14:00
Break
14:00-15:00
RNA-seq Analysis (Practicals and Troubleshooting)
Alexey Lorionov
15:00-16:00
Networking/Poster Presentation
All
16:00
End of the day
Day 5 – Friday 03 July 2020
9:30-10:45
Single Cell Transcriptomics
Wendi Bacon
10:45-11:00
Break
11:00-12:30
Single Cell Transcriptomics continued
Wendi Bacon
11:45-12:45
Single cell approaches/keynote
To be confirmed
12:30-13:00
Course wrap-up and feedback
Ajay Mishra
13:00
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 which will also ask you to:
- Provide three short paragraphs with a biography, work history and description of your current research interests; each paragraph should be no more than 100 words
- Upload 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 online by 23:59 GMT on Friday 13 March, 2020.
Incomplete applications will not be considered.
EMBL-EBI, UK
EMBL-EBI, UK
McGill University, Canada
EMBL, Heidelberg, Germany
EMBL-EBI, UK
Cancer Research UK Cambridge Institute
Wellcome Sanger Institute, UK
McGill University and Genome Quebec Innovation Centre, Canada
Programme
Day 1 – Monday 06 July 2020 |
||
|---|---|---|
| 10:00-10:30 | EMBL-EBI introduction | Ajay Mishra |
| 10:30-11:00 | Course introduction | Moritz Gerstung |
| 11:00-11:15 | Break | |
| 11:15-12:15 | Introduction to High Throughput Sequencing and its Application in Cancer (Lecture Recap and Live Q&A Session) | Mathieu Bourgey |
| 12:15-14:00 | Break | |
| 14:00-15:00 | Introduction to cancer genomics and its caveats (Lecture Recap and Live Q&A Session) | Tobias Rausch |
| 15:00-15:15 | Break | |
| 15:15-15:45 | Cancer epigenetics and whole-genome haplotyping (Lecture Recap and Live Q&A Session) | Tobias Rausch |
| 15:45-16:45 | Networking/Poster session | All |
| 16:45 | End of the day |
Day 2 – Tuesday 30 June 2020 |
||
|---|---|---|
| 09:45-10:00 | Morning challenge | All |
| 10:00-10:45 | Structural Variation (Lecture Recap and Live Q&A) | Tobias Rausch |
| 10:45-11:00 | break | |
| 11:00-11:30 | SNV Analysis (Lecture recap and Live Q&A) | Mathieu Bourgey |
| 11:30-12:30 | Variant Annotation, Filtration and Visualisation (Practical Demonstration) | Robert Eveleigh |
| 12:30-13:30 | Break | |
| 13:30-14:15 | Variant Annotation, Filtration and Visualisation (Troubleshooting) | Robert Eveleigh |
| 14:15 | Quick comfort break | |
| 14:15-15:15 | Variant Annotation, Filtration and Visualisation (Troubleshooting) | Robert Eveleigh |
| 15:15-16:15 | Networking/Poster session | All |
| 16:15 | End of the day |
Day 3 – Wednesday 01 July 2020 |
||
|---|---|---|
| 09:45-10:00 | Morning challenge | All |
| 10:00-11:25 | Copy Number Variation (CNV) Analysis Using NGS data (Lecture Recap and Live Q&A Session) | Mathieu Bourgey |
| 11:25-11:30 | Break | |
| 11:30-12:15 | CNV Analysis: Deletion/Amplification, Calling CNVs, Visualisation, Interpretation | Robert Eveleigh |
| 12:15-13:05 | Lunch | |
| 13:05-14:05 | CNV Analysis: Deletion/Amplification, Calling CNVs, Visualisation, Interpretation | Robert Eveleigh |
| 14:05-14:15 | Tea/coffee break | |
| 14:15-15:15 | Data Visualisation (Practical Demonstration and Troubleshooting) | Robert Eveleigh |
| 15:15-16:16 | Networking/Poster session | All |
| 16:15 | End of the day |
Day 4 – Thursday 02 July 2020 |
||
|---|---|---|
| 09:45-10:00 | Morning challenge | All |
| 10:00-10:45 | CRISPR-Cas9 Genome Editing for Identifying Cancer Dependencies and New Therapeutic Targets (Lecture Recap and Live Q&A Session) | Francesco Iorio |
| 10:45-11:00 | Break | |
| 11:00-12:00 | Pre-processing, QC Assessment and Visualization of Gene Essentiality Profiles from CRISPR-Cas9 Screens (Practicals and Troubleshooting) | Francesco Iorio |
| 12:00-13:00 | Break | |
| 13:00-13:45 | RNA-seq Analysis (Lecture Recap and Live Q&A Session) | Alexey Lorionov |
| 13:45-14:00 | Break | |
| 14:00-15:00 | RNA-seq Analysis (Practicals and Troubleshooting) | Alexey Lorionov |
| 15:00-16:00 | Networking/Poster Presentation | All |
| 16:00 | End of the day |
Day 5 – Friday 03 July 2020 |
||
|---|---|---|
| 9:30-10:45 | Single Cell Transcriptomics | Wendi Bacon |
| 10:45-11:00 | Break | |
| 11:00-12:30 | Single Cell Transcriptomics continued | Wendi Bacon |
| 11:45-12:45 | Single cell approaches/keynote | To be confirmed |
| 12:30-13:00 | Course wrap-up and feedback | Ajay Mishra |
| 13:00 | 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 which will also ask you to:
- Provide three short paragraphs with a biography, work history and description of your current research interests; each paragraph should be no more than 100 words
- Upload 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 online by 23:59 GMT on Friday 13 March, 2020.
Incomplete applications will not be considered.