Course at EMBL-EBI
Exploring human genetic variation
Do you want to understand more about genetic variation? Are you aware of the resources available for finding, viewing and exploring variant data? Are you trying to link variant data to phenotypes?
This two-day workshop will demonstrate resources and bioinformatics tools available at EMBL-EBI and the Sanger Institute that will aid understanding of human genetic variation.
Who is this course for?
No prior experience of bioinformatics is required, but an interest in finding out more about genetic variation resources and an undergraduate level understanding of biology would be of benefit. Experience with command line usage would be very beneficial.
This workshop will focus specifically on human genetic variation.
Prerequisite
We encourage the audience to go through our online course on human genetic variation prior to attending the workshop - www.ebi.ac.uk/training/online/course/human-genetic-variation-i-introduction-2019 .
What will I learn?
Learning outcomes
At the end of this workshop you should be able to:
- Access and explore a range of appropriate variation resources
- Use these resources to retrieve relevant variant information
- Apply the information that you have discovered to your reserach
Course content
This workshop will cover:
- European Variation Archive (EVA)
- Ensembl variation resources, Variant Effect Predictor (VEP)
- International Genome Sample Resource (IGSR)
- UniProt
- GWAS Catalog
- Locus Reference Genomic (LRG)
- Matched Annotation from the NCBI and EMBL-EBI (MANE)
- European Genome-Phenome Archive (EGA)
- DECIPHER
- Catalog of Somatic Mutations in Cancer (COSMIC)
Trainers
Ajay Mishra
EMBL-EBI, UK Julia Foreman
Wellcome Sanger Institute, UK Baron Koylass
EMBL-EBI, UK Matthieu Vizuete-Forster
EMBL-EBI, UK Andrew Nightingale
EMBL-EBI, UK Maria Cerezo
EMBL-EBI, UK Simon Forbes
Wellcome Sanger Institute, UK Joannella Morales
EMBL-EBI, UK Claire Rye
Wellcome Sanger Institute, UK Jackie MacArthur
EMBL-EBI, UK Emily Perry
EMBL-EBI, UK Michal Szpak
EMBL-EBI, UK Nidhi Bindal
Wellcome Sanger Institute, UK Zbyslaw Sondka
Wellcome Sanger Institute, UK
Programme
Day 1 - Tuesday 11th February
Where can I find human genetic variation data?
08:15
Shuttle from Cambridge Station (Stop 5)
09:00-09:15
Arrival and registration
09:15-09:30
Welcome and workshop introduction
Ajay Mishra
09:30-11:00
Variation data in Ensembl
Michal Szpak, Ensembl team
11:00-11:15
Tea/Coffee Break
11:15-12:45
UniProt variation and interpretation
Andrew Nightingale
12:45-13:30
Lunch
13:30-15:00
GWAS Catalog
Jackie MacArthur/Maria Cerezo
15:00-15:15
Tea/Coffee Break
15:15-16:15
International Genome Sample Resource (IGSR)
Emily Perry, Ensembl team
16:15-17:15
European Genome-Phenome Archive (EGA)
Matthieu Vizuete-Forster
17:15-18:00
European Variation Archive (EVA)
Baron Koylass
18:15
Shuttle to Cambridge railway station
Day 2 – Wednesday 12th February
How do I interpret genetic variants?
08:15
Shuttle from Cambridge Station (Stop 5)
09:15-10:15
Variation Effect Predictor (VEP)
Michal Szpak, Ensembl team
10:15-11:00
European Variation Archive (EVA) practicals
Baron Koylass
11:00-11:15
Tea/Coffee Break
11:15-12:45
Reference sequences for variant reporting (LRG/MANE)
Joannella Morales
12:45-13:30
Lunch
13:30-15:00
DECIPHER - Mapping the Clinical Genome
Julia Foreman and the DECIPHER team
15:00-15:15
Tea/Coffee Break
15:15-16:45
Catalogue of Somatic Mutations in Cancer (COSMIC)
Claire Rye, Nidhi Bindal and Zbyslaw Sondka
16:45-17:00
Wrap up and feedback
Ajay Mishra
17:15
Shuttle to Cambridge railway station
Attendance at this workshop is allocated on a first come, first served basis.
The registration fee covers your lunch, refreshments and a shuttle between Cambridge station and the Wellcome Genome Campus. Accommodation is not included and you will need to make your own arrangements.
Please note that registration closes two weeks prior to the workshop, so please register as soon as you can. Once you have registered and we have received payment we can provide a letter of support should you require a visa to travel to the UK. Applying for a visa can take several weeks, and it might not be possible to be granted a visa if you register just before the closing date. If you are unable to attend, then please notify us as quickly as possible so that we can offer your place to someone else.
Once you have registered please send Rebecca Nicholl a picture of yourself and 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.
EMBL-EBI, UK
Wellcome Sanger Institute, UK
EMBL-EBI, UK
EMBL-EBI, UK
EMBL-EBI, UK
EMBL-EBI, UK
Wellcome Sanger Institute, UK
EMBL-EBI, UK
Wellcome Sanger Institute, UK
EMBL-EBI, UK
EMBL-EBI, UK
EMBL-EBI, UK
Wellcome Sanger Institute, UK
Wellcome Sanger Institute, UK
Programme
Day 1 - Tuesday 11th February |
||
|---|---|---|
| Where can I find human genetic variation data? | ||
| 08:15 | Shuttle from Cambridge Station (Stop 5) | |
| 09:00-09:15 | Arrival and registration | |
| 09:15-09:30 | Welcome and workshop introduction | Ajay Mishra |
| 09:30-11:00 | Variation data in Ensembl | Michal Szpak, Ensembl team |
| 11:00-11:15 | Tea/Coffee Break | |
| 11:15-12:45 | UniProt variation and interpretation | Andrew Nightingale |
| 12:45-13:30 | Lunch | |
| 13:30-15:00 | GWAS Catalog | Jackie MacArthur/Maria Cerezo |
| 15:00-15:15 | Tea/Coffee Break | |
| 15:15-16:15 | International Genome Sample Resource (IGSR) | Emily Perry, Ensembl team |
| 16:15-17:15 | European Genome-Phenome Archive (EGA) | Matthieu Vizuete-Forster |
| 17:15-18:00 | European Variation Archive (EVA) | Baron Koylass |
| 18:15 | Shuttle to Cambridge railway station | |
Day 2 – Wednesday 12th February |
||
|---|---|---|
| How do I interpret genetic variants? | ||
| 08:15 | Shuttle from Cambridge Station (Stop 5) | |
| 09:15-10:15 | Variation Effect Predictor (VEP) | Michal Szpak, Ensembl team |
| 10:15-11:00 | European Variation Archive (EVA) practicals | Baron Koylass |
| 11:00-11:15 | Tea/Coffee Break | |
| 11:15-12:45 | Reference sequences for variant reporting (LRG/MANE) | Joannella Morales |
| 12:45-13:30 | Lunch | |
| 13:30-15:00 | DECIPHER - Mapping the Clinical Genome | Julia Foreman and the DECIPHER team |
| 15:00-15:15 | Tea/Coffee Break | |
| 15:15-16:45 | Catalogue of Somatic Mutations in Cancer (COSMIC) | Claire Rye, Nidhi Bindal and Zbyslaw Sondka |
| 16:45-17:00 | Wrap up and feedback | Ajay Mishra |
| 17:15 | Shuttle to Cambridge railway station | |
Attendance at this workshop is allocated on a first come, first served basis.
The registration fee covers your lunch, refreshments and a shuttle between Cambridge station and the Wellcome Genome Campus. Accommodation is not included and you will need to make your own arrangements.
Please note that registration closes two weeks prior to the workshop, so please register as soon as you can. Once you have registered and we have received payment we can provide a letter of support should you require a visa to travel to the UK. Applying for a visa can take several weeks, and it might not be possible to be granted a visa if you register just before the closing date. If you are unable to attend, then please notify us as quickly as possible so that we can offer your place to someone else.
Once you have registered please send Rebecca Nicholl a picture of yourself and 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.