Virtual course
Exploring human genetic variation
Do you want to learn 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 four-day workshop will demonstrate resources and bioinformatics tools available at EMBL-EBI and the Wellcome Sanger Institute that will aid understanding of human genetic variation.
During the first three days, you will learn how to browse, retrieve, and use human genetic variation data via talks, demos, and tutorials. You will then be provided with exercises to work through the resources on your own with remote trainer support available if needed and provided space to meet other participants if you wish to do so. We will meet again on 30 March for a Q&A session and discussion about any questions or issues that occurred while working on the materials provided.
Virtual course
Participants will learn via a mix of live talks, demos, hands-on exercises, and trainer Q&A sessions. Practical experience will be developed through homework activities with remote trainer support. Live sessions will be delivered using Zoom with additional support and asynchronous communication via Slack.
Participants will need to be available between the hours of 09:30 – 15:30 GMT each day of the course from 21 – 23 March 2023 and from 09:30 – 12:00 BST on 30 March 2023. Trainers will be available to assist, answer questions, and provide further explanations during these times.
Who is this course for?
No prior experience in 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.
Prerequisites
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
After this course 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 research
Course content
During this course you will learn about:
- European Variation Archive (EVA)
- Ensembl variation resources, Variant Effect Predictor (VEP)
- UniProt
- GWAS Catalog
- Matched Annotation from the NCBI and EMBL-EBI (MANE)
- European Genome-Phenome Archive (EGA)
- DECIPHER
- Catalog of Somatic Mutations in Cancer (COSMIC)
Trainers
Julia Foreman
EMBL-EBI Silvia Bahena Hernandez
EMBL-EBI Baron Koylass
EMBL-EBI Adam Frankish
EMBL-EBI Dona Shaju
EMBL-EBI James Stephenson
EMBL-EBI Louisse Paola Mirabueno
EMBL-EBI Elliot Sollis
EMBL-EBI Rebecca White
Wellcome Sanger Institute Leonie Hodges
Wellcome Sanger Institute Zbyslaw Sondka
Wellcome Sanger Institute Helder Pedro
Wellcome Sanger Institute Prabhat Totoo
EMBL-EBI
Programme
Times from 21 March – 23 March are listed in GMT; times on 30 March are listed in BST.
Time (GMT) Topic Trainer Day one – Tuesday 21 March 2023 – Where can I find human genetic variation data? 09:30 – 10:00 Welcome and introductions Dayane Araújo 10:00 – 10:30 Variation data in Ensembl Louisse Mirabueno 10:30 – 10:45 Break 10:45 – 12:00 Variation data in Ensembl Louisse Mirabueno 12:00 – 13:00 Lunch Break 13:00 – 14:00 UniProt variation and interpretation James Stepherson and Prabhat Totoo 14:00 – 15:00 GWAS Elliot Sollis 15:00 – 15:30 Networking
Time (GMT) Topic Trainer Day two – Wednesday 22 March 2023 – Where can I find human genetic variation? 09:30 – 09:45 Morning activity Dayane Araújo 09:45 – 10:45 European Genome-Phenome Archive (EGA) Dona Shaju and Silvia Bahena 10:45 – 11:15 Break 11:15 – 12:30 European Variation Archive (EVA) Baron Koylass 12:30 – 13:30 Lunch break 13:30 – 14:30 The MANE Collaboration Adam Frankish 14:30 – 15:30 Variation Effect Predictor (VEP) Louisse Mirabueno
Time (GMT) Topic Trainer Day three – Thursday 23 March 2023 – How do I interpret genetic variants? 09:30 – 10:00 DECIPHER – Mapping the clinical genome Julia Foreman 10:00 – 10:15 Break 10:15 – 12:00 DECIPHER – Mapping the clinical genome Julia Foreman 12:00 – 13:00 Lunch break 13:00 – 14:30 Catalogue of Somatic Mutations in Cancer (COSMIC) Rebecca White and Leonie Hodges 14:30 – 15:00 Intro to self-paced hands-on training Dayane Araújo 15:00 - 15:30 Networking
Time (BST) Topic Trainer Day four – Thursday 30 March 2023 – Q&A, and discussions 09:30 – 09:45 Welcome Dayane Araújo 09:45 – 10:30 Q&A and discussion with all trainers Louisse Mirabueno, James Stepherson, Silvia Bahena, Baron Koylass, Adam Frankish, Zbyslaw Sondka and Helder Pedro 10:30 – 10:45 Break 10:45 – 11:30 Talk to the trainers Louisse Mirabueno, Prabhat Totoo, Silvia Bahena, Baron Koylass, Adam Frankish, Zbyslaw Sondka and Helder Pedro 11:30 – 12:00 Wrap-up and feedback Dayane Araújo
Please read our page on application support 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
- Ensure you add relevant information to the ‘submission details’ section where you are asked to provide information on your:
- pre-requisite skills and knowledge
- current work and course expectations
- data availability
Please complete your application by midnight on Friday 2 December 2022. Items marked * in the application are mandatory. Incomplete registrations will not be processed.
If you have any questions regarding the application process please contact Juanita Riveros.
Flash talks
All participants will be asked to prepare two slides and record a short presentation about their research work as part of the course (two minutes). These provide an opportunity to share their research with the other participants and provide a forum for discussion.
EMBL-EBI
EMBL-EBI
EMBL-EBI
EMBL-EBI
EMBL-EBI
EMBL-EBI
EMBL-EBI
EMBL-EBI
Wellcome Sanger Institute
Wellcome Sanger Institute
Wellcome Sanger Institute
Wellcome Sanger Institute
EMBL-EBI
Programme
Times from 21 March – 23 March are listed in GMT; times on 30 March are listed in BST.
| Time (GMT) | Topic | Trainer |
| Day one – Tuesday 21 March 2023 – Where can I find human genetic variation data? | ||
| 09:30 – 10:00 | Welcome and introductions | Dayane Araújo |
| 10:00 – 10:30 | Variation data in Ensembl | Louisse Mirabueno |
| 10:30 – 10:45 | Break | |
| 10:45 – 12:00 | Variation data in Ensembl | Louisse Mirabueno |
| 12:00 – 13:00 | Lunch Break | |
| 13:00 – 14:00 | UniProt variation and interpretation | James Stepherson and Prabhat Totoo |
| 14:00 – 15:00 | GWAS | Elliot Sollis |
| 15:00 – 15:30 | Networking | |
| Time (GMT) | Topic | Trainer |
| Day two – Wednesday 22 March 2023 – Where can I find human genetic variation? | ||
| 09:30 – 09:45 | Morning activity | Dayane Araújo |
| 09:45 – 10:45 | European Genome-Phenome Archive (EGA) | Dona Shaju and Silvia Bahena |
| 10:45 – 11:15 | Break | |
| 11:15 – 12:30 | European Variation Archive (EVA) | Baron Koylass |
| 12:30 – 13:30 | Lunch break | |
| 13:30 – 14:30 | The MANE Collaboration | Adam Frankish |
| 14:30 – 15:30 | Variation Effect Predictor (VEP) | Louisse Mirabueno |
| Time (GMT) | Topic | Trainer |
| Day three – Thursday 23 March 2023 – How do I interpret genetic variants? | ||
| 09:30 – 10:00 | DECIPHER – Mapping the clinical genome | Julia Foreman |
| 10:00 – 10:15 | Break | |
| 10:15 – 12:00 | DECIPHER – Mapping the clinical genome | Julia Foreman |
| 12:00 – 13:00 | Lunch break | |
| 13:00 – 14:30 | Catalogue of Somatic Mutations in Cancer (COSMIC) | Rebecca White and Leonie Hodges |
| 14:30 – 15:00 | Intro to self-paced hands-on training | Dayane Araújo |
| 15:00 - 15:30 | Networking | |
| Time (BST) | Topic | Trainer |
| Day four – Thursday 30 March 2023 – Q&A, and discussions | ||
| 09:30 – 09:45 | Welcome | Dayane Araújo |
| 09:45 – 10:30 | Q&A and discussion with all trainers | Louisse Mirabueno, James Stepherson, Silvia Bahena, Baron Koylass, Adam Frankish, Zbyslaw Sondka and Helder Pedro |
| 10:30 – 10:45 | Break | |
| 10:45 – 11:30 | Talk to the trainers | Louisse Mirabueno, Prabhat Totoo, Silvia Bahena, Baron Koylass, Adam Frankish, Zbyslaw Sondka and Helder Pedro |
| 11:30 – 12:00 | Wrap-up and feedback | Dayane Araújo |
Please read our page on application support 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
- Ensure you add relevant information to the ‘submission details’ section where you are asked to provide information on your:
- pre-requisite skills and knowledge
- current work and course expectations
- data availability
Please complete your application by midnight on Friday 2 December 2022. Items marked * in the application are mandatory. Incomplete registrations will not be processed.
If you have any questions regarding the application process please contact Juanita Riveros.
Flash talks
All participants will be asked to prepare two slides and record a short presentation about their research work as part of the course (two minutes). These provide an opportunity to share their research with the other participants and provide a forum for discussion.