Genetic variation analysis course

Course Description

Next-generation sequencing (NGS) technologies have revolutionized medicine and are changing its practice. As a joint state-of-the-art research and training facility of the ETH and the University of Zurich, the Functional Genomics Centre Zurich (FGCZ) offers a three-day course on variant analysis with hands-on tutorials. The aim is to help scientists interested in human genetic variation and interpretation, in particular heritable, to gain a better understanding of the tools and resources available and their use.

The course starts with the raw reads and cover pre-processing, alignment, variant calling, several quality-control checkpoints, annotation and impact of variation on protein function and structure. Additionally, the course will have a taster session on somatic variant calling. The hands-on sessions do neither require a pre-existing knowledge of Unix nor the command line environment. 
By the end of the course participants should be able to make informed decisions about NGS experimental designs, workflows and tools for variant analysis.

Course Program

• Read QC: Metrics for evaluating read quality
• Pre-processing of the raw data
• Mapping reads to a reference genome,
• Mapping QC: Metrics for mapping of DNA-seq reads
• Germline variant calling and differences to somatic variant calling
• Variant filtering and annotation
• Variant interpretation
• Visualization of mapping and variant calling results
• Challenges and pitfalls of variant analysis

Didactical Approach

This course is conceived as highly interactive, this includes:

• Theoretical inputs (lectures)
• Hands-on activities for data analysis (computer sessions)
• Interactive discussions on case studies (group discussions)
• Q&A sessions, feedback and discussions with other participants and instructors
• Flash presentations by means of whiteboards or slides

Learning Outcomes

At the end of this course, participants will be able to:

1. Understand file formats commonly used in variant analysis
2. Perform quality assessment of variant analysis data, raw and processed
3. Follow and evaluate data processing steps in heritable variant analysis, from raw reads to variant calls, variant annotation and prioritization
4. Assess the use of tools for variant interpretation
5. Perform basic data analysis using a workflow manager for variant calling
 

Important facts and how to apply

Language

The course will be entirely taught in English.

Participants

The course is limited to 20 participants.

Target audience and prerequisites

Applicants should be postdoctoral scientists, PhD students or masters’ students actively engaged in or soon to commence research involving variant analysis or NGS data.

Cost

The course tuition fees for members of the University of Zürich and ETHZ is CHF 150.00 (Swiss francs) per person. Please note, that this price can only be applied if the tuition fee is paid through an internal, i.e. University of Zürich or ETHZ, account.
For all other academics (paying through a non-UZH and non-ETHZ account) the cost is CHF 500.00 per person. For industrial delegates the cost is CHF 1,000.00 per person.

An invoice will be issued upon registration. This invoice will be sent out by email as well as a hard copy by regular mail/post. Those participants that register will be sent an email reserving their place together with an ‘Application Form’ to be signed by their correspondent supervisor and emailed back to the FGCZ. Upon receiving the signed ‘Application Form’, the participant will be considered and their place in the course will be confirmed.

Cancellation Policy

Please note that due to the high demand for this course any change related to your participation should be informed as soon as possible, but not later than ten (10) working days prior to the course start date. The notice must be e-mailed to .
If the cancellation of the course occurs after this time period, the tuition fee will not be refunded.

Please do not hesitate to contact us should you need any additional information or encounter any problems.

Expenses

Please beware that travel expenses, accommodation and meals are not included in the Tuition Fee. These will have to be covered by the participant entirely.