DNA Next Generation Sequencing

Course Description

Next-generation sequencing (NGS) technologies have revolutionized many fields in biology and are changing the practice of medicine. As a joint state-of-the-art research and training facility of the ETH and the University of Zurich, the Functional Genomics Center Zurich (FGCZ) offers a five-day course with hands-on practicals. The aim is to help scientists interested in NGS technologies, particularly applied to DNA sequencing, to gain a better understanding of the techniques available and their applications. This course is not meant to replace any manufacturers’ training normally supplied with an instrument.
 The practical consists of a library preparation and sequencing starting from genomic DNA, followed by short and a long read sequencing workflows using Illumina and Oxford Nanopore Technologies, respectively. An introduction to the analysis of the resulting data and some exercises will be offered as well. The lectures cover existing and upcoming NGS technologies, their applications and the principles of downstream data analysis. 
The data analysis part starts off from the raw reads, as generated by the instrument, and cover pre-processing, alignment, variant calling and several quality control checkpoints. The hands-on sessions for data analysis does neither require a pre-existing knowledge of Unix nor the command line environment. This course is not intended to be a training course for those solely interested in next-generation sequencing bioinformatics.
By the end of the course participants should be able to make informed decisions about which technology and workflow to apply to solve specific research questions.

Course Programme

Library Prep

• DNA library generation: principles and types

Sequencing

• Detailed description of available sequencing technologies platforms
• Hands-on laboratory work: preparing chips for sequencing and
  performing sequencing runs on various platforms

Data analysis

• Run QC: Criteria for run performance
• Read QC: Metrics for evaluating read quality
• Preprocessing of raw reads
• Mapping reads to a reference genome
• Mapping QC: Metrics for mapping of DNA-seq reads
• Variant calling
• Visualization of mapping and variant calling results
• Introduction to de novo assembly applications
• IT and awareness of the data storage and its size

Didactical approach

The course is conceived as highly interactive which includes:

• Theoretical inputs (lectures)
• Interactive discussions on case studies (group discussions)
• Pair and group work in the laboratory
• Instrument handling for the practical part
• Hands-on activities for data analysis (computer sessions)
• 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 the course, participants will be able to:
1. Demonstrate an understanding of NGS technologies;
2. Assess the challenges involved in investigating the genome;
3. Perform library preparation and sequencing procedures in the laboratory;
5. Assess the quality of the library as well as the data obtained
6. Perform basic data analysis using the Sushi pipeline
7. Apply NGS into a research-based context by:
a. formulating a meaningful research question
b. designing an experimental setup (based on the analytical techniques learned during the course) to address this specific question on genomics
c. presenting their strategy to the class

Important facts and how to apply

Target audience and prerequisites

Applicants should be postdoctoral scientists, PhD students or masters students actively engaged in or soon to commence research involving next generation sequencing technology. 

Cost

The course tuition fees for Ph.D. students and post-docs from the University of Zürich and ETHZ is CHF 300.00 (Swiss francs) and CHF 500.00 (Swiss francs), respectively . For external academics (non-UZH and non-ETHZ) the cost is CHF 1200.00 per person. For industrial delegates the cost is CHF 1500.00 per person.

IMPORTANT: The internal prices can be applied only, when paid by internal account.

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.