Immunoinformatics

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Overview

Immunoinformatics is a cross-disciplinary research field at the interface between computer science, mathematics and experimental immunology. Immunoinformatics serves practical applications in clinical medicine, such as antibody and T-cell discovery for therapeutics and vaccine design. Furthermore, it enables to profile the complexity of the immune repertoire providing a method for establishing novel diagnostics and identifying immune biomarkers across diseases.

In this course, participants will learn about Next-Generation Sequencing (NGS) of antibody repertoires. Part 1 will provide an introduction to the antibody repertoires, it will cover genetic background, generation of diversity, some of the sequencing technologies currently in use and a hand-on session on the computational tools available for the analysis of antibody repertoire NGS data. Part 2 will focus on the pre-processing and analysis of data. Each step of the preprocessing will be elucidated using the programming platforms of R and/or Python, along with existing bioinformatics pipelines available. Repertoire analysis content will provide statistical quantification and visualization of high-dimensional data. The course will be fully interactive with case studies, and the participants will be able to download data and example scripts.

Audience

This course is addressed to scientists who need to pre-process and analyze B- and T-cell receptor high-throughput sequencing (HTS) data.

Learning objectives

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

• describe the general concepts of adaptive immunity, B- and T-cell receptors (BCR and TCR)
• find and download BCR/TCR HTS data
• preprocess BCR/TCR sequences
• annotate V, D, J germline genes
• analyze BCR/TCR immune repertoires
• use data visualization tools and select methods to represent a large dataset graphically
• produce data visualizations with the R software (basic R and ggplot2)

Prerequisites

Knowledge / competencies

This course is designed for beginners in R, for instance those who have attended the First Steps in R. However a short introduction to R will be provided.

Technical

You are required to bring your own laptop with a wifi connection, and the following software installed PRIOR to the course: R, R Studio, Python, Jupyter notebook. A list of packages will be provided in due time.

Venue and Time

This course will be streamed.

On day 1, the course will start at 9:00 and end around 17:00. On day 2, the course will start at 9:00 and end around 12:30.

Precise information will be provided to the participants in due time.

Application

The registration fees for academics are 90 CHF and 450 for for-profit companies.

You will be informed by email of your registration confirmation. Upon reception of the confirmation email, participants will be asked to confirm attendance by paying the fees within 5 days.

Applications close as soon as the course will be full. Deadline for free-of-charge cancellation is set to 11/Jan/2022. Cancellation after this date will not be reimbursed. Please note that participation in SIB courses is subject to our general conditions.

Additional information

Instructor: Prof. Dr. Enkelejda Miho, FHNW University of Applied Sciences and Arts Northwestern Switzerland, School of Life Sciences, Institute of Medical Engineering and Medical Informatics

Coordination: Patricia Palagi

We will recommend 0.5 ECTS credits for this course (given a passed exam at the end of the course).

You are welcome to register to the SIB courses mailing list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

Please note that participation in SIB courses is subject to our general conditions.

SIB abides by the ELIXIR Code of Conduct. Participants of SIB courses are also required to abide by the same code.

For more information, please contact training@sib.swiss.