Graduate School of health and Medical Sciences

Genomics
Provider: Faculty of Health and Medical Sciences

Activity no.: 3279-25-00-00	There are 14 available seats
	Enrollment deadline: 24/02/2025

Date and time	24.03.2025, at: 09:00 - 27.03.2025, at: 16:30
Regular seats	20
Course fee	4,320.00 kr.
Lecturers	Anders Krogh
ECTS credits	2.60

Contact person	HeaDS Administration E-mail address: heads-admin@sund.ku.dk

Enrolment Handling/Course Organiser	PhD administration E-mail address: phdkursus@sund.ku.dk

Aim and content This course is free of charge for PhD students at Danish universities (except Copenhagen Business School), and for PhD Students from NorDoc member faculties. All other participants must pay the course fee. Anyone can apply for the course, but if you are not a PhD student at a Danish university, you will be placed on the waiting list until enrollment deadline. This also applies to PhD students from NorDoc member faculties. After the enrollment deadline, available seats will be allocated to applicants on the waiting list. Learning objectives A student who has met the objectives of the course will be able to: 1. Explain basic population genetics concepts and elaborate on them when analyzing data. 2. Understand and apply in practice the basics of GWAS (Linkage disequilibrium and linear regression). 3. Perform and generalize approaches to data preprocessing and imputation of missing genotypes. 4. Discuss and reproduce basic GWAS applications from literature. 5. Interpret GWAS results and have a critical approach towards their limitations. Content The Sandbox Genomics course is a four-day program designed to provide comprehensive training in GWAS (Genome-Wide Association Studies). On the first day, participants will engage in lectures and discussions on foundational genetics concepts, setting the stage for the rest of the course. Attendees will then be guided through every step of a typical GWAS study, from data preprocessing and quality control to the interpretation of results. A key feature of the course is a hands-on GWAS case study, where participants will work through the entire process from start to finish. This will include handling missing genotypes, performing linear regression analyses for association testing, and understanding linkage disequilibrium for fine-mapping and haplotype construction. Throughout the course, participants will gain practical insights into the technical challenges and best practices for conducting GWAS using high-performance computing resources. In addition to real-world case studies and recent applications, the course will highlight common limitations and biases in GWAS studies that researchers should be aware of. Exercises will be run on an HPC platform, and participants will be expected to build on existing familiarity with bioinformatics tools and the scripting languages bash and R/Python. Participants Seats: 20 The course is intended for PhD students at SUND who are interested in learning the different steps involved in a GWAS study and using them to build a structured pipeline for semi-automated GWAS analyses using high-performance computing resources. Requirements The course is for PhD students and researchers at SUND who are interested in building an analysis pipeline for Genome-Wide Association Studies (GWAS). It will cover all essential steps in a typical GWAS study, from quality control to the interpretation of results, enabling participants to create a reusable and reproducible bioinformatics pipeline. The course is suitable for both beginners and intermediate users, combining lectures with hands-on practical exercises using R, the Linux command line, and custom software. A basic understanding of R programming and Unix is strongly recommended, along with familiarity with genomic data, such as those generated from next-generation sequencing (NGS) experiments. Relevance to graduate programs The course is relevant to PhD students from the following graduate programs at the Graduate School of Health and Medical Sciences, UCPH: All graduate programmes Language English Form The course will feature lectures with active discussion sessions, interactive demonstrations on an HPC platform, and group exercises aimed at navigating HPC systems. Participants will gain hands-on experience with state-of-the-art genomics tools. Course director Anders Krogh, Professor, Head of Center for Health Data Science, Head of Health Data Science Sandbox Center for Health Data Science, anders.krogh@sund.ku.dk Teachers The workshop is provided by project members of the Health Data Science Sandbox, a national training and research infrastructure project. The Sandbox team is building training resources and guides for learning bioinformatics, predictive modeling in precision medicine, high performance computing and data carpentry. These resources are accessible to all Danish university employees (PhD students and up) via academic supercomputing infrastructure. Jennifer Bartell PhD, Senior consultant and Sandbox project manager Center for Health Data Science, KU bartell@sund.ku.dk Alba Refoyo Martinez PhD, Data Scientist, Sandbox Team Center for Health Data Science, KU alba.martinez@sund.ku.dk Samuele Soraggi PhD, Special Consultant Bioinformatics Research Center, Dept of Molecular Biology, Aarhus University, samuele@birc.au.dk Dates 24-26 March 2025 - 9:00 – 16:30 27 March 2025 - 9:00 – 12:00 Course location TBD Faculty of Health and Medical Sciences, Panum, Blegdamsvej 3B, 2200 København. Registration 24 February 2025 Expected frequency This course will be repeated in Autumn 2025. Seats to PhD students from other Danish universities will be allocated on a first-come, first-served basis and according to the applicable rules. Applications from other participants will be considered after the last day of enrollment. Note: All applicants are asked to submit invoice details in case of no-show, late cancellation or obligation to pay the course fee (typically non-PhD students). If you are a PhD student, your participation in the course must be in agreement with your principal supervisor.

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