GWAS with the Genomics Sandbox

Repository for the GWAS with the genomics Sandbox. Tutorials can be found under the Notebooks folder.

This course introduces and applies bioinformatic tools to perform a whole population genomics analysis.

This workshop is based on the materials from A tutorial on conducting genome-wide association studies: Quality control and statistical analysis: https://pmc.ncbi.nlm.nih.gov/articles/PMC6001694/.

Goals:

• Learn and explain fundamental population genetics concepts, applying them during data analysis.
• Understand the principles of GWAS, including linkage disequilibrium and linear regression, and apply them in practice.
• Develop skills to preprocess data and perform genotype imputation for missing values.
• Explore, discuss, and replicate basic GWAS applications from the scientific literature.
• Interpret GWAS results critically, recognizing their limitations.

Syllabus:

• Introduction to GWAS
• Quality control
• Population structure
• Types of association tests
• Polygenic (risk) scores
• Other applications

Workshop requirements:

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.

Authors:

• Samuele Soraggi
• Alba Refoyo Martinez
• Conor O'Hare

Acknowledgements:

• Center for Health Data Science, University of Copenhagen
• Matti Pirinen, PhD, University of Helsinki
• Andries T. Marees, Vrije Universiteit Amsterdam

Resources

• GWAS course at the University of Helsinki by Marri Pirinen: https://www.mv.helsinki.fi/home/mjxpirin/GWAS_course/
• GWAS tutorials by Andries T. Marees, check out repo accompanying the paper A Tutorial on Conducting Genome‐Wide Association Studies: Quality Control and Statistical Analysis. DOI: 10.1002/mpr.1608.
• Basic GWAS tutorial for PRS by Shing Wan Choi Shing Wan Choi website