Topics

This week’s assignments will guide you through the following topics depending on what your team has decided to do for the Quarter 2 Project.

Reading

For the team of Gurman, Lihao, and Anton, please consult the follwing reading materials:

• SuSiE fine-mapping
• An example research study using SuSiE (Read sections pertaining to the use of SuSiE and parameters that were set)
• Gene Burden Testing (This paper has a convenient R script for computing the burden of a gene)

For the team of John, Tyler, and Ethan, please consult the following reading materials:

• COLOC software
• A study that uses the COLOC software (Consult this paper for parameters to use when running COLOC)
• Gene set enrichment analysis software
• Evaluating the importance of gene sets (Consult this paper for how to interpret the gene sets you will find from performing PCA on a matrix of genes x traits/diseases with colocalization statistics)

Tasks

Complete the following tasks: For the team of Gurman, Lihao, and Anton:

• Install the SuSiE R package and experiment with it by following the vignette
• Acquire genome-wide GWAS summary statistics for multiple traits/diseases of interest
• Identify a gene burden testing software of choice, or write your own script based on our conversation in class.

For the team of John, Tyler, and Ethan:

• Install the COLOC software and supply two summary statistics results from eQTL analysis that you’ve already run for 2 genes just to make sure it runs.
• Acquire genome-wide GWAS summary statistics for multiple traits/diseases of interest
• Install the gene set enrichment analysis software and provide a random set of genes just to make sure it runs.

Weekly Questions

On Gradescope, describe your progress with the software installation required for each group and report a table of the GWAS summary statistics you found on the GWAS catalog website, including the citation for the study, the year, the first author, the sample size, and the name of the trait/disease.