Robbin Nameki, Anamay Shetty, Eileen Dareng, Jonathan Tyrer, the Ovarian Cancer Research Consortium, Paul Pharoah, Rosario I. Corona, Siddhartha Kar, Kate Lawrenson
R.N. & A.S. Equally contributed to the study
K.L. & S.K. Joint directed the study
This is a step-by-step tutorial on how to conduct chromMAGMA, a bioinformatic pipeline that builds on MAGMA (Leeuw et al., 2015) by assigning genome-wide association (GWAS) statistics to epigenomic profiles, followed by assignment to genes. As proof-of-concept in this tutorial we will apply chromMAGMA to Epithelial Ovarian Cancer (EOC) datasets.
There are two key parts to this tutorial.
The first part includes running MAGMA with modified .annot files that assign SNPs to regulatory elements. In this case, we will use .annot files of EOC GWAS statistics from Coetzee, et al. 2021 ,'Integrative multi-omics analyses to identify the genetic and functional mechanisms underlying ovarian cancer risk regions' (under review) assigned to genomic regions consisting of a union set of primary EOC H3K27ac ChIP-seq data from Corona et al. 2020. The regulatory elements are then assigned back to genes using the Genehancer (Fishilevich et al., 2017) database in a Rscript.
The second part includes the process of cleaning outputs and assigning the most significant regulatory element to a gene. This part of the tutorial will then delve into various annotations, descriptive statistics, and analysis to explore the gene-level outputs from chromMAGMA. This part is conveniently available as GitHub Pages https://lawrenson-lab.github.io/chromMAGMA-public
Create a chromMAGMA folder within directories
cd /path-to-your-folder
mkdir chromMAGMA
Next, download MAGMA and the associated files from the MAGMA website:
https://ctg.cncr.nl/software/magma
GWAS statistics are to be released with our forthocoming paper:
[OCAC Paper Reference]
Map to the Processing Directory. Everything pertaining to processing is in this directory.
cd /path-to-your-folder/chromMAGMA/Processing
The key processing steps are found in magma_preparation_and_execution.Rmd which lays out the key steps to run chromMAGMA. This will create a .RDS file which can then be used in the Analysis portion onwards.
MAGMA v1.08 was used and downloaded from the MAGMA website:
https://ctg.cncr.nl/software/magma
Broad GSEA Preranked for the command line was used and downloaded from the Broad GSEA website. We used v3.0.
http://www.gsea-msigdb.org/gsea/downloads.jsp
Please ensure these are downloaded to the apps folder of chromMAGMA.
Map to the Analysis directory. Corresponding Rmarkdowns and the Utility Source Code (Utils.R) are available in this directory.
cd /path-to-your-folder/chromMAGMA/Analysis
This part is also available as a step-by-step github pages at https://lawrenson-lab.github.io/chromMAGMA-public .