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MAGMA

I applied the MAGMA1 pipeline to summary statistics from a GWAS of C-Reactive Protein (CRP) from Said at el.2.

In the gene set analysis step, I incorporated tissue-specific RNAseq data from GTEx3 to try to link genes associated with LDL to specific tissues.

The results are shown below:

Result of MAGMA GTEx applied to Said et al.'s CRP GWAS. The x axis corresponds to tissue type, while the y axis measures MAGMA significance level.

All the significant tissue are liver-related. This is consistent with the liver's role as a primary site of acute-phase-reactant synthesis.

  1. Christiaan A De Leeuw, Joris M Mooij, Tom Heskes, and Danielle Posthuma. MAGMA: generalized gene-set analysis of GWAS data. PLoS Computational Biology, 11(4):e1004219, 2015. URL: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004219. ↩

  2. Saredo Said, Raha Pazoki, Ville Karhunen, Urmo Võsa, Symen Ligthart, Barbara Bodinier, Fotios Koskeridis, Paul Welsh, Behrooz Z Alizadeh, Daniel I Chasman, and others. Genetic analysis of over half a million people characterises C-reactive protein loci. Nature Communications, 13(1):2198, 2022. URL: https://www.nature.com/articles/s41467-022-29650-5. ↩

  3. GTEx Consortium. The GTEx consortium atlas of genetic regulatory effects across human tissues. Science, 369(6509):1318–1330, 2020. URL: https://www.science.org/doi/full/10.1126/science.aaz1776. ↩