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MAGMA GTEx

I applied MAGMA1 to EBV DNA GWAS of Nyeo et al.2 using bulk RNAseq data from GTEx3 as a reference. The gene-property analysis results are plotted below.

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

The four significant tissue/cell types are Ileum Lymphode Aggregate, Whole Blood, Spleen, and EBV-Transformed Lymphocytes. All are immune-related. Given that the primary determinant of a person's EBV DNA levels is the ability of their immune system to keep their EBV infection under control and in a dormant state, this makes sense.

  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. Sherry S Nyeo, Erin M Cumming, Oliver S Burren, Meghana S Pagadala, Jacob C Gutierrez, Thahmina A Ali, Laura C Kida, Yifan Chen, Hoyin Chu, Fengyuan Hu, and others. Population-scale sequencing resolves determinants of persistent ebv dna. Nature, pages 1–9, 2026. URL: https://www.nature.com/articles/s41586-025-10020-2. ↩

  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. ↩