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MAGMA GTEx

I applied MAGMA1 to the whole brainstem volume GWAS of Xue 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 Xue et al.'s whole brainstem GWAS. The x axis corresponds to tissue type, while the y axis measures MAGMA significance level.

As would be expected from a GWAS of the volume of a region of the brain, all 4 significant tissue types relate to the nervous system. These consist of three central nervous system cell types: Brain_Cerebellum, Brain_Cerebellar_Hemisphere, and Brain_Spinal_cord_cervical_c-1; as well as one peripheral nervous system cell type: Nerve_Tibial. It is unclear why these specific nervous system cell types are selected by MAGMA over other nervous-system related cell types.

  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. Hui Xue, Jilian Fu, Zuojun Geng, Jingliang Cheng, Meiyun Wang, Longjiang Zhang, Guangbin Cui, Yongqiang Yu, Weihua Liao, Hui Zhang, and others. The genetic architecture of brainstem structures. Nature Communications, 2025. URL: https://www.nature.com/articles/s41467-025-67221-6_reference.pdf. ↩

  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. ↩